Commit f182365f authored by Matthieu Muffato's avatar Matthieu Muffato
Browse files

Patched the Compara test-databases

parent ca892b40
--
-- Created by SQL::Translator::Producer::SQLite
-- Created on Thu Jan 5 13:47:00 2017
-- Created on Tue Jan 24 12:49:38 2017
--
BEGIN TRANSACTION;
......@@ -59,10 +59,12 @@ CREATE TABLE constrained_element (
CREATE TABLE dnafrag (
dnafrag_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
length integer NOT NULL DEFAULT 0,
name varchar(40) NOT NULL DEFAULT '',
name varchar(255) NOT NULL DEFAULT '',
genome_db_id integer NOT NULL,
coord_system_name varchar(40) NOT NULL DEFAULT '',
is_reference tinyint NOT NULL DEFAULT 1
cellular_component enum NOT NULL DEFAULT 'NUC',
is_reference tinyint NOT NULL DEFAULT 1,
codon_table_id tinyint NOT NULL DEFAULT 1
);
CREATE UNIQUE INDEX name ON dnafrag (genome_db_id, name);
......@@ -78,6 +80,18 @@ CREATE TABLE dnafrag_region (
dnafrag_strand tinyint NOT NULL DEFAULT 0
);
--
-- Table: exon_boundaries
--
CREATE TABLE exon_boundaries (
gene_member_id integer NOT NULL,
seq_member_id integer NOT NULL,
dnafrag_start integer NOT NULL,
dnafrag_end integer NOT NULL,
sequence_length integer NOT NULL,
left_over tinyint NOT NULL DEFAULT 0
);
--
-- Table: external_db
--
......@@ -150,6 +164,7 @@ CREATE TABLE gene_member (
source_name enum NOT NULL,
taxon_id integer NOT NULL,
genome_db_id integer,
biotype_group enum NOT NULL DEFAULT 'coding',
canonical_member_id integer,
description text,
dnafrag_id bigint,
......@@ -176,6 +191,19 @@ CREATE TABLE gene_member_hom_stats (
PRIMARY KEY (gene_member_id, collection)
);
--
-- Table: gene_member_qc
--
CREATE TABLE gene_member_qc (
gene_member_stable_id varchar(128) NOT NULL,
genome_db_id integer NOT NULL,
seq_member_id integer,
n_species integer,
n_orth integer,
avg_cov float,
status varchar(50) NOT NULL
);
--
-- Table: gene_tree_node
--
......@@ -289,6 +317,8 @@ CREATE TABLE genome_db (
has_karyotype tinyint NOT NULL DEFAULT 0,
is_high_coverage tinyint NOT NULL DEFAULT 0,
genome_component varchar(5),
strain_name varchar(40),
display_name varchar(255),
locator varchar(400),
first_release smallint,
last_release smallint
......@@ -567,6 +597,8 @@ CREATE TABLE seq_member (
genome_db_id integer,
sequence_id integer,
gene_member_id integer,
has_transcript_edits tinyint NOT NULL DEFAULT 0,
has_translation_edits tinyint NOT NULL DEFAULT 0,
description text,
dnafrag_id bigint,
dnafrag_start integer,
......
13705552 151834684 5 134 chromosome 1
4514314 7320470 15 65 chromosome 1
36722 675822 scaffold_166 4 scaffold 1
4514338 107808587 Un_random 65 chromosome 1
2039125 16798506 groupIII 36 group 1
4346076 202140232 3 60 chromosome 1
2039164 31848461 17 37 chromosome 1
1045569 169801366 7 31 chromosome 1
1045563 189746636 2 31 chromosome 1
12160504 27241186 9 87 chromosome 1
2175916 723 Contig213555 43 supercontig 1
13094385 1346504 GL172955.1 116 scaffold 1
13200476 158337067 1 122 chromosome 1
13203820 199944510 3 123 chromosome 1
12966556 163896628 14 108 chromosome 1
13049389 1378627 GL343321.1 111 scaffold 1
13705560 98207768 16 134 chromosome 1
13636391 3303274 JH126603.1 129 scaffold 1
13211504 202329955 3 125 chromosome 1
13785441 2670181 KB743644.1 144 scaffold 1
13783415 23441680 9 142 chromosome 1
13688462 12481155 GL831134.1 130 scaffold 1
13055709 24221871 11 112 chromosome 1
13705633 42124431 34 135 chromosome 1
12753243 22517 GeneScaffold_6359 91 genescaffold 1
13955520 133797422 10 150 chromosome 1
13862672 17670860 JH603178.1 145 scaffold 1
14022783 91754291 15 153 chromosome 1
13203897 11483068 GL873579.1 124 scaffold 1
13955574 162156779 7 151 chromosome 1
14026375 59543403 2 154 chromosome 1
14022801 84932903 24 153 chromosome 1
13902789 32369425 LG14 148 chromosome 1
13902799 275612895 1 147 chromosome 1
3570454 260857928 7 46 chromosome 1
14018859 2562819 KI519677.1 152 scaffold 1
13701661 218635234 13 132 chromosome 1
4346125 59975221 19 61 chromosome 1
14026979 90463843 11 155 chromosome 1
13955539 198295559 3 150 chromosome 1
11302777 39289 GeneScaffold_5302 82 genescaffold 1
13955536 248956422 1 150 chromosome 1
13955530 135086622 11 150 chromosome 1
13955535 133275309 12 150 chromosome 1
13955524 107043718 14 150 chromosome 1
13955534 101991189 15 150 chromosome 1
13955537 90338345 16 150 chromosome 1
13955531 83257441 17 150 chromosome 1
13955525 80373285 18 150 chromosome 1
13955522 58617616 19 150 chromosome 1
13955526 242193529 2 150 chromosome 1
13955515 64444167 20 150 chromosome 1
13955528 46709983 21 150 chromosome 1
13955519 50818468 22 150 chromosome 1
13955527 190214555 4 150 chromosome 1
13955538 181538259 5 150 chromosome 1
13955521 170805979 6 150 chromosome 1
13955533 159345973 7 150 chromosome 1
13955532 145138636 8 150 chromosome 1
13955529 138394717 9 150 chromosome 1
3955517 156040895 X 150 chromosome 1
13955512 57227415 Y 150 chromosome 1
