RetrogeneDB ID: retro_ocun_663

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 13:103123494..103125005(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TRIP4
• Ensembl ID: ENSOCUG00000002322
• Aliases: None
• Description: thyroid hormone receptor interactor 4 [Source:HGNC Symbol;Acc:12310]

Sequence

>retro_ocun_663
AGGCACGTTTTTTTAATTGAGAGTGCCAAAGAGATAGGAAAATATGTTACTGAATTCCTCCAGGGAAATGAGGGCCCAAA
TGATCAATTCATAGAACAACTTATAACCAAATGGAAGAAGAATGATCAGGAGCTGATTTCTGATCCTATGCAGCAGTACT
TCAAAAAAGATGGAATTTTAGATGGTCAAAGATCAGGAGACCAGCTAACACGAGGTTGAGGGAAAGGGAGAAACCAATAG
AAAGTTCCTGCATTTGCTGAGCCTGACACAGCTGTAGAGGTCAAATCACCTTTTGATTTGGCCAAGGCACAAGAGAACAG
CAACTCTGTGGAGAAGACAACAAGGTTTGTCAATTTACACAGAAGAGAGGGACAGCACAAGCTTGCAGTCCCACTCCACA
GTTGCCACCCTTGGACTGCCTGGGCCAGAAGCACAAGCTCATCAAAAGTGTGATCTGTGGGCATGTTGTCCATGAGCAAG
AGGGTTCTGGCCCCTGCGTATTCTGTGGCTCTCTGGTACATACACATGAACAGGGTATTTTACAGGGTGACTCAAACAAG
AGCCAGAAACTATTAAAAGGGCTCATGTCAGGGACAAACAACTCCAGAAAGGCAGATGTCTCTACCCAGGACCTTCTTCC
TCACCAAGAATCATGCGTTAAGTCTGGTCTGGAGAAGACCATCAAGTGTAAGATAAACTATTAGCGTTTGATGGAACTAG
CATCTGAACCCCCAAGTCACTGATGAGGACTCAGATTACATTGCCAGTGATTCTAACCAGTGGTGGTCCAAAGTCGAGCA
TGAAGCCCTGAAGAAGTGAGAGAAAGAGCTGAGAGAGCTTCAGTGTGCCTCTCGACTCTCAAAGGTGGTCACCATTGACT
TTGCAGGTCGGAAGATCCTGGAAGAGAACCTCCACTAGCCGAGCATCACAGCAGACTAGATGAACTAGCGATACAGACCT
TTACCAGTGGAACTTCGAACCAGTCACTGATCAAATTGGATGGATCTTCTGAAGATGCCTTGGGAGTTATGGTGAATCCC
AGCCTGTACCAGACCCCTTCCCAGTGGGTTGACTAGACATGTGCAGCCTCGCAGAAGAAGGCTTTCCATTTAGCAGAATT
GGGACTAGAGTGCAACTTACATCAACACCAGCTGTGAATGCAGAAAGAAGAATTTCAGGAAGGCTTTGGTGGTGGCCGGT
GCCTTTCTACATATCAGCTATGGGCTGCTTTGCTTGGCAGAGTGATTAAAAGGGTGGAGGGAAGATCCTGGTACACCCCA
CACAGAGGATAACTTTAAATAGCAGCCACAGACCAAAAACTCTCCCCTCAAGCAGTCCAAAAACTCCAGGCTATGGTATG
GTCTCCTTCATGGAAACATGTGGAATTTTCCAATGACTATCCCTCAGTGTGTCTTCTGGGCTGTGTGGCCCTAACTGACT
GCTTATCTCAGAAAGAATTTACAGAGCAATTTCCATACATCAGTCAAGAATCTGGTTCTCCATTTGTTTTC

Alignment

ORF - retro_ocun_663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.49 %
• Parental protein coverage: 87.09 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  QYVLSIESAEEIREYVTDLLQGNEGPKGQFIEELINKWQKNDQELISDPMQQSFKKDEILDGQKSGDQLK
          ..V..IESA.EI..YVT..LQGNEGP..QFIE.LI.KW.KNDQELISDPMQQ.FKKD.ILDGQ.SGDQL.
Retrocopy RHVFLIESAKEIGKYVTEFLQGNEGPNDQFIEQLITKWKKNDQELISDPMQQYFKKDGILDGQRSGDQLT

