RetrogeneDB ID: | retro_xtro_13 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL173263.1:21879..23421(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | ENSXETG00000015938 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | cyp1b1 | ||
| Ensembl ID: | ENSXETG00000025303 | ||
| Aliases: | None | ||
| Description: | cytochrome P450, family 1, subfamily B, polypeptide 1 [Source:Jamboree;Acc:XB-GENE-951460] |
Retrocopy-Parental alignment summary:
>retro_xtro_13
GAATGGAAAGACAGTGTCCAACCAGCCCTGGTGTTCTCTTTCTTGATACTCATCTGCCTAGAGGTGTGCCTATGGCTGAG
GAACAATGGGCAGAGGAGGTCTCCCCCTGGACCCTTTCCCTGGCCTGTGGTGGGCAATGCAATGCAACTCGGGCAACTTC
CCCATCTCACCTTTTGTAAAATGTCTCAGAAATATGGCAACGTATTCCAGATCAGACTGGGTACCCAAGACATTGTGGTG
CTGAATGGAGATTCCACCATAAGGGAAGCTCTGGTGAAGCATAGCAAGGAATTTGCTGGGAGACCCAACTTCTCCTCCTT
CCAGCTTATCTCTGGGGGCAAAAGCATTGCTTTTGGGGGCTATTCTACTCTCTGGAAGGCTCAAAAGAAAATTGCTCACT
CAACCCTTAGAGCGTTTTCTACTGTCAACAGCAAAACGCAGAAGCTATTTGAGAAGCATGTGGTGGCAGAGGCGCAGGAC
CTCATTGACGTTTTTCTGCGCTTGACCTCTGAGGAGGAATATTTTGATCCTACACGTGAGTGCACGGTGGCCGCTGCCAA
TGTCATCTGTGCCTTGTGCTTTGGCAAACGTTACAGCCACGATGATGAGGAGTTCAAAGCCCTGATTGGGAGAAATGACA
AGTTTGGCCAAACCGTGGGCGCTGGTAGCCTTGTAGACATCATGCCCTGGCTTCTAACTTTCCCAAACCCAGTGCGCAGC
CTCTATCAGAGCTTCAAAGATCTCAACTGGGAATTTTATGGTTTTGTCAAGGAGAAGGTAAGCCACCACCGGCAAACCTA
CAACCCAGAGATCACCAGGGACATGAGTGATGCCTTCATCAGTCATATAGACAATGCAGAAGGGATAGAAGCAGGTGATG
GTCTGAGCAAGGACTATGTGGAAAGCATTGTCAATGATATCCTGGGCGCAGGGCAAGACACCACTGCTACTGCCCTCACC
TGGATTCTGCTCTTACTCATTAAATACCCTGACATTCAGCAGAAGCTGCAGGAAGAGATAGACCTGGTGGTGGGACCCAA
CCGACTTCCCACAGCAGATGACAAAGTTCAGCTCCCCTATGTCCAAGCCTTTATCTATGAAGCCCTGCGTTTCAGCAGCT
TCGTGCCAGTCACTATCCCGCACTCTACCACCAGTGATGTGGTCATTGATGGCTTCTACATTCCCAAGGACACGGTGGTC
TTTGTTAACCAGTGGTCAGTCAACCATGATGAATCCAAATGGAAAAACCCAGATGTTTTTGACCCCAGCAGGTTTTTGGA
TGAAGAGGGTCAGCTGGACAGAGATGCTGCTTTCGGGGTGATGATCTTCTCCGTGGGCAAAAGGAGATGTATTGGGGACC
AGCTATCTATGCTACAGATATTTCTATTCACGGCCATCTTTCTCCACCAGTGCACCCTCCATGGCAACCCTAAGGAGATA
CCCACCATGGACTGTATCAGTGGCTTATCTCTCAAACCACTGCCCTATGGGATGTCCGTTAGAGCCAGAGTTGGTAGAAC
AACCATGAAAGAACCTGTCTGA
ORF - retro_xtro_13 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 53.64 % |
| Parental protein coverage: | 91.14 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | WIRSS----QPPGPFPWPLFGNALQMGSYPHLAFIDLAKRYGNIFQIKLGSQKIVVLNGDLVIRHALLHK |