13705553 195471971 1 134 chromosome 1
13705557 130694993 10 134 chromosome 1
13705565 122082543 11 134 chromosome 1
13705564 120129022 12 134 chromosome 1
13705559 120421639 13 134 chromosome 1
13705556 124902244 14 134 chromosome 1
13705558 104043685 15 134 chromosome 1
13705563 94987271 17 134 chromosome 1
13705549 90702639 18 134 chromosome 1
13705554 61431566 19 134 chromosome 1
13705568 182113224 2 134 chromosome 1
13705562 160039680 3 134 chromosome 1
13705567 156508116 4 134 chromosome 1
13705550 149736546 6 134 chromosome 1
13705551 145441459 7 134 chromosome 1
13705555 129401213 8 134 chromosome 1
13705552 151834684 5 134 chromosome NUC 1 1
4514314 7320470 15 65 chromosome NUC 1 1
36722 675822 scaffold_166 4 scaffold NUC 1 1
4514338 107808587 Un_random 65 chromosome NUC 1 1
2039125 16798506 groupIII 36 group NUC 1 1
4346076 202140232 3 60 chromosome NUC 1 1
2039164 31848461 17 37 chromosome NUC 1 1
1045569 169801366 7 31 chromosome NUC 1 1
1045563 189746636 2 31 chromosome NUC 1 1
12160504 27241186 9 87 chromosome NUC 1 1
2175916 723 Contig213555 43 supercontig NUC 1 1
13094385 1346504 GL172955.1 116 scaffold NUC 1 1
13200476 158337067 1 122 chromosome NUC 1 1
13203820 199944510 3 123 chromosome NUC 1 1
12966556 163896628 14 108 chromosome NUC 1 1
13049389 1378627 GL343321.1 111 scaffold NUC 1 1
13705560 98207768 16 134 chromosome NUC 1 1
13636391 3303274 JH126603.1 129 scaffold NUC 1 1
13211504 202329955 3 125 chromosome NUC 1 1
13785441 2670181 KB743644.1 144 scaffold NUC 1 1
13783415 23441680 9 142 chromosome NUC 1 1
13688462 12481155 GL831134.1 130 scaffold NUC 1 1
13055709 24221871 11 112 chromosome NUC 1 1
13705633 42124431 34 135 chromosome NUC 1 1
12753243 22517 GeneScaffold_6359 91 genescaffold NUC 1 1
13955520 133797422 10 150 chromosome NUC 1 1
13862672 17670860 JH603178.1 145 scaffold NUC 1 1
14022783 91754291 15 153 chromosome NUC 1 1
13203897 11483068 GL873579.1 124 scaffold NUC 1 1
13955574 162156779 7 151 chromosome NUC 1 1
14026375 59543403 2 154 chromosome NUC 1 1
14022801 84932903 24 153 chromosome NUC 1 1
13902789 32369425 LG14 148 chromosome NUC 1 1
13902799 275612895 1 147 chromosome NUC 1 1
3570454 260857928 7 46 chromosome NUC 1 1
14018859 2562819 KI519677.1 152 scaffold NUC 1 1
13701661 218635234 13 132 chromosome NUC 1 1
4346125 59975221 19 61 chromosome NUC 1 1
14026979 90463843 11 155 chromosome NUC 1 1
13955539 198295559 3 150 chromosome NUC 1 1
11302777 39289 GeneScaffold_5302 82 genescaffold NUC 1 1
13955536 248956422 1 150 chromosome NUC 1 1
13955530 135086622 11 150 chromosome NUC 1 1
13955535 133275309 12 150 chromosome NUC 1 1
13955524 107043718 14 150 chromosome NUC 1 1
13955534 101991189 15 150 chromosome NUC 1 1
13955537 90338345 16 150 chromosome NUC 1 1
13955531 83257441 17 150 chromosome NUC 1 1
13955525 80373285 18 150 chromosome NUC 1 1
13955522 58617616 19 150 chromosome NUC 1 1
13955526 242193529 2 150 chromosome NUC 1 1
13955515 64444167 20 150 chromosome NUC 1 1
13955528 46709983 21 150 chromosome NUC 1 1
13955519 50818468 22 150 chromosome NUC 1 1
13955527 190214555 4 150 chromosome NUC 1 1
13955538 181538259 5 150 chromosome NUC 1 1
13955521 170805979 6 150 chromosome NUC 1 1
13955533 159345973 7 150 chromosome NUC 1 1
13955532 145138636 8 150 chromosome NUC 1 1
13955529 138394717 9 150 chromosome NUC 1 1
3955517 156040895 X 150 chromosome NUC 1 1
13955512 57227415 Y 150 chromosome NUC 1 1
13705553 195471971 1 134 chromosome NUC 1 1
13705557 130694993 10 134 chromosome NUC 1 1
13705565 122082543 11 134 chromosome NUC 1 1
13705564 120129022 12 134 chromosome NUC 1 1
13705559 120421639 13 134 chromosome NUC 1 1
13705556 124902244 14 134 chromosome NUC 1 1
13705558 104043685 15 134 chromosome NUC 1 1
13705563 94987271 17 134 chromosome NUC 1 1
13705549 90702639 18 134 chromosome NUC 1 1
13705554 61431566 19 134 chromosome NUC 1 1
13705568 182113224 2 134 chromosome NUC 1 1
13705562 160039680 3 134 chromosome NUC 1 1
13705567 156508116 4 134 chromosome NUC 1 1
13705550 149736546 6 134 chromosome NUC 1 1
13705551 145441459 7 134 chromosome NUC 1 1
13705555 129401213 8 134 chromosome NUC 1 1
100000065 ENSTNIG00000020505 0 ENSEMBLGENE 99883 65 100000065 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4514314 3306094 3306168 1 SNORD2
100002261 ENSTRUG00000019469 0 ENSEMBLGENE 31033 4 100002260 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 36722 268619 268692 1 SNORD2
100002264 ENSTRUG00000019394 0 ENSEMBLGENE 31033 4 100002264 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 36722 269022 269095 1 SNORD2
100003686 ENSTNIG00000020529 0 ENSEMBLGENE 99883 65 100003686 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4514338 52669397 52669470 -1 SNORD2
100003687 ENSTNIG00000020519 0 ENSEMBLGENE 99883 65 100003688 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4514338 52669729 52669803 -1 SNORD2