Parental  RSRRKGRNKQEVPAFAEPDTTVEVKTPFDLAKAQENSNSVKKKTKFVNLYTREGQDKLAVLLPGRHP-CD
          R...KGRN...VPAFAEPDT.VEVK.PFDLAKAQENSNSV.K.T.FVNL..REGQ.KLAV.L...HP..D
Retrocopy RG*GKGRNQ*KVPAFAEPDTAVEVKSPFDLAKAQENSNSVEKTTRFVNLHRREGQHKLAVPLHSCHP<LD

Parental  CLGQKHKLINNCLICGRIVCEQEGSGPCLFCGSLVCTHEERDILQRDSNKSQKLLKKLMSGADNSVKMDI
          CLGQKHKLI....ICG..V.EQEGSGPC.FCGSLV.THE...ILQ.DSNKSQKLLK.LMSG..NS.K.D.
Retrocopy CLGQKHKLIKS-VICGHVVHEQEGSGPCVFCGSLVHTHEQ-GILQGDSNKSQKLLKGLMSGTNNSRKADV

Parental  SSQDLLPHQELRIKSGLEKAIKHK-DKLLEFDRTSI-RRTQVIDDESDYFASDSNQWLSKVEREALQKRE
          S.QDLLPHQE...KSGLEK.IK.K.DKLL.FD.TSI....QV.D..SDY.ASDSNQW.SKVE.EAL.K.E
Retrocopy STQDLLPHQESCVKSGLEKTIKCK<DKLLAFDGTSI<LNPQVTDEDSDYIASDSNQWWSKVEHEALKK*E

Parental  EELRELRHASRLSKKVTIDFAGRKILEE-ENPLAEYHSRLDE-AIQAIANGTLNQPQIKLDRSSEDPLGV
          .ELREL..ASRLSK.VTIDFAGRKILEE.E.PLAE.HSRLDE.AIQ....GT.NQ..IKLD.SSED.LGV
Retrocopy KELRELQCASRLSKVVTIDFAGRKILEE<EPPLAEHHSRLDELAIQTFTSGTSNQSLIKLDGSSEDALGV

Parental  LVNPNLYQPPPQWVDHTCAASQKKAFHSARLGSEFNLHQHQLRIQDEEFQEGFDGGWCLSMHQPWASLLV
          .VNP.LYQ.P.QWVD.TCAASQKKAFH.A.LG.E.NLHQHQL..Q.EEFQEGF.GG.CLS..Q.WA.LL.
Retrocopy MVNPSLYQTPSQWVD*TCAASQKKAFHLAELGLECNLHQHQL*MQKEEFQEGFGGGRCLSTYQLWAALLG

Parental  RGIKRVEGRSWYTPHRGRLWIAATGKKPSPQEVSELQAT-YRLLRG-KDVEFPNDYPSGCLLGCVDLIDC
          R.IKRVEGRSWYTPHRG.L.IAAT..K.SPQ.V..LQA..Y.LL.G.K.VEF.NDYPS.CLLGCV.L.DC
Retrocopy RVIKRVEGRSWYTPHRG*L*IAATDQKLSPQAVQKLQAM>YGLLHG<KHVEFSNDYPSVCLLGCVALTDC

Parental  LSQKEFKEQFPDISQESDSPFVF
          LSQKEF.EQFP.ISQES.SPFVF
Retrocopy LSQKEFTEQFPYISQESGSPFVF

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
SRP017611_brain	0.00 RPM	13.74 RPM
SRP017611_kidney	0.00 RPM	25.24 RPM
SRP017611_liver	0.00 RPM	9.87 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_663 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_663 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_663 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000032766	1 retrocopy	retro_cjac_2382,
Macaca mulatta	ENSMMUG00000009882	1 retrocopy	retro_mmul_1853,
Oryctolagus cuniculus	ENSOCUG00000002322	1 retrocopy	retro_ocun_663 ,