Table 1.
Trusted U7 snRNA sequences*
| Species | Assembly | Sequence | Start | Stop | Ori. | Database ID | ψ |
|---|---|---|---|---|---|---|---|
| Mus musculus | Ensembl 43 | Chr.6 | 124,706,844 | 124,706,905 | − | ENSMUSG00000065217 | 27 |
| Rattus norvegicus | Ensembl 43 | Chr.X | 118,163,804 | 118,163,865 | − | ENSRNOG00000034996 | 31 |
| Rattus norvegicus | Ensembl 43 | Chr.4 | 160,870,934 | 160,870,995 | − | ENSRNOG00000035016 | 31 |
| Homo sapiens | Ensembl 43 | Chr.12 | 6,923,240 | 6,923,302 | + | ENSG00000200368 | 91 |
| Macaca mulatta | Ensembl 43 | Chr.11 | 7,125,496 | 7,125,557 | + | ENSMMUG00000027525 | 95 |
| Otolemur garnettii | PreEnsembl 43 | Scaffold_102959 | 117,572 | 117,633 | − | 0 | |
| Oryctolagus cuniculus | Ensembl 43 | GeneScaffold_1693 | 111,485 | 111,546 | + | 3 | |
| Procavia capensis | NCBI TRACE | 175719230 | 275 | 336 | + | – | |
| Loxodonta africana | Ensembl 43 | Scaffold_60301 | 4,254 | 4,314 | − | 2 | |
| Echinops telfairi | Ensembl 43 | GeneScaffold_2204 | 10,742 | 10,803 | + | ENSETEG00000020899 | 57 |
| Felis catus | Ensembl 43 | GeneScaffold_69 | 192,907 | 192,968 | + | 7 | |
| Canis familiaris | Ensembl 43 | Chr.27 | 41,131,749 | 41,131,810 | − | ENSCAFG00000021852 | 2 |
| Myotis lucifugus | PreEnsembl 43 | Scaffold_168837 | 32,294 | 32,356 | − | 0 | |
| Equus caballus | PreEnsembl 43 | Scaffold_58 | 7,463,562 | 7,463,623 | + | 0 | |
| Bos taurus | Ensembl 43 | Chr.5 | 10,349,126 | 10,349,187 | − | AAFC03061782 | 8 |
| Tursiops truncatus | NCBI TRACE | 194072802 | 598 | 659 | + | – | |
| Dasypus novemcinctus | Ensembl 43 | GeneScaffold_1944 | 24,469 | 24,530 | + | 16 | |
| Spermophilus tridec. | PreEnsembl 43 | Scaffold_139061 | 45,428 | 45,489 | − | 0 | |
| Erinaceus europaeus | Ensembl 43 | GeneScaffold_2232 | 5,133 | 5,194 | + | 30 | |
| Monodelphis domestica | Ensembl 43 | Un | 131,411,333 | 131,411,393 | + | ENSMODG00000022029 | 1 |
| Gallus gallus | Ensembl 43 | Chr.1 | 80,484,148 | 80,484,212 | + | ENSGALG00000017891 | 1 |
| Taeniopygia guttata | NCBI TRACE | TGAB-afg09c06.b1 | 683 | 748 | − | – | |
| Anolis carolinensis | NCBI TRACE | G889P8207RM16.T0 | 106 | 171 | − | – | |
| Xenopus tropicalis | Ensembl 43 | Scaffold_883 | Cluster: ~20 copies from 272,500 to end | ||||
| Xenopus laevis | GenBank | X64404 | Cluster (partial) | ||||
|
Xenopus borealis |
GenBank |
Z54313 |
Cluster (partial) |
||||
| Danio rerio | Ensembl 43 | Chr.16 | Cluster: 4 copies from 13,708,000 to 13,723,000 | ||||
| Takifugu rubripes | Ensembl 43 | Scaffold_205 | 229,679 | 229,736 | + | 0 | |
| Tetraodon nigroviridis | Ensembl 43 | Chr.8 | 9,059,483 | 9,059,541 | + | (1) | |
| Gasterosteus aculeatus | Ensembl 43 | GroupXX | 11,616,333 | 11,616,392 | − | 0 | |
| Oryzias latipes | Ensembl 43 | Chr.16 | 17,393,002 | 17,393,059 | + | 0 | |
| Strongylocentrotus p. | BCM_Spur_v2.1 | Cluster: 2 sequences each on scaffolds 83935 and 88560 | |||||
|
Psammechinus miliaris |
GenBank |
Cluster: 5 genes, 1 sequence=M13311.1 |
|||||
| Drosophila melanogaster | UCSC | 3L | 3,577,355 | 3,577,425 | + | CR33504 | 0 |
| Drosophila ananassae | CAF-1 | CH902618.1 | 9,849,345 | 9,849,414 | − | 0 | |
| Drosophila erecta | CAF-1 | CH954178.1 | 6,292,889 | 6,292,959 | + | 1 | |
| Drosophila grimshawi | CAF-1 | CH916366.1 | 10,347,991 | 10,348,062 | + | 1 | |
| Drosophila mojavensis | CAF-1 | CH933809.1 | 2,924,982 | 2,925,053 | − | 1 | |
| Drosophila persimilis | CAF-1 | CH479328.1 | 89,311 | 89,383 | − | 0 | |
| Drosophila pseudoobscura | CAF-1 | CH379070.2 | 5,738,714 | 5,738,786 | + | 1 | |
| Drosophila simulans | CAF-1 | CM000363.1 | 3,136,652 | 3,136,582 | − | 1 | |
| Drosophila virilis | CAF-1 | CH940647.1 | 4,512,836 | 4,512,907 | − | 1 | |
| Drosophila willistoni | CAF-1 | CH964101.1 | 1,418,210 | 1,418,280 | + | 0 | |
| Drosophila yakuba | CAF-1 | CM000159.2 | 4,146,836 | 4,146,905 | + | 0 | |
*
ψ gives the number of paralog loci, most likely U7 pseudogenes, defined by a BLAST E-value less than 0.001 compared with the functional copy. CAF-1 refers to the genome freezes provided by the Drosophila Comparative Genomics Consortium. These sequences were retrieved from http://rana.lbl.gov/drosophila/caf1.html in December 2006. The D. melanogaster sequence is the one used by the UCSC Genome Browser (http://genome.ucsc.edu/) (Release 4; Apr. 2004, UCSC version dm2). The sea urchin genome BCM_Spur_v2.1 was obtained from ftp://ftp.hgsc.bcm.tmc.edu/pub/data/Spurpuratus/fasta/Spur_v2.1/linearScaff.