100008184 ENSGACG00000022790 0 ENSEMBLGENE 69293 36 100008184 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2039125 9224992 9225064 1 SNORD2
100008186 ENSGACG00000022791 0 ENSEMBLGENE 69293 36 100008186 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2039125 9225550 9225621 1 SNORD2
100009977 ENSPPYG00000028034 0 ENSEMBLGENE 9601 60 100009977 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4346076 190574508 190574576 1 SNORD2
100016849 ENSORLG00000021574 0 ENSEMBLGENE 8090 37 100016849 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2039164 14653720 14653794 1 SNORD2
100016850 ENSORLG00000021634 0 ENSEMBLGENE 8090 37 100016850 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2039164 14654245 14654320 1 SNORD2
100029371 ENSMMUG00000036232 0 ENSEMBLGENE 9544 31 100029371 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 1045569 164954481 164954549 1 SNORD2
100033919 ENSMMUG00000037192 0 ENSEMBLGENE 9544 31 100033919 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 1045563 179142348 179142416 1 SNORD2
100046335 ENSTGUG00000018017 0 ENSEMBLGENE 59729 87 100046335 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 12160504 18582628 18582698 1 SNORD2
100047101 ENSOANG00000027382 0 ENSEMBLGENE 9258 43 100047100 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2175916 513 593 -1 SNORD2
100054945 ENSXETG00000029617 0 ENSEMBLGENE 8364 116 100054945 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13094385 381059 381128 -1 SNORD2
100054946 ENSXETG00000029793 0 ENSEMBLGENE 8364 116 100054946 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13094385 385005 385076 -1 SNORD2
100065013 ENSBTAG00000044311 0 ENSEMBLGENE 9913 122 100065013 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13200476 81062767 81062835 -1 SNORD2
100071636 ENSGGOG00000032407 0 ENSEMBLGENE 9595 123 100071636 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13203820 188240400 188240468 1 SNORD2
100087720 ENSOCUG00000023265 0 ENSEMBLGENE 9986 108 100088181 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 12966556 78843854 78843921 -1 SNORD2
100093454 ENSACAG00000018292 0 ENSEMBLGENE 28377 111 100094079 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13049389 118621 118692 -1 SNORD2
100099604 ENSMUSG00000088524 0 ENSEMBLGENE 10090 134 100100368 small nucleolar RNA, C/D box 2 [Source:MGI Symbol;Acc:MGI:3819528] 13705560 23108953 23109021 1 Snord2
100099742 ENSLACG00000021456 0 ENSEMBLGENE 7897 129 100100505 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13636391 2411690 2411759 1 SNORD2
100113582 ENSPTRG00000037854 0 ENSEMBLGENE 9598 125 100114678 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13211504 190852362 190852430 1 SNORD2
100123418 ENSAPLG00000000068 0 ENSEMBLGENE 8839 144 100124975 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13785441 276440 276510 1 SNORD2
100130549 ENSGALG00000025617 0 ENSEMBLGENE 9031 142 100132105 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13783415 15672950 15673019 1 SNORD2
100137301 ENSONIG00000022215 0 ENSEMBLGENE 8128 130 100138857 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13688462 12140155 12140229 1 SNORD2
100137304 ENSONIG00000022099 0 ENSEMBLGENE 8128 130 100138860 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13688462 12140712 12140786 1 SNORD2
100151878 ENSMGAG00000000091 0 ENSEMBLGENE 9103 112 100153475 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13055709 16212140 16212209 1 SNORD2
100162160 ENSCAFG00000027814 0 ENSEMBLGENE 9615 135 100164038 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13705633 19356118 19356186 1 SNORD2
100164895 ENSMEUG00000017324 0 ENSEMBLGENE 9315 91 100166821 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 12753243 17043 17112 1 SNORD2
100176264 ENSG00000238707 0 ENSEMBLGENE 9606 150 100178494 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13955520 56595963 56596031 -1 SNORD2
100182621 ENSFALG00000015549 0 ENSEMBLGENE 59894 145 100185036 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13862672 11103001 11103071 1 SNORD2
100184508 ENSCSAG00000026646 0 ENSEMBLGENE 60711 153 100186963 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14022783 81076307 81076375 1 SNORD2
100191757 ENSOGAG00000023959 0 ENSEMBLGENE 30611 124 100194492 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13203897 9863584 9863651 -1 SNORD2
100204308 ENSPANG00000010082 0 ENSEMBLGENE 9555 151 100207705 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13955574 157844257 157844325 1 SNORD2
100215815 ENSDARG00000082639 0 ENSEMBLGENE 7955 154 100220003 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14026375 7922554 7922624 1 SNORD2
100215819 ENSDARG00000083056 0 ENSEMBLGENE 7955 154 100220007 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14026375 7922934 7923004 1 SNORD2
