RetrogeneDB ID: | retro_itri_1694 | ||
Retrocopy location | Organism: | Squirrel (Ictidomys tridecemlineatus) | |
| Coordinates: | JH393641.1:674288..675761(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSSTOG00000024553 | |
| Aliases: | None | ||
| Status: | KNOWN_PSEUDOGENE | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | TFE3 | ||
| Ensembl ID: | ENSSTOG00000014237 | ||
| Aliases: | None | ||
| Description: | transcription factor binding to IGHM enhancer 3 [Source:HGNC Symbol;Acc:11752] |
Retrocopy-Parental alignment summary:
>retro_itri_1694
CTACAAGCTCAAAAGCCAACCCCTACCCCTACGCTCCAGGCCACACCAACCACCCCAGCTACATTCACTACATCGTCTTC
TGCAGGGGGCTCCAGGACCCCTGCCATGATGTCATCTTCTTCACACCGGGCCTTGCTGCAGGAGAGGCCTGAGCGTCGCG
AACAGAGTGCAGCTGCTTCCTTCCCCAGTCCTGCTCCTGCCTCGCCTGCCATCTCTGTGGTTGGTGTCTCTGCTGGGGGC
CACACGATGGGCCGGCCACTCCCTGCTCAGGTGCCCAGGGAGGTGCTCAAGGTACAGACCCCCCTGGAGAACCCAACGCG
CTACCACCTGCAGCAGGTGAGTCGGCAGCAGGTGAAACAGTACCTGTCCACTACACTTGGGCCCAGGCTGGCTTCCCAGG
CTCTCACCCCACCACCAGGGCCCACCAGTGCCCAGCCGCTGCCTGCCCTTGAGGCTGCTCACGCCACTGGTCCCACAGGC
CGCACTCCCAGCAGCCCCACAGCACTGCTCACCACCAGGTCCAGCTCAGAGCAGGAGATTGATGACGACATTGATGAGAT
CATCAGCCTGGAGTCCAGTTCCAGTGATGAGATGCTCAGCTACCTGCCCGGAGGCACCGCAGGGCTGCAGCTCCCCAGCT
CGCTGCCTGCCTCAGGGAATCTGCTTGACTTGTACAGTAATCAGGGTGTGGCCACGCCAGCCATCACTGTCAGCAACTCC
TGTCCAGCTGAGCTGCCTAACATCAAACGGGAGATCTCTGGAACCAAGGCAAAGGCCCTGTTGAAGGAACGCCAGAAGAA
AGACAATCACAACCGACGCAGGCGATTCAACATTGACTATAGGATCAAGGAGTTGGGCACCCTCATTCCCAAGTCCAATG
ATCCAGAGATGTGCTGGAACAAGGGCACCATCCTGGATGCCTCTGTGGATTATATCCGCAAGTTGCAGAAGGAACAACAG
CGCTCCAAAGATCTGGAAAGTCATCTTCGGTCCCTGGAGCAAGCCAATGGCATCCTGCAGCTTCGAATTCAGGAGCTAGA
ACTGCAGGCCCAGATCCATGGTTTGCCAGTGCCTCCCACCCCAGGGCTGCTCTCCCTAACCACGACTTCAGCCTCTGACA
GCCTCAAGCCAGAGCAGCTGGACATTGAGGAGGAGGGCAGGTCAGGCACAGCAGCATTTCATGTAGCAGGGGGACCTGCC
CAGAATGCTCCCCATCAGCAGCCCCCAGAACCACCTTCAGATGCTCTTCTGGACCTGCATTTTCCCAGTGATCACCTGGG
GGACCTGGGAGACCCCTTCCACCTGGAGCTGGAGGACATTCTGATGGAGGAGGAGGAGGTGGTGGGAGGACTGTGTGGGA
GGGGTATCCTGTCTCCACTGCGGGCTGCCTCTGACCCCCTGCTTTCTTCAGTATCCCCGGCTGTCTCAAAGGCCAGCAGC
CAGGGCAGCAGCTTCAGCAAGGAGGAAGAGTCC
ORF - retro_itri_1694 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 80.16 % |