| W.R.......PPGPFPWP..GNA.Q.G..PHL.F......YGN.FQI.LG.Q.IVVLNGD..IR.AL... | |
| Retrocopy | WLRNNGQRRSPPGPFPWPVVGNAMQLGQLPHLTFCKMSQKYGNVFQIRLGTQDIVVLNGDSTIREALVKH |
| Parental | GEDFAGRPKFTSYQFVSGGRSLAFGCYTEKWKAHRKLAHSTVRAFSTGNPQTKRCLAENVLKEARDLIAL |
| ...FAGRP.F.S.Q..SGG.S.AFG.Y...WKA..K.AHST.RAFST.N..T.......V..EA.DLI.. | |
| Retrocopy | SKEFAGRPNFSSFQLISGGKSIAFGGYSTLWKAQKKIAHSTLRAFSTVNSKTQKLFEKHVVAEAQDLIDV |
| Parental | FSELGQGGKYFYPGRHTVVSVANVMSAVCFGRRYQHGDLEFQSLLSNNDKFTRSVGAGSLVDVMPWLQRF |
| F..L.....YF.P.R...V..ANV..A.CFG.RY.H.D.EF..L...NDKF...VGAGSLVD.MPWL..F | |
| Retrocopy | FLRLTSEEEYFDPTRECTVAAANVICALCFGKRYSHDDEEFKALIGRNDKFGQTVGAGSLVDIMPWLLTF |
| Parental | PNPVRSVFRSFQQVNYEFYDFVYKKFLLHRNTANQAVTRDMMDAFIHILITKEG----KSLEAEHVPSTV |
| PNPVRS...SF...N.EFY.FV..K...HR.T.N...TRDM.DAFI......EG......L....V.S.V | |
| Retrocopy | PNPVRSLYQSFKDLNWEFYGFVKEKVSHHRQTYNPEITRDMSDAFISHIDNAEGIEAGDGLSKDYVESIV |
| Parental | TDIFGASQDTLSTALQWVIFFLVRYPEIQTKLQDEMDRVIGKDRLPCIEDQPKLPYLMAFLYEFMRFSSF |
| .DI.GA.QDT..TAL.W....L..YP.IQ.KLQ.E.D.V.G..RLP...D...LPY..AF.YE..RFSSF | |
| Retrocopy | NDILGAGQDTTATALTWILLLLIKYPDIQQKLQEEIDLVVGPNRLPTADDKVQLPYVQAFIYEALRFSSF |
| Parental | VPITIPHATTKNTTIMGYQIPKDTVVFVNQWSVNHDPQKWSNPGEFNPSRFLDDNGLINKDLVSNIMIFS |
| VP.TIPH.TT....I.G..IPKDTVVFVNQWSVNHD..KW.NP..F.PSRFLD..G....D.....MIFS | |
| Retrocopy | VPVTIPHSTTSDVVIDGFYIPKDTVVFVNQWSVNHDESKWKNPDVFDPSRFLDEEGQLDRDAAFGVMIFS |
| Parental | VGKRRCIGEELSKIQLFMFSSILLHQCIFTALPADNLNPKGDYGLSIKPKPFRISMTLRHG |
| VGKRRCIG..LS..Q.F.F..I.LHQC.....P..........GLS.KP.P...S...R.G | |
| Retrocopy | VGKRRCIGDQLSMLQIFLFTAIFLHQCTLHGNPKEIPTMDCISGLSLKPLPYGMSVRARVG |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain | 5 .47 RPM | 1 .04 RPM |
| SRP007412_heart | 6 .33 RPM | 0 .00 RPM |
| SRP007412_kidney | 6 .33 RPM | 0 .00 RPM |
| SRP007412_liver | 20 .82 RPM | 0 .00 RPM |
| SRP007412_skeletal_muscle | 3 .88 RPM | 0 .00 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_13 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_13 was not experimentally validated.
Retrocopy orthology:
Xenopus tropicalis 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 | |
|---|---|---|---|
| Xenopus tropicalis | ENSXETG00000025303 | 1 retrocopy |
retro_xtro_13 ,
|