100215833 ENSDARG00000080523 0 ENSEMBLGENE 7955 154 100220025 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14026375 7925865 7925936 1 SNORD2
100220485 ENSCSAG00000027032 0 ENSEMBLGENE 60711 153 100225049 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14022801 79602435 79602503 1 SNORD2
100223263 ENSLOCG00000019102 0 ENSEMBLGENE 7918 148 100227949 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13902789 461949 462018 1 SNORD2
100226195 ENSOARG00000022667 0 ENSEMBLGENE 9940 147 100231022 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13902799 198671751 198671819 -1 SNORD2
100235573 ENSMODG00000026826 0 ENSEMBLGENE 13616 46 100240803 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 3570454 206772418 206772486 -1 SNORD2
100238959 ENSPFOG00000021602 0 ENSEMBLGENE 48698 152 100244296 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14018859 380507 380583 1 SNORD2
100238967 ENSPFOG00000021430 0 ENSEMBLGENE 48698 152 100244304 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14018859 381062 381137 1 SNORD2
100242730 ENSSSCG00000018746 0 ENSEMBLGENE 9823 132 100248134 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13701661 133974703 133974771 1 SNORD2
100246488 ENSECAG00000027514 0 ENSEMBLGENE 9796 61 100252028 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4346125 24791922 24791988 1 SNORD2
100263700 ENSRNOG00000053621 0 ENSEMBLGENE 10116 155 100270056 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14026979 81378396 81378464 -1 SNORD2
100277999 ENSG00000174852 0 ENSEMBLGENE 9606 150 100285954 small nucleolar RNA, C/D box 2 [Source:HGNC Symbol;Acc:HGNC:32678] 13955539 186784796 186784864 1 SNORD2
100281324 ENSTSYG00000021671 0 ENSEMBLGENE 9478 82 100289437 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 11302777 17893 17961 1 SNORD2
100000065 ENSTNIG00000020505 0 ENSEMBLGENE 99883 65 snoncoding 100000065 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4514314 3306094 3306168 1 SNORD2
100002261 ENSTRUG00000019469 0 ENSEMBLGENE 31033 4 snoncoding 100002260 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 36722 268619 268692 1 SNORD2
100002264 ENSTRUG00000019394 0 ENSEMBLGENE 31033 4 snoncoding 100002264 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 36722 269022 269095 1 SNORD2
100003686 ENSTNIG00000020529 0 ENSEMBLGENE 99883 65 snoncoding 100003686 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4514338 52669397 52669470 -1 SNORD2
100003687 ENSTNIG00000020519 0 ENSEMBLGENE 99883 65 snoncoding 100003688 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4514338 52669729 52669803 -1 SNORD2
100008184 ENSGACG00000022790 0 ENSEMBLGENE 69293 36 snoncoding 100008184 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2039125 9224992 9225064 1 SNORD2
100008186 ENSGACG00000022791 0 ENSEMBLGENE 69293 36 snoncoding 100008186 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2039125 9225550 9225621 1 SNORD2
100009977 ENSPPYG00000028034 0 ENSEMBLGENE 9601 60 snoncoding 100009977 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4346076 190574508 190574576 1 SNORD2
100016849 ENSORLG00000021574 0 ENSEMBLGENE 8090 37 snoncoding 100016849 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2039164 14653720 14653794 1 SNORD2
100016850 ENSORLG00000021634 0 ENSEMBLGENE 8090 37 snoncoding 100016850 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2039164 14654245 14654320 1 SNORD2
100029371 ENSMMUG00000036232 0 ENSEMBLGENE 9544 31 snoncoding 100029371 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 1045569 164954481 164954549 1 SNORD2
100033919 ENSMMUG00000037192 0 ENSEMBLGENE 9544 31 snoncoding 100033919 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 1045563 179142348 179142416 1 SNORD2
100046335 ENSTGUG00000018017 0 ENSEMBLGENE 59729 87 snoncoding 100046335 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 12160504 18582628 18582698 1 SNORD2
100047101 ENSOANG00000027382 0 ENSEMBLGENE 9258 43 snoncoding 100047100 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 2175916 513 593 -1 SNORD2
100054945 ENSXETG00000029617 0 ENSEMBLGENE 8364 116 snoncoding 100054945 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13094385 381059 381128 -1 SNORD2
100054946 ENSXETG00000029793 0 ENSEMBLGENE 8364 116 snoncoding 100054946 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13094385 385005 385076 -1 SNORD2
100065013 ENSBTAG00000044311 0 ENSEMBLGENE 9913 122 snoncoding 100065013 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13200476 81062767 81062835 -1 SNORD2
100071636 ENSGGOG00000032407 0 ENSEMBLGENE 9595 123 snoncoding 100071636 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13203820 188240400 188240468 1 SNORD2
100087720 ENSOCUG00000023265 0 ENSEMBLGENE 9986 108 snoncoding 100088181 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 12966556 78843854 78843921 -1 SNORD2
