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 symbol: NCOA4
• Ensembl ID: ENSBTAG00000019565
• Aliases: None
• Description: nuclear receptor coactivator 4 [Source:RefSeq peptide;Acc:NP_001069336]

Sequence

>retro_btau_1761
CAGGTCATCATCACATTTGGGTCTCTAAGGACCATTCCAAATTGAGAACATGATGGTTCATGCTAGTTCATCAAACATTG
GATTCTCTCTGGAGAAAAGAGGCTGTACCACATTGCCAGAGCAGAAGTCAGCATCCAGCACCATAGCTGTCCCTCACAGG
AAATGGCTCCATTGGGATCAAACCTGCCAATGGTCACCAGGCTCCCTAAATACCCATAACTAGTCTCCAGGATGAGCTCA
CTCAAAAGTAGACCTTGTCAAAGAGTCAGAATTCTTCCAGAGCCTGAAATTTCTTCAGTAATGTCTGCGCCAACCTAAGA
TGCTTGGAAAACTGGCTCCACAAGAGTCAGAAACAAGAAATTTCTGAAAAACAAAGTTACCAAAATGTAATGGCTATTCT
ATTATCAATTCTTCATTGAAAATGAAAATGTTGGATGTTTAAGGCTTCTTAGTCAAGATGAAATGGACATTTCTGATTGA
GTTACCAGTCTGGTAACTCCCCAGGAATCACATAATCTTGAGAAGCCTGGGAATGACAGCTATGAAACCAGTGAGAAGTT
CTTGTTCAAGGTGTTTCCAGTAGTCCTACAGTGTGAATGATTGGCTTGTCAAGCCTGATTCCTGTGCCAGTTGTCAGAGT
AACCAGCATAAAGGTGGGGAGACTGGAAATCTGGGCAATCTGAAGTGCCTAGATTGCCACTTGGAGGCCACAAAACCCAT
GCTCACTCCCAGTGTCATTACTTAAGATTGGCTTGTCCAGAACTGTCAAGATCCATACAAAGTAGAGGAGGTCAACAAAG
CCAATGAACCCTATGTAAGCTTTGCAGAGTGCATGGATGATGAAAACTGTGAGAAGGAATCTCTGTGTAAAGACTTCTGA
AGAAAGAAGGAAAGGATAAAATGGTATGTCTTTGGAACAAAAACCTGAACCTGAGAAATACTCCCTGAATATGTGGCTCT
GTCCATCCAGAAAATAGGCAACTGAGAAAGCTACGACATTCAAGACAGTGTACTCTTTTAGAATTGCTGATTCCTTCCAA
GTTATAAGTAACAATTGCTTGTTAGAGTGGCACATTACCCCCTCATGCAAAGAAGGATGTCCCAAGGAAGTGCCTCTTAC
TGAGGACAGAGCTGTCAAACAAAAGCTTACGGGCCTCTTGGCCACTTTCTGGTGTCCCTTTATCACAACTGACTGGGTCT
TTCCAGGAAAG

Alignment

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

Expression

RNA-Seq

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

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1761 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1761 was not experimentally validated.

Homology

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	retro_chof_2540,
Callithrix jacchus	ENSCJAG00000013352	1 retrocopy	retro_cjac_916,
Myotis lucifugus	ENSMLUG00000000619	1 retrocopy	retro_mluc_2161,
Mus musculus	ENSMUSG00000056234	1 retrocopy	retro_mmus_14,