RetrogeneDB ID: retro_ocun_1896

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: X:68255992..68256626(+)
• Located in intron of: ENSOCUG00000016730

Retrocopy information

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

Parental gene information

• Parental gene symbol: HIBADH
• Ensembl ID: ENSOCUG00000010349
• Aliases: None
• Description: 3-hydroxyisobutyrate dehydrogenase [Source:UniProtKB/Swiss-Prot;Acc:P32185]

Sequence

>retro_ocun_1896
GAGTTTCAAGAGGAAGGAGAACAGGTAGTACCTTCCCCAGCAGATGTAGCCAAAAAAGCTGACAGAATTATTAAAAATGC
TGCCCACCACTATCAGTGCAATAGAAGCTCATTCTGGAGCAAACGGAATTCTAAAATACGTGGAGACAGGCTCATCCAGT
ACTACTGATCCTGCAGTTTCAAAAGAATTGGCCAAAAAAGTTGAGAAAATGGGAGTTTTCATGGATGCCCTGTTTCTGGT
GGTGTAGGAGCTGCTCGGTCTGAGAACCTCATGTTCATGGTGGGAGGAGTCAAAGATGAATTTTCTGCTTCCACAGAGTT
GCTGAGGTGCATGGGCTCCAAGGTGATGTACTATGGAACTGTTGGGACTGAGCAGGCTTCAAAGATCTGAAACAACATGC
TGTTAGCTATTAGTATGATTGTAACGGCTGGAGCTGTGAATCTTGGAATCAGGTTAGGGCTTGACCCAAAACTATTGGCT
AAAATTCTAAATAGGAGCTCAGGACGGCGTTGATCAAGTGACACTTATAAATCGCGTACCCAGTGTGATGGATGGTAGTC
CCTCTTCTAATAACTATCAGGGTAGATTCAGAATGACATTCACAGTACAAGACTCTTCCACTAGAACAGACAGC

Alignment

ORF - retro_ocun_1896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.43 %
• Parental protein coverage: 64.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EFQEAGEQVVSSPADVAEKADRIIT-MLPTSINAIEAYSGANGILKKVKKGSLLIDSSTIDPAVSKELAK
          EFQE.GEQVV.SPADVA.KADRII..MLPT.I.AIEA.SGANGILK.V..GS....SST.DPAVSKELAK
Retrocopy EFQEEGEQVVPSPADVAKKADRIIK>MLPTTISAIEAHSGANGILKYVETGS----SSTTDPAVSKELAK

Parental  EVEKMGAVFMDA-PVSGGVGAARSGNLTFMVGGVEDEFAAAKELLGCMGSNVVYCGAVGTGQAAKICNNM
          .VEKMG.VFMDA.PVSGGVGAARS.NL.FMVGGV.DEF.A..ELL.CMGS.V.Y.G.VGT.QA.KI.NNM
Retrocopy KVEKMG-VFMDA<PVSGGVGAARSENLMFMVGGVKDEFSASTELLRCMGSKVMYYGTVGTEQASKI*NNM

Parental  LLAISMIGTAEAMNLGIRLGLDPKLLAKILNMSSGRCWSSDTY-NPVPGVMDGVPSANNYQGGFGTTLMA
          LLAISMI.TA.A.NLGIRLGLDPKLLAKILN.SSGR..SSDTY.N.VP.VMDG.PS.NNYQG.F..T...
Retrocopy LLAISMIVTAGAVNLGIRLGLDPKLLAKILNRSSGRR*SSDTY>NRVPSVMDGSPSSNNYQGRFRMTFTV

Parental  KDLGLAQDS
          .D.....DS
Retrocopy QDSSTRTDS

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	0.17 RPM	32.29 RPM
SRP017611_kidney	0.00 RPM	469.38 RPM
SRP017611_liver	0.00 RPM	125.94 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1896 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1896 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1896 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003153	1 retrocopy	retro_chof_1225,
Dasypus novemcinctus	ENSDNOG00000008640	2 retrocopies	retro_dnov_1465, retro_dnov_1997,
Mus musculus	ENSMUSG00000029776	1 retrocopy	retro_mmus_2360,
Oryctolagus cuniculus	ENSOCUG00000010349	1 retrocopy	retro_ocun_1896 ,
Oryctolagus cuniculus	ENSOCUG00000010486	1 retrocopy	retro_ocun_680,
Sus scrofa	ENSSSCG00000016695	1 retrocopy	retro_sscr_792,
Ictidomys tridecemlineatus	ENSSTOG00000004108	1 retrocopy	retro_itri_395,
Tarsius syrichta	ENSTSYG00000014191	1 retrocopy	retro_tsyr_1136,
Vicugna pacos	ENSVPAG00000012531	1 retrocopy	retro_vpac_571,