100093454 ENSACAG00000018292 0 ENSEMBLGENE 28377 111 snoncoding 100094079 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13049389 118621 118692 -1 SNORD2
100099604 ENSMUSG00000088524 0 ENSEMBLGENE 10090 134 snoncoding 100100368 small nucleolar RNA, C/D box 2 [Source:MGI Symbol;Acc:MGI:3819528] 13705560 23108953 23109021 1 Snord2
100099742 ENSLACG00000021456 0 ENSEMBLGENE 7897 129 snoncoding 100100505 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13636391 2411690 2411759 1 SNORD2
100113582 ENSPTRG00000037854 0 ENSEMBLGENE 9598 125 snoncoding 100114678 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13211504 190852362 190852430 1 SNORD2
100123418 ENSAPLG00000000068 0 ENSEMBLGENE 8839 144 snoncoding 100124975 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13785441 276440 276510 1 SNORD2
100130549 ENSGALG00000025617 0 ENSEMBLGENE 9031 142 snoncoding 100132105 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13783415 15672950 15673019 1 SNORD2
100137301 ENSONIG00000022215 0 ENSEMBLGENE 8128 130 snoncoding 100138857 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13688462 12140155 12140229 1 SNORD2
100137304 ENSONIG00000022099 0 ENSEMBLGENE 8128 130 snoncoding 100138860 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13688462 12140712 12140786 1 SNORD2
100151878 ENSMGAG00000000091 0 ENSEMBLGENE 9103 112 snoncoding 100153475 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13055709 16212140 16212209 1 SNORD2
100162160 ENSCAFG00000027814 0 ENSEMBLGENE 9615 135 snoncoding 100164038 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13705633 19356118 19356186 1 SNORD2
100164895 ENSMEUG00000017324 0 ENSEMBLGENE 9315 91 snoncoding 100166821 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 12753243 17043 17112 1 SNORD2
100176264 ENSG00000238707 0 ENSEMBLGENE 9606 150 snoncoding 100178494 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13955520 56595963 56596031 -1 SNORD2
100182621 ENSFALG00000015549 0 ENSEMBLGENE 59894 145 snoncoding 100185036 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13862672 11103001 11103071 1 SNORD2
100184508 ENSCSAG00000026646 0 ENSEMBLGENE 60711 153 snoncoding 100186963 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14022783 81076307 81076375 1 SNORD2
100191757 ENSOGAG00000023959 0 ENSEMBLGENE 30611 124 snoncoding 100194492 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13203897 9863584 9863651 -1 SNORD2
100204308 ENSPANG00000010082 0 ENSEMBLGENE 9555 151 snoncoding 100207705 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13955574 157844257 157844325 1 SNORD2
100215815 ENSDARG00000082639 0 ENSEMBLGENE 7955 154 snoncoding 100220003 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14026375 7922554 7922624 1 SNORD2
100215819 ENSDARG00000083056 0 ENSEMBLGENE 7955 154 snoncoding 100220007 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14026375 7922934 7923004 1 SNORD2
100215833 ENSDARG00000080523 0 ENSEMBLGENE 7955 154 snoncoding 100220025 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14026375 7925865 7925936 1 SNORD2
100220485 ENSCSAG00000027032 0 ENSEMBLGENE 60711 153 snoncoding 100225049 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14022801 79602435 79602503 1 SNORD2
100223263 ENSLOCG00000019102 0 ENSEMBLGENE 7918 148 snoncoding 100227949 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13902789 461949 462018 1 SNORD2
100226195 ENSOARG00000022667 0 ENSEMBLGENE 9940 147 snoncoding 100231022 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13902799 198671751 198671819 -1 SNORD2
100235573 ENSMODG00000026826 0 ENSEMBLGENE 13616 46 snoncoding 100240803 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 3570454 206772418 206772486 -1 SNORD2
100238959 ENSPFOG00000021602 0 ENSEMBLGENE 48698 152 snoncoding 100244296 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14018859 380507 380583 1 SNORD2
100238967 ENSPFOG00000021430 0 ENSEMBLGENE 48698 152 snoncoding 100244304 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14018859 381062 381137 1 SNORD2
100242730 ENSSSCG00000018746 0 ENSEMBLGENE 9823 132 snoncoding 100248134 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 13701661 133974703 133974771 1 SNORD2
100246488 ENSECAG00000027514 0 ENSEMBLGENE 9796 61 snoncoding 100252028 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 4346125 24791922 24791988 1 SNORD2
100263700 ENSRNOG00000053621 0 ENSEMBLGENE 10116 155 snoncoding 100270056 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 14026979 81378396 81378464 -1 SNORD2
100277999 ENSG00000174852 0 ENSEMBLGENE 9606 150 snoncoding 100285954 small nucleolar RNA, C/D box 2 [Source:HGNC Symbol;Acc:HGNC:32678] 13955539 186784796 186784864 1 SNORD2
100281324 ENSTSYG00000021671 0 ENSEMBLGENE 9478 82 snoncoding 100289437 Small nucleolar RNA SNORD2 [Source:RFAM;Acc:RF01299] 11302777 17893 17961 1 SNORD2
