RetrogeneDB ID: retro_ocun_1439

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 8:26867650..26868429(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AZIN1
• Ensembl ID: ENSOCUG00000015196
• Aliases: None
• Description: antizyme inhibitor 1 [Source:HGNC Symbol;Acc:16432]

Sequence

>retro_ocun_1439
TTACTACATGTTGCAGCAGAAGATAATATTGGAGCTGAAGAGGGTAACATGAAGTTTGGCACCTCACTGAAGAACTGTAG
GCATCTCTTGGAATGTGCTAAGGAACTAGATGTGCAAAATTGGGGTTAAATTTCATGTTTCAAGTGCTTTCAAATAATCT
CAAGTATATGTCCATTCCCTGTCTGATGTATGATATGCTTTTGACATGGCTGGAGAATTTGGCTATTCAGTGAGCATGTT
AGACCTGGGTGGACGCTTCACAGGAACTGAGTTTCAATTGGAAGAAGTTAATCATGTTATCAGCCCTCTGTTGGATGTCT
GGTTTCCTGAAGGATCTGGTAATAAGATCACTTCAGAACCTGCAAGCTACTGTGTGTCTTCTGCATTCACACTTGCAGTT
AGTATCACTGCAAGGAAAGTTGTTGAAAATGGTAAGCTTTCCTCTCGAGTAGAAAAAACCAGATGTGATGAAGCAGCCTT
CCTGTATTATGTGAATGATGGTATTTATGGTTCTTTTGCAAGTAAGCCATCTGAGAACTTAAAAGCCATTCCAGAGGTTC
ACAAGAAATGCAAGGAAGATGAGCCTCTGTTTACAAGCAGCCTTTGAGGTCCATCCTGTGATGAGCTGGATCAAATTGTG
GAAAACTGTCTTATTCCTGAGCTGAATGTGGGAGATTGGCTTATCTTTGATAACATGGGAGCAGATTCTTCCCATGAGCC
ATCTGCTTTTAATAATTTTCAGAGGCTTAGCTATTTATTAAATGATGTCATTCAGTGAT

Alignment

ORF - retro_ocun_1439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.37 %
• Parental protein coverage: 98.11 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LLHIATEDYIGGEEGNMKFGTSLKNCRHLLECAKELDVQ-IIGVKF-HVSSACKESQVYVHALSDARCVF
          LLH.A.ED.IG.EEGNMKFGTSLKNCRHLLECAKELDVQ...G..F.HVSSA.K.SQVYVH.LSD....F
Retrocopy LLHVAAEDNIGAEEGNMKFGTSLKNCRHLLECAKELDVQ<KLGLNF<HVSSAFK*SQVYVHSLSDV*YAF

Parental  DMAGEFGYTMNMLDIGGGFTGTEFQLEEVNHVISPLLDVYFPEGSGIKIISEPGSYYVSSAFTLAVNIIA
          DMAGEFGY...MLD.GG.FTGTEFQLEEVNHVISPLLDV.FPEGSG.KI.SEP.SY.VSSAFTLAV.I.A
Retrocopy DMAGEFGYSVSMLDLGGRFTGTEFQLEEVNHVISPLLDVWFPEGSGNKITSEPASYCVSSAFTLAVSITA

Parental  KKVVENGKLSSG-EKTGSDEPAFVYYMNDGVYGSFASKLSENLNAIPEVHKKCKEDEPLFTSSLWGPSCD
          .KVVENGKLSS..EKT..DE.AF.YY.NDG.YGSFASK.SENL.AIPEVHKKCKEDEPLFTSSL.GPSCD
Retrocopy RKVVENGKLSSRVEKTRCDEAAFLYYVNDGIYGSFASKPSENLKAIPEVHKKCKEDEPLFTSSL*GPSCD

Parental  ELDLIVENCLLPELNVGDWLIFDNMGADSFHEPSAFNDFQR-PAVYYMMSFSD
          ELD.IVENCL.PELNVGDWLIFDNMGADS.HEPSAFN.FQR..A.Y.MMSFSD
Retrocopy ELDQIVENCLIPELNVGDWLIFDNMGADSSHEPSAFNNFQR>LAIY*MMSFSD

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	2.43 RPM	167.83 RPM
SRP017611_kidney	1.11 RPM	79.36 RPM
SRP017611_liver	0.23 RPM	21.81 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1439 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1439 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005164	2 retrocopies	retro_chof_1086, retro_chof_1522,
Equus caballus	ENSECAG00000016922	1 retrocopy	retro_ecab_1096,
Oryctolagus cuniculus	ENSOCUG00000015196	1 retrocopy	retro_ocun_1439 ,
Tursiops truncatus	ENSTTRG00000000140	1 retrocopy	retro_ttru_1210,