RetrogeneDB ID: retro_ocun_1167

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 3:41449214..41450182(+)
• Located in intron of: ENSOCUG00000005724

Retrocopy information

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

Parental gene information

• Parental gene symbol: IRF1
• Ensembl ID: ENSOCUG00000004165
• Aliases: None
• Description: interferon regulatory factor 1 (IRF1), mRNA [Source:RefSeq mRNA;Acc:NM_001171347]

Sequence

>retro_ocun_1167
GTGCCCATCACTAGGATGCACATGAGACCCTGGCTAGCAATACAGGTTAATTCCAACCAGATCCCCGGGCTGATCTGGAT
TAATAAAGAGGAGATGATCTTCCAGATCCCGTGGAAGCACGCCATCAAGCACGGCTGGGACATCAACAAGGACGCCTGTC
TGTTCCAGAGCTGGGCCGTTCATACAGGCCAACACAAAGCTGGGGAAAAGAGCTGGATCTGAAGACGTGGAAGGCCAACT
TCCACTGTGCTGTGAACTCCCTGCCGGACCTCGAGTAGGTGAAGGACCAGAGCAGGAACAAGGGCAGCTTGGCTGTGTGG
GTGTACCAGATGCTCCCACCCCTCATCAGGAACCAGAAAAAAGAGAGGAAGTCCAAGTCCACCTGAGATGCTAAGGGCAA
GGCCCAGAGGAAGTCCTGTGGGGATTCCAGCCTGGACACCTTCTCTGATGGACTCAGCAGCTCCACCCTGCCTGATGACC
ACAGTGACTACACTGCCCAAGGCTACATTGGGCAGGACTTGGAAGTGGAACAGGCCCTCACTCCAGCACTGTCACCACAT
AGCACTCTCCTCTTCTGGAGCATCCCAGGGGACATCGTGCCAGGTAGCACCAGTGACCCGTACAGCTTCCAGGTATCTCC
CATGCTGGCCACCTCTGAAGCTGCAACAGATGAGGATGAGGAAGGGGAATTACCAGAGGGCATCATGAAGCTCTTTGAGC
AGCCAGAGTGGCGGCGGACAAACGTGGATGGGAAGGGGTACCTGCTTAAAGAGCCTGGGACCCAGGCCGCTGCTGTCTAC
GGAGACTTCAGCTGCAAGGAGGAGCCAGAAGTTGACAGCCATGGAGGGGACGTTGGTCTGAGCCTTCCCTGCATCTTCAC
AGATGTCAGGAACATAGACAGCAGCTGGCTGGACAGCCTGCTGCCCCCAGTCAAGCTGCCTTCTATCCAGGCCATTCCTT
GTGCACCA

Alignment

ORF - retro_ocun_1167 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPITRMRMRPWLEMQINSNQIPGLIWINKEEMIFQIPWKHAAKHGWDINKDACLFRSWAIHTGRYKAGEK
          .PITRM.MRPWL..Q.NSNQIPGLIWINKEEMIFQIPWKHA.KHGWDINKDACLF.SWA.HTG..KAGEK
Retrocopy VPITRMHMRPWLAIQVNSNQIPGLIWINKEEMIFQIPWKHAIKHGWDINKDACLFQSWAVHTGQHKAGEK

Parental  -EPDPKTWKANFRCAMNSLPDIEEVKDQSRNKGSSAVRVYRMLPPLTRNQRKERKSKSTRDAKGKAKRKQ
          .E.D.KTWKANF.CA.NSLPD.E.VKDQSRNKGS.AV.VY.MLPPL.RNQ.KERKSKST.DAKGKA.RK.
Retrocopy <ELDLKTWKANFHCAVNSLPDLE*VKDQSRNKGSLAVWVYQMLPPLIRNQKKERKSKST*DAKGKAQRK-

Parental  SCGDSSPDTFSDGLSSSTLPDDHSGYTAQGYIGQDSEVEQALTPALSPHSTLPSW---GDIVPDSTSDLY
          SCGDSS.DTFSDGLSSSTLPDDHS.YTAQGYIGQD.EVEQALTPALSPHSTL..W...GDIVP.STSD.Y
Retrocopy SCGDSSLDTFSDGLSSSTLPDDHSDYTAQGYIGQDLEVEQALTPALSPHSTLLFWSIPGDIVPGSTSDPY

Parental  SFQVSPMPSASEAATDEDEEGKLPEDIMKLLEQPEWQPTHVDGKGYLLNEPGAQATAVYGDFSCKEEPEV
          SFQVSPM...SEAATDEDEEG.LPE.IMKL.EQPEW..T.VDGKGYLL.EPG.QA.AVYGDFSCKEEPEV
Retrocopy SFQVSPMLATSEAATDEDEEGELPEGIMKLFEQPEWRRTNVDGKGYLLKEPGTQAAAVYGDFSCKEEPEV

Parental  DSPGGDIGLSLHRVFTDLKNMDSSWLDSLLPQVRLPSIQAIPCAP
          DS.GGD.GLSL...FTD..N.DSSWLDSLLP.V.LPSIQAIPCAP
Retrocopy DSHGGDVGLSLPCIFTDVRNIDSSWLDSLLPPVKLPSIQAIPCAP

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	0.33 RPM	6.46 RPM
SRP017611_kidney	0.51 RPM	23.11 RPM
SRP017611_liver	0.08 RPM	9.25 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1167 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1167 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1167 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000004165	1 retrocopy	retro_ocun_1167 ,