4 31033 takifugu_rubripes FUGU4 2007-11-Ensembl 0 1 \N \N 24 \N
27 51511 ciona_savignyi CSAV2.0 2006-04-Ensembl 0 1 \N \N 39 \N
31 9544 macaca_mulatta MMUL_1 2006-01-Ensembl 1 1 \N \N 40 \N
33 9371 echinops_telfairi TENREC 2006-01-Ensembl 0 0 \N \N 40 \N
36 69293 gasterosteus_aculeatus BROADS1 2006-06-Ensembl 1 1 \N \N 40 \N
37 8090 oryzias_latipes MEDAKA1 2006-05-Ensembl 1 1 \N \N 41 \N
43 9258 ornithorhynchus_anatinus OANA5 2007-01-Ensembl 1 1 \N \N 42 \N
46 13616 monodelphis_domestica BROADO5 2007-02-Ensembl 1 1 \N \N 44 \N
48 37347 tupaia_belangeri TREESHREW 2006-10-Ensembl 0 0 \N \N 43 \N
49 9365 erinaceus_europaeus HEDGEHOG 2006-10-Ensembl 0 0 \N \N 43 \N
55 42254 sorex_araneus COMMON_SHREW1 2007-04-Ensembl 0 0 \N \N 45 \N
58 30608 microcebus_murinus micMur1 2007-07-Ensembl 0 0 \N \N 48 \N
60 9601 pongo_abelii PPYG2 2007-10-Ensembl 1 1 \N \N 49 \N
61 9796 equus_caballus EquCab2 2007-09-Ensembl 1 1 \N \N 49 \N
65 99883 tetraodon_nigroviridis TETRAODON8 2007-11-Ensembl 1 1 \N \N 50 \N
67 9978 ochotona_princeps pika 2008-01-Ensembl 0 0 \N \N 50 \N
69 10141 cavia_porcellus cavPor3 2008-03-Ensembl 0 1 \N \N 51 \N
78 9358 choloepus_hoffmanni choHof1 2008-11-Ensembl 0 0 \N \N 53 \N
79 9813 procavia_capensis proCap1 2008-11-Ensembl 0 0 \N \N 53 \N
80 9739 tursiops_truncatus turTru1 2008-11-Ensembl 0 0 \N \N 53 \N
82 9478 tarsius_syrichta tarSyr1 2008-11-Ensembl 0 0 \N \N 53 \N
83 10020 dipodomys_ordii dipOrd1 2008-11-Ensembl 0 0 \N \N 53 \N
84 30538 vicugna_pacos vicPac1 2008-11-Ensembl 0 0 \N \N 53 \N
85 132908 pteropus_vampyrus pteVam1 2008-11-Ensembl 0 0 \N \N 53 \N
87 59729 taeniopygia_guttata taeGut3.2.4 2008-08-Ensembl 1 1 \N \N 53 \N
91 9315 macropus_eugenii Meug_1.0 2009-02-Ensembl 0 0 \N \N 55 \N
98 9785 loxodonta_africana loxAfr3 2009-07-Ensembl 0 1 \N \N 57 \N
108 9986 oryctolagus_cuniculus OryCun2.0 2009-11-Ensembl 1 1 \N \N 60 \N
109 9646 ailuropoda_melanoleuca ailMel1 2010-01-Ensembl 0 1 \N \N 60 \N
111 28377 anolis_carolinensis AnoCar2.0 2010-09-Ensembl 1 1 \N \N 61 \N
112 9103 meleagris_gallopavo UMD2 2010-09-Ensembl 1 1 \N \N 61 \N
115 61853 nomascus_leucogenys Nleu1.0 2010-10-Ensembl 0 1 \N \N 62 \N
116 8364 xenopus_tropicalis JGI_4.2 2010-09-Ensembl 0 1 \N \N 62 \N
117 9483 callithrix_jacchus C_jacchus3.2.1 2010-02-Ensembl 1 1 \N \N 63 \N
118 59463 myotis_lucifugus Myoluc2.0 2010-12-Ensembl 0 1 \N \N 63 \N
120 7757 petromyzon_marinus Pmarinus_7.0 2011-02-Ensembl 0 1 \N \N 64 \N
121 9305 sarcophilus_harrisii DEVIL7.0 2011-03-Ensembl 0 1 \N \N 64 \N
122 9913 bos_taurus UMD3.1 2011-04-Ensembl 1 1 \N \N 64 \N
123 9595 gorilla_gorilla gorGor3.1 2009-08-Ensembl 1 0 \N \N 64 \N
124 30611 otolemur_garnettii OtoGar3 2011-06-Ensembl 0 1 \N \N 65 \N
125 9598 pan_troglodytes CHIMP2.1.4 2011-05-Ensembl 1 1 \N \N 65 \N
126 8049 gadus_morhua gadMor1 2010-01-Ensembl 0 0 \N \N 65 \N
127 4932 saccharomyces_cerevisiae R64-1-1 2011-09-SGD 1 1 \N \N 65 \N
128 7719 ciona_intestinalis KH 2011-08-Ensembl 1 1 \N \N 66 \N
129 7897 latimeria_chalumnae LatCha1 2011-09-Ensembl 0 1 \N \N 66 \N
130 8128 oreochromis_niloticus Orenil1.0 2011-05-Ensembl 0 1 \N \N 67 \N
131 43179 ictidomys_tridecemlineatus spetri2 2011-12-Ensembl 0 1 \N \N 67 \N
132 9823 sus_scrofa Sscrofa10.2 2011-09-Ensembl 1 1 \N \N 67 \N
134 10090 mus_musculus GRCm38 2012-01-Ensembl 1 1 \N \N 68 \N
135 9615 canis_familiaris CanFam3.1 2011-11-Ensembl 1 1 \N \N 68 \N
136 13735 pelodiscus_sinensis PelSin_1.0 2011-11-Ensembl 0 1 \N \N 68 \N
137 8083 xiphophorus_maculatus Xipmac4.4.2 2012-01-Ensembl 0 1 \N \N 69 \N
138 9669 mustela_putorius_furo MusPutFur1.0 2012-04-Ensembl 0 1 \N \N 69 \N
139 9685 felis_catus Felis_catus_6.2 2011-12-Ensembl 1 1 \N \N 70 \N
142 9031 gallus_gallus Galgal4 2011-12-Ensembl 1 1 \N \N 71 \N
143 6239 caenorhabditis_elegans WBcel235 2014-09-WormBase 1 1 \N \N 71 \N
144 8839 anas_platyrhynchos BGI_duck_1.0 2009-09-Ensembl 0 1 \N \N 73 \N
145 59894 ficedula_albicollis FicAlb_1.4 2012-05-Ensembl 0 1 \N \N 73 \N
146 7994 astyanax_mexicanus AstMex102 2013-04-Ensembl 0 1 \N \N 74 \N
147 9940 ovis_aries Oar_v3.1 2012-12-Ensembl 1 1 \N \N 74 \N
148 7918 lepisosteus_oculatus LepOcu1 2012-01-Ensembl 1 1 \N \N 74 \N
149 9361 dasypus_novemcinctus Dasnov3.0 2013-06-Ensembl 0 1 \N \N 74 \N
150 9606 homo_sapiens NCBI33 2014-01-Ensembl 1 1 \N \N 76 \N
151 9555 papio_anubis PapAnu2.0 2013-01-Ensembl 1 1 \N \N 76 \N
152 48698 poecilia_formosa PoeFor_5.1.2 2013-11-Ensembl 0 1 \N \N 76 \N
153 60711 chlorocebus_sabaeus ChlSab1.1 2014-03-Ensembl 1 1 \N \N 77 \N
154 7955 danio_rerio GRCz10 2014-09-Ensembl 1 1 \N \N 80 \N
155 10116 rattus_norvegicus Rnor_6.0 2014-09-Ensembl 1 1 \N \N 80 \N
156 7227 drosophila_melanogaster BDGP6 2014-05-FlyBase 1 1 \N \N 79 \N
4 31033 takifugu_rubripes FUGU4 2007-11-Ensembl 0 1 \N \N \N \N 24 \N
27 51511 ciona_savignyi CSAV2.0 2006-04-Ensembl 0 1 \N \N \N \N 39 \N
