RetrogeneDB ID: | retro_xtro_2 | ||
Retrocopy location | Organism: | Xenopus (Xenopus tropicalis) | |
| Coordinates: | GL173441.1:386499..387861(-) | ||
| Located in intron of: | ENSXETG00000005043 | ||
Retrocopy information | Ensembl ID: | ENSXETG00000032820 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | fbxw7 | ||
| Ensembl ID: | ENSXETG00000009388 | ||
| Aliases: | None | ||
| Description: | F-box and WD repeat domain containing 7 [Source:Jamboree;Acc:XB-GENE-1000486] |
Retrocopy-Parental alignment summary:
>retro_xtro_2
ACTGGGGCCTCCCACCAGCCTACAGGAGGAGCCCAAATTGCTGCTAAACTGGTCGGCCGGAAGGAGAAGCAGAAGAAAAT
GGAAGCCGGGGAGCCCCAGGACTTTATCTCTTCATTCCCTGATGAGTTGGCATTGCGCATCCTCTCGTACCTTGATGCCA
AGGATATCCTGCAGGTGGCGCAGACTTGCCAGCGCTGGAGAGAGTTGGCTGAGGATGAAGGCCTGTGGCAGGGAAAGTGC
AAAGTGGATCGGATCGACGTGGCGAGAAGCAGAGATCCGGGTTCGCCGGCCGACCCATGGAAAAGCGCCTACATCCGTCA
GCACCAGATCAACACCAACTGGCGCCGGGGGAGATTCCGATCCATAAACTTACGCCTGCGGCACGACGACGAGGTCATTA
CCTGCTTGGAGTTTGATGGGAGCCGAATACTCAGCAGCGACAGTTGGAAGACAATCAAGGTCTGGTCGGCGGTTACGGGC
GAATGTCTGAGGACGCTCGTCGGTCACGCGGATATTATATTTACAATGCAAATGAGCTCGGAGATTATAATTAGCGGATC
CCTGGATCAGACCTTGAAAGTGTGGGACGCAGAGACCGGGGATTGTATTCACACGTTACGCGGCCATAGCGCCGGCGTGG
AGTGCGTGCATCTCTGCGGGAAAAGGGCCGTCAGTGGCTCCCAAGACAGAACCATCAGAGTCTGGGACATCGAGACCGGC
CGCTGCCTTCACCTCCTCACCGGGCACCGAGACTTCATCAAATGTGTTCGGTATCACGGGCAAAGGGTGGTGAGCTTTGC
GTACGATTCCACCGTGAAAATATGGGACCCCGAGAGTGAGAGCTGCGTGCGCACCCTGCAAGGCCGCGCCGACAAGACCT
CCAGTTTAGAGTCCGACGGGGTCCACGTGGTCACCGTGTCCGACAGAACCACCATAAGAGTCTGGGATGAGGCGACGGGG
CGATGTATCCAAACACTGACCGGATACCCGTTCGCCATTAGTGCGGTGGCGCTGGCGGGCAATATCCTCGTGTCCGGAAA
CGCTGATTGCACCGCTAACGTGTGGGACATAAAAACGGGGCGGTGCTTGCACACTCTGCGCGGCCCTGCCCACATGAGAA
GCCGATTGGAAAGCGTTCAGCTGAGGAGGGACTGCGTCATAGCCAGCGCCGAAGACGGAACCGTCACCCTGTGGGACTGG
AAAAGTGGGGCCTTCTTGCAGAACCTGGCGCTGTCGCACACCAAGGGGCCCTGTTCCATCCAGTTCCAAGTCTCCAACAC
AAAACTCGTCTGCGCCGTCTCGAAAAGATCCAGAGTCGCGTTCGAGCCAACAAAGGTGGTGGTTCTGGACTTTGGTGCCG
AC
ORF - retro_xtro_2 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 56.87 % |
| Parental protein coverage: | 51.49 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | PGFTHSPWKSAYIRQHRIDTNWRRGELKSPKVLKGHDDHVITCLQFCGNRIVSGSDDNTLKVWSAVTGKC |
| PG....PWKSAYIRQH.I.TNWRRG...S......HDD.VITCL.F.G.RI.S.....T.KVWSAVTG.C | |
| Retrocopy | PGSPADPWKSAYIRQHQINTNWRRGRFRSINLRLRHDDEVITCLEFDGSRILSSDSWKTIKVWSAVTGEC |
| Parental | LRTLVGHTGGVWSSQMRDNIIISGSTDRTLKVWNAETGECIHTLYGHTSTVRCMHLHEKRVVSGSRDATL |
| LRTLVGH.......QM...IIISGS.D.TLKVW.AETG.CIHTL.GH...V.C.HL..KR.VSGS.D.T. | |
| Retrocopy | LRTLVGHADIIFTMQMSSEIIISGSLDQTLKVWDAETGDCIHTLRGHSAGVECVHLCGKRAVSGSQDRTI |
| Parental | RVWDIETGQCLHVLMGHVAAVRCVQYDGRRVVSGAYDFMVKVWDPETETCLHTLQGHTNRVYSLQFDGIH |
| RVWDIETG.CLH.L.GH.....CV.Y.G.RVVS.AYD..VK.WDPE.E.C..TLQG......SL..DG.H | |
| Retrocopy | RVWDIETGRCLHLLTGHRDFIKCVRYHGQRVVSFAYDSTVKIWDPESESCVRTLQGRADKTSSLESDGVH |
| Parental | VVSGSLDTSIRVWDVETGNCIHTLTGHQSLTSGMELKDNILVSGNADSTVKIWDIKTGQCLQTLQGPNKH |
| VV..S..T.IRVWD..TG.CI.TLTG.....S...L..NILVSGNAD.T...WDIKTG.CL.TL.GP... | |
| Retrocopy | VVTVSDRTTIRVWDEATGRCIQTLTGYPFAISAVALAGNILVSGNADCTANVWDIKTGRCLHTLRGPAHM |
| Parental | QSAVTCLQFNKNFVITSSDDGTVKLWDLKTGEFIRNLVTLESGGSGGVVWRIRASNTKLVCAVG--SRNG |
| .S.....Q.....VI.S..DGTV.LWD.K.G.F..NL......G..........SNTKLVCAV...SR.. | |
| Retrocopy | RSRLESVQLRRDCVIASAEDGTVTLWDWKSGAFLQNLALSHTKGPCSIQFQV--SNTKLVCAVSKRSRVA |
| Parental | TEETKLLVLDFDVD |
| .E.TK..VLDF..D | |
| Retrocopy | FEPTKVVVLDFGAD |
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 | 0 .14 RPM | 68 .47 RPM |
| SRP007412_heart | 0 .06 RPM | 9 .81 RPM |
| SRP007412_kidney | 0 .06 RPM | 9 .81 RPM |
| SRP007412_liver | 0 .76 RPM | 3 .45 RPM |
| SRP007412_skeletal_muscle | 0 .12 RPM | 7 .09 RPM |
Xenopus tropicalis was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_xtro_2 retrocopy.
Xenopus tropicalis was not studied using FANTOM5 data.
retro_xtro_2 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 | ENSXETG00000009388 | 1 retrocopy |
retro_xtro_2 ,
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