RetrogeneDB ID: | retro_btau_1761 | ||
Retrocopy location | Organism: | Cow (Bos taurus) | |
| Coordinates: | X:100752826..100754037(+) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | NCOA4 | ||
| Ensembl ID: | ENSBTAG00000019565 | ||
| Aliases: | None | ||
| Description: | nuclear receptor coactivator 4 [Source:RefSeq peptide;Acc:NP_001069336] |
Retrocopy-Parental alignment summary:
>retro_btau_1761
CAGGTCATCATCACATTTGGGTCTCTAAGGACCATTCCAAATTGAGAACATGATGGTTCATGCTAGTTCATCAAACATTG
GATTCTCTCTGGAGAAAAGAGGCTGTACCACATTGCCAGAGCAGAAGTCAGCATCCAGCACCATAGCTGTCCCTCACAGG
AAATGGCTCCATTGGGATCAAACCTGCCAATGGTCACCAGGCTCCCTAAATACCCATAACTAGTCTCCAGGATGAGCTCA
CTCAAAAGTAGACCTTGTCAAAGAGTCAGAATTCTTCCAGAGCCTGAAATTTCTTCAGTAATGTCTGCGCCAACCTAAGA
TGCTTGGAAAACTGGCTCCACAAGAGTCAGAAACAAGAAATTTCTGAAAAACAAAGTTACCAAAATGTAATGGCTATTCT
ATTATCAATTCTTCATTGAAAATGAAAATGTTGGATGTTTAAGGCTTCTTAGTCAAGATGAAATGGACATTTCTGATTGA
GTTACCAGTCTGGTAACTCCCCAGGAATCACATAATCTTGAGAAGCCTGGGAATGACAGCTATGAAACCAGTGAGAAGTT
CTTGTTCAAGGTGTTTCCAGTAGTCCTACAGTGTGAATGATTGGCTTGTCAAGCCTGATTCCTGTGCCAGTTGTCAGAGT
AACCAGCATAAAGGTGGGGAGACTGGAAATCTGGGCAATCTGAAGTGCCTAGATTGCCACTTGGAGGCCACAAAACCCAT
GCTCACTCCCAGTGTCATTACTTAAGATTGGCTTGTCCAGAACTGTCAAGATCCATACAAAGTAGAGGAGGTCAACAAAG
CCAATGAACCCTATGTAAGCTTTGCAGAGTGCATGGATGATGAAAACTGTGAGAAGGAATCTCTGTGTAAAGACTTCTGA
AGAAAGAAGGAAAGGATAAAATGGTATGTCTTTGGAACAAAAACCTGAACCTGAGAAATACTCCCTGAATATGTGGCTCT
GTCCATCCAGAAAATAGGCAACTGAGAAAGCTACGACATTCAAGACAGTGTACTCTTTTAGAATTGCTGATTCCTTCCAA
GTTATAAGTAACAATTGCTTGTTAGAGTGGCACATTACCCCCTCATGCAAAGAAGGATGTCCCAAGGAAGTGCCTCTTAC
TGAGGACAGAGCTGTCAAACAAAAGCTTACGGGCCTCTTGGCCACTTTCTGGTGTCCCTTTATCACAACTGACTGGGTCT
TTCCAGGAAAG
ORF - retro_btau_1761 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 63.96 % |
| Parental protein coverage: | 65.18 % |
| Number of stop codons detected: | 7 |
| Number of frameshifts detected: | 7 |
Retrocopy - Parental Gene Alignment:
| Parental | QAITTFGSLKTI-QIPEHLMAHASSSNIGSFLEKRGYIPLPEQKSASSTTAAPLSEWL-LGSKPAVGHQA |
| Q.I.TFGSL.TI.QI.E..M.HASSSNIG..LEKRG...LPEQKSASST.A.P...WL..G.KPA.GHQA | |
| Retrocopy | QVIITFGSLRTI>QI-ENMMVHASSSNIGFSLEKRGCTTLPEQKSASSTIAVPHRKWL>IGIKPANGHQA |
| Parental | PYLPSTNLQDWLNHKQTLENSQTSARACSFLNKVWGNLKGLENWLHKSQQQEVSEKPSFQ-KSNSYSTTS |
| P..P.T.LQD.L..K.TL..SQ.S.RA..F...V..NL..LENWLHKSQ.QE.SEK.S.Q.K.N.YS... | |
| Retrocopy | P*IPITSLQDELTQK*TLSKSQNSSRA*NFFSNVCANLRCLENWLHKSQKQEISEKQSYQ<KCNGYSIIN |
| Parental | SYSMEI-EKVGDLEPLDQDEMDLSD---WLVTPQESHKLEKPENGGCETTSEKFKLLFQV-FHESYNVND |
| S.S....E.VG.L..L.QDEMD.SD....LVTPQESH.LEKP.N...E.TSEKF..LF.V.F..SY.VND | |
| Retrocopy | S-SLKM<ENVGCLRLLSQDEMDISD*VTSLVTPQESHNLEKPGNDSYE-TSEKF--LFKV>FQ*SYSVND |
| Parental | WLVKSDSCTYCQGNQPKGVEIENLGNLKCLNDHLEAKKPLSTPSLTTEDWLVQNHQDPYKVEEVCKANEP |
| WLVK.DSC..CQ.NQ.KG.E..NLGNLKCL..HLEA.KP..TPS..T.DWLVQN.QDPYKVEEV.KANEP | |
| Retrocopy | WLVKPDSCASCQSNQHKGGETGNLGNLKCLDCHLEATKPMLTPSVIT*DWLVQNCQDPYKVEEVNKANEP |
| Parental | CTSFAECVCDENCEKEALCK-WLLKKEGKDK-NGMPVDPKPEPGKHKDSLNTWLSPSGREAAEQARAPQA |
| ..SFAEC..DENCEKE.LCK..LLKKEGKDK.NGM....KPEP.K...SLN.WL.PS...A.E.A..... | |
| Retrocopy | YVSFAECMDDENCEKESLCK<RLLKKEGKDK<NGMSLEQKPEPEKY--SLNMWLCPSRK*ATEKATTFKT |
| Parental | T-AAGVADSFQVIRSSPLSEWLMTPSHKEGCPNKEAPLTEDRAGKQKLTSPLATAWCPFNTADWVLPAK |
| ......ADSFQVI....L.EW..TPS.KEGCP.KE.PLTEDRA.KQKLT..LAT.WCPF.T.DWV.P.K | |
| Retrocopy | VYSFRIADSFQVISNNCLLEWHITPSCKEGCP-KEVPLTEDRAVKQKLTGLLATFWCPFITTDWVFPGK |
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 |
|---|---|---|
| ERP005899_liver | 0 .00 RPM | 144 .05 RPM |
| ERP005899_muscle | 0 .00 RPM | 322 .91 RPM |
| SRP017611_brain | 0 .00 RPM | 71 .85 RPM |
| SRP017611_kidney | 0 .00 RPM | 144 .39 RPM |
| SRP017611_liver | 0 .00 RPM | 170 .50 RPM |
| SRP030211_testis | 0 .00 RPM | 34 .05 RPM |
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1761 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1761 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_btau_1761 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Bos taurus | ENSBTAG00000019565 | 1 retrocopy |
retro_btau_1761 ,
|
| Choloepus hoffmanni | ENSCHOG00000004343 | 1 retrocopy | |
| Callithrix jacchus | ENSCJAG00000013352 | 1 retrocopy | |
| Myotis lucifugus | ENSMLUG00000000619 | 1 retrocopy | |
| Mus musculus | ENSMUSG00000056234 | 1 retrocopy |