31 9544 macaca_mulatta MMUL_1 2006-01-Ensembl 1 1 \N \N \N \N 40 \N
33 9371 echinops_telfairi TENREC 2006-01-Ensembl 0 0 \N \N \N \N 40 \N
36 69293 gasterosteus_aculeatus BROADS1 2006-06-Ensembl 1 1 \N \N \N \N 40 \N
37 8090 oryzias_latipes MEDAKA1 2006-05-Ensembl 1 1 \N \N \N \N 41 \N
43 9258 ornithorhynchus_anatinus OANA5 2007-01-Ensembl 1 1 \N \N \N \N 42 \N
46 13616 monodelphis_domestica BROADO5 2007-02-Ensembl 1 1 \N \N \N \N 44 \N
48 37347 tupaia_belangeri TREESHREW 2006-10-Ensembl 0 0 \N \N \N \N 43 \N
49 9365 erinaceus_europaeus HEDGEHOG 2006-10-Ensembl 0 0 \N \N \N \N 43 \N
55 42254 sorex_araneus COMMON_SHREW1 2007-04-Ensembl 0 0 \N \N \N \N 45 \N
58 30608 microcebus_murinus micMur1 2007-07-Ensembl 0 0 \N \N \N \N 48 \N
60 9601 pongo_abelii PPYG2 2007-10-Ensembl 1 1 \N \N \N \N 49 \N
61 9796 equus_caballus EquCab2 2007-09-Ensembl 1 1 \N \N \N \N 49 \N
65 99883 tetraodon_nigroviridis TETRAODON8 2007-11-Ensembl 1 1 \N \N \N \N 50 \N
67 9978 ochotona_princeps pika 2008-01-Ensembl 0 0 \N \N \N \N 50 \N
69 10141 cavia_porcellus cavPor3 2008-03-Ensembl 0 1 \N \N \N \N 51 \N
78 9358 choloepus_hoffmanni choHof1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
79 9813 procavia_capensis proCap1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
80 9739 tursiops_truncatus turTru1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
82 9478 tarsius_syrichta tarSyr1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
83 10020 dipodomys_ordii dipOrd1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
84 30538 vicugna_pacos vicPac1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
85 132908 pteropus_vampyrus pteVam1 2008-11-Ensembl 0 0 \N \N \N \N 53 \N
87 59729 taeniopygia_guttata taeGut3.2.4 2008-08-Ensembl 1 1 \N \N \N \N 53 \N
91 9315 macropus_eugenii Meug_1.0 2009-02-Ensembl 0 0 \N \N \N \N 55 \N
98 9785 loxodonta_africana loxAfr3 2009-07-Ensembl 0 1 \N \N \N \N 57 \N
108 9986 oryctolagus_cuniculus OryCun2.0 2009-11-Ensembl 1 1 \N \N \N \N 60 \N
109 9646 ailuropoda_melanoleuca ailMel1 2010-01-Ensembl 0 1 \N \N \N \N 60 \N
111 28377 anolis_carolinensis AnoCar2.0 2010-09-Ensembl 1 1 \N \N \N \N 61 \N
112 9103 meleagris_gallopavo UMD2 2010-09-Ensembl 1 1 \N \N \N \N 61 \N
115 61853 nomascus_leucogenys Nleu1.0 2010-10-Ensembl 0 1 \N \N \N \N 62 \N
116 8364 xenopus_tropicalis JGI_4.2 2010-09-Ensembl 0 1 \N \N \N \N 62 \N
117 9483 callithrix_jacchus C_jacchus3.2.1 2010-02-Ensembl 1 1 \N \N \N \N 63 \N
118 59463 myotis_lucifugus Myoluc2.0 2010-12-Ensembl 0 1 \N \N \N \N 63 \N
120 7757 petromyzon_marinus Pmarinus_7.0 2011-02-Ensembl 0 1 \N \N \N \N 64 \N
121 9305 sarcophilus_harrisii DEVIL7.0 2011-03-Ensembl 0 1 \N \N \N \N 64 \N
122 9913 bos_taurus UMD3.1 2011-04-Ensembl 1 1 \N \N \N \N 64 \N
123 9595 gorilla_gorilla gorGor3.1 2009-08-Ensembl 1 0 \N \N \N \N 64 \N
124 30611 otolemur_garnettii OtoGar3 2011-06-Ensembl 0 1 \N \N \N \N 65 \N
125 9598 pan_troglodytes CHIMP2.1.4 2011-05-Ensembl 1 1 \N \N \N \N 65 \N
126 8049 gadus_morhua gadMor1 2010-01-Ensembl 0 0 \N \N \N \N 65 \N
127 4932 saccharomyces_cerevisiae R64-1-1 2011-09-SGD 1 1 \N \N \N \N 65 \N
128 7719 ciona_intestinalis KH 2011-08-Ensembl 1 1 \N \N \N \N 66 \N
129 7897 latimeria_chalumnae LatCha1 2011-09-Ensembl 0 1 \N \N \N \N 66 \N
130 8128 oreochromis_niloticus Orenil1.0 2011-05-Ensembl 0 1 \N \N \N \N 67 \N
131 43179 ictidomys_tridecemlineatus spetri2 2011-12-Ensembl 0 1 \N \N \N \N 67 \N
132 9823 sus_scrofa Sscrofa10.2 2011-09-Ensembl 1 1 \N \N \N \N 67 \N
134 10090 mus_musculus GRCm38 2012-01-Ensembl 1 1 \N \N \N \N 68 \N
135 9615 canis_familiaris CanFam3.1 2011-11-Ensembl 1 1 \N \N \N \N 68 \N
136 13735 pelodiscus_sinensis PelSin_1.0 2011-11-Ensembl 0 1 \N \N \N \N 68 \N
137 8083 xiphophorus_maculatus Xipmac4.4.2 2012-01-Ensembl 0 1 \N \N \N \N 69 \N
138 9669 mustela_putorius_furo MusPutFur1.0 2012-04-Ensembl 0 1 \N \N \N \N 69 \N
139 9685 felis_catus Felis_catus_6.2 2011-12-Ensembl 1 1 \N \N \N \N 70 \N
142 9031 gallus_gallus Galgal4 2011-12-Ensembl 1 1 \N \N \N \N 71 \N
143 6239 caenorhabditis_elegans WBcel235 2014-09-WormBase 1 1 \N \N \N \N 71 \N
144 8839 anas_platyrhynchos BGI_duck_1.0 2009-09-Ensembl 0 1 \N \N \N \N 73 \N
145 59894 ficedula_albicollis FicAlb_1.4 2012-05-Ensembl 0 1 \N \N \N \N 73 \N
146 7994 astyanax_mexicanus AstMex102 2013-04-Ensembl 0 1 \N \N \N \N 74 \N
147 9940 ovis_aries Oar_v3.1 2012-12-Ensembl 1 1 \N \N \N \N 74 \N
148 7918 lepisosteus_oculatus LepOcu1 2012-01-Ensembl 1 1 \N \N \N \N 74 \N
149 9361 dasypus_novemcinctus Dasnov3.0 2013-06-Ensembl 0 1 \N \N \N \N 74 \N
150 9606 homo_sapiens NCBI33 2014-01-Ensembl 1 1 \N \N \N \N 76 \N
151 9555 papio_anubis PapAnu2.0 2013-01-Ensembl 1 1 \N \N \N \N 76 \N
152 48698 poecilia_formosa PoeFor_5.1.2 2013-11-Ensembl 0 1 \N \N \N \N 76 \N
153 60711 chlorocebus_sabaeus ChlSab1.1 2014-03-Ensembl 1 1 \N \N \N \N 77 \N