| Parental protein coverage: | 85.91 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | LQATPTTPATLSTSSSAGGSRTPAMSSSSSSRVLLRQQLMRAQAQEQERRERREQAAAASFPSPAPASPA |
| LQA...TP.................SS...SR...........A..QER.ERREQ.AAASFPSPAPASPA | |
| Retrocopy | LQAQKPTPTPTLQATPTTPATFTTSSSAGGSRTPAMMSSSSHRALLQERPERREQSAAASFPSPAPASPA |
| Parental | ISVVGVSAGGHTLGRPPPAQVPREVLKVQTHLENPTRYHLQQARRQQVKQYLSTTLGPKLASQALTPPPG |
| ISVVGVSAGGHT.GRP.PAQVPREVLKVQT.LENPTRYHLQQ..RQQVKQYLSTTLGP.LASQALTPPPG | |
| Retrocopy | ISVVGVSAGGHTMGRPLPAQVPREVLKVQTPLENPTRYHLQQVSRQQVKQYLSTTLGPRLASQALTPPPG |
| Parental | PTSAQPLPAPEAAHTTGPTGSAPNSPMALLTIGSSSEKEIDDVIDEIISLESSYNDEMLSYLPGGTAGLQ |
| PTSAQPLPA.EAAH.TGPTG..P.SP.ALLT..SSSE.EIDD.IDEIISLESS..DEMLSYLPGGTAGLQ | |
| Retrocopy | PTSAQPLPALEAAHATGPTGRTPSSPTALLTTRSSSEQEIDDDIDEIISLESSSSDEMLSYLPGGTAGLQ |
| Parental | LPSTLPVSGNLLDVYSNQGVATPAITVSNSCPAELPNIKREISETEAKALLKERQKKDNHNLIERRRRFN |
| LPS.LP.SGNLLD.YSNQGVATPAITVSNSCPAELPNIKREIS.T.AKALLKERQKKDNHN...RRRRFN | |
| Retrocopy | LPSSLPASGNLLDLYSNQGVATPAITVSNSCPAELPNIKREISGTKAKALLKERQKKDNHN---RRRRFN |
| Parental | INDRIKELGTLIPKSNDPEMRWNKGTILKASVDYIRKLQKEQQRSKDLESRQRSLEQANRSLQLRIQELE |
| I..RIKELGTLIPKSNDPEM.WNKGTIL.ASVDYIRKLQKEQQRSKDLES..RSLEQAN..LQLRIQELE | |
| Retrocopy | IDYRIKELGTLIPKSNDPEMCWNKGTILDASVDYIRKLQKEQQRSKDLESHLRSLEQANGILQLRIQELE |
| Parental | LQAQIHGLPVPPTPGLLSLTTTSASDSLKPEQLDIEEEGRPGTAAFHVAGGPAQNAPHQQPPAPPSDALL |
| LQAQIHGLPVPPTPGLLSLTTTSASDSLKPEQLDIEEEGR.GTAAFHVAGGPAQNAPHQQPP.PPSDALL | |
| Retrocopy | LQAQIHGLPVPPTPGLLSLTTTSASDSLKPEQLDIEEEGRSGTAAFHVAGGPAQNAPHQQPPEPPSDALL |
| Parental | DLHFPSDHLGDLGDPFHLGLEDILMEEEEGVVGGLSGGALSPLRAASDPLLSSVSPAVSKASSRRSSFSM |
| DLHFPSDHLGDLGDPFH....................G.LSPLRAASDPLLSSVSPAVSKASS..SSFS. | |
| Retrocopy | DLHFPSDHLGDLGDPFHXXXXXXXXXXXXXXXXXXXXGILSPLRAASDPLLSSVSPAVSKASSQGSSFSK |
| Parental | EEES |
| EEES | |
| Retrocopy | EEES |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_1694 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1694 was not experimentally validated.
Retrocopy orthology:
Ictidomys tridecemlineatus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Ictidomys tridecemlineatus | ENSSTOG00000014237 | 1 retrocopy |
retro_itri_1694 ,
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