154 7955 danio_rerio GRCz10 2014-09-Ensembl 1 1 \N \N \N \N 80 \N
155 10116 rattus_norvegicus Rnor_6.0 2014-09-Ensembl 1 1 \N \N \N \N 80 \N
156 7227 drosophila_melanogaster BDGP6 2014-05-FlyBase 1 1 \N \N \N \N 79 \N
13 \N schema_version 86
23 \N schema_version 88
2 \N schema_type compara
3 \N patch patch_84_85_a.sql|schema_version
4 \N patch patch_84_85_b.sql|gene_tree_root_attr
......@@ -15,3 +15,15 @@
16 \N patch patch_85_86_c.sql|gene_tree_root.species_tree_root_id
17 \N patch patch_85_86_d.sql|homology.high_confidence
18 \N patch patch_85_86_e.sql|gene_member_hom_stats
20 \N patch patch_86_87_a.sql|schema_version
21 \N patch patch_86_87_b.sql|gene_member_qc
22 \N patch patch_86_87_c.sql|msa_stats_to_stn_tag
24 \N patch patch_87_88_a.sql|schema_version
25 \N patch patch_87_88_b.sql|dnafrag_name_255
26 \N patch patch_87_88_c.sql|codon_table_id
27 \N patch patch_87_88_d.sql|cellular_component
28 \N patch patch_87_88_e.sql|biotype_group
29 \N patch patch_87_88_f.sql|has_seq_edits
30 \N patch patch_87_88_g.sql|genome_db.strain_name
31 \N patch patch_87_88_h.sql|exon_boundaries
32 \N patch patch_87_88_i.sql|genome_db.display_name
......@@ -48,10 +48,12 @@ CREATE TABLE `constrained_element` (
CREATE TABLE `dnafrag` (
`dnafrag_id` bigint(20) unsigned NOT NULL AUTO_INCREMENT,
`length` int(11) NOT NULL DEFAULT '0',
`name` varchar(40) NOT NULL DEFAULT '',
`name` varchar(255) NOT NULL DEFAULT '',
`genome_db_id` int(10) unsigned NOT NULL,
`coord_system_name` varchar(40) NOT NULL DEFAULT '',
`cellular_component` enum('NUC','MT','PT') NOT NULL DEFAULT 'NUC',
`is_reference` tinyint(1) NOT NULL DEFAULT '1',
`codon_table_id` tinyint(2) unsigned NOT NULL DEFAULT '1',
PRIMARY KEY (`dnafrag_id`),
UNIQUE KEY `name` (`genome_db_id`,`name`)
) ENGINE=MyISAM AUTO_INCREMENT=14026981 DEFAULT CHARSET=latin1;
......@@ -66,6 +68,17 @@ CREATE TABLE `dnafrag_region` (
KEY `synteny_reversed` (`dnafrag_id`,`synteny_region_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `exon_boundaries` (
`gene_member_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) unsigned NOT NULL,
`dnafrag_start` int(11) NOT NULL,
`dnafrag_end` int(11) NOT NULL,
`sequence_length` int(10) unsigned NOT NULL,
`left_over` tinyint(1) NOT NULL DEFAULT '0',
KEY `seq_member_id` (`seq_member_id`),
KEY `gene_member_id` (`gene_member_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `external_db` (
`external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`db_name` varchar(100) NOT NULL,
......@@ -126,6 +139,7 @@ CREATE TABLE `gene_member` (
`source_name` enum('ENSEMBLGENE','EXTERNALGENE') NOT NULL,
`taxon_id` int(10) unsigned NOT NULL,
`genome_db_id` int(10) unsigned DEFAULT NULL,
`biotype_group` enum('coding','snoncoding','lnoncoding','mnoncoding','LRG') NOT NULL DEFAULT 'coding',
`canonical_member_id` int(10) unsigned DEFAULT NULL,
`description` text,
`dnafrag_id` bigint(20) unsigned DEFAULT NULL,
......@@ -155,6 +169,18 @@ CREATE TABLE `gene_member_hom_stats` (
PRIMARY KEY (`gene_member_id`,`collection`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_member_qc` (
`gene_member_stable_id` varchar(128) NOT NULL,
`genome_db_id` int(10) unsigned NOT NULL,
`seq_member_id` int(10) DEFAULT NULL,
`n_species` int(11) DEFAULT NULL,
`n_orth` int(11) DEFAULT NULL,
`avg_cov` float DEFAULT NULL,
`status` varchar(50) NOT NULL,
KEY `genome_db_id` (`genome_db_id`),
KEY `gene_member_stable_id` (`gene_member_stable_id`)
) ENGINE=MyISAM DEFAULT CHARSET=latin1;
CREATE TABLE `gene_tree_node` (
`node_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
`parent_id` int(10) unsigned DEFAULT NULL,
......@@ -262,6 +288,8 @@ CREATE TABLE `genome_db` (
`has_karyotype` tinyint(1) NOT NULL DEFAULT '0',
`is_high_coverage` tinyint(1) NOT NULL DEFAULT '0',
`genome_component` varchar(5) DEFAULT NULL,
`strain_name` varchar(40) DEFAULT NULL,
`display_name` varchar(255) DEFAULT NULL,
`locator` varchar(400) DEFAULT NULL,
`first_release` smallint(6) DEFAULT NULL,
`last_release` smallint(6) DEFAULT NULL,
......@@ -406,7 +434,7 @@ CREATE TABLE `meta` (
PRIMARY KEY (`meta_id`),
UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
KEY `species_value_idx` (`species_id`,`meta_value`(255))
) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1;
) ENGINE=MyISAM AUTO_INCREMENT=33 DEFAULT CHARSET=latin1;
CREATE TABLE `method_link` (
`method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
......@@ -517,6 +545,8 @@ CREATE TABLE `seq_member` (
`genome_db_id` int(10) unsigned DEFAULT NULL,
`sequence_id` int(10) unsigned DEFAULT NULL,
`gene_member_id` int(10) unsigned DEFAULT NULL,
`has_transcript_edits` tinyint(1) NOT NULL DEFAULT '0',
`has_translation_edits` tinyint(1) NOT NULL DEFAULT '0',
`description` text,
`dnafrag_id` bigint(20) unsigned DEFAULT NULL,
`dnafrag_start` int(10) DEFAULT NULL,
......
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