RetrogeneDB ID: retro_ocun_1628

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018724:3338621..3339051(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SWI5
• Ensembl ID: ENSOCUG00000005318
• Aliases: None
• Description: SWI5 recombination repair homolog (yeast) [Source:HGNC Symbol;Acc:31412]

Sequence

>retro_ocun_1628
CCGAGGCGTCAAAATGGGAGCTGCGTGTGCAGCTCTGTCACCTCCCACTCTGGGGGCGGGGCGATTTCCCTTGGGTGCGT
GCGCAGCTTTCTGGGAGCCCTCTCATGGCGTCCGTCACAGAATTCTAGTCAGTCTGCGGACCCCAGAGGCCGCTCTCCGG
CCCACGCCCTGGACCCCCTTTCTCCACAGGCGCCCCCGAACCGGGGCCCTCGGACCCCAGGGCTCAGGAGGTGGGCGCAG
AGCAGGGGACACTGCATCAGTTCACGACCCCTTTCTGACTCCTCCCAGATGTGCCCCAGACGTTCTCCTTTCAGAAATCC
CCTCGGGGTCCCTTTCACGCCCTCCAGACACTGCCCTCTCACACCCAGCCCTTCCTCGAGGGGCCCCACGCTGACCCCGC
CCAGCTGGATCCAGTCGGGCGCTCCCAGGT

Alignment

ORF - retro_ocun_1628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.16 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PRRQKGSCARSSGTAHS-GGGTDFRWMRA---QLSGRAVMASLTSADPGGRSPARALDPLSPQAPPHRGP
          PRRQ.GSC..SS.T.HS.GG.......R.....LS.R....S..SADP.GRSPA.ALDPLSPQAPP.RGP
Retrocopy PRRQNGSCVCSSVTSHSGGGAISLGCVRSFLGALSWRPSQNSSQSADPRGRSPAHALDPLSPQAPPNRGP

Parental  RTPGLRRWARSAERGHC-SRHSPFLTPPRGAQASSSQKAPQGLLSRP--TAAGPSRRCRGAFRSPRPTST
          RTPGLRRWA.S..RGHC.S.H.PFLTPPR.A........P.G.LSRP..TA.......RGA.R.PRP...
Retrocopy RTPGLRRWAQS--RGHC>SVHDPFLTPPRCAPDVLLSEIPSGSLSRPPDTALSHPALPRGAPR*PRPAGS

Parental  TGQAEG
          .....G
Retrocopy SRALPG

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	21.52 RPM
SRP017611_kidney	0.00 RPM	34.46 RPM
SRP017611_liver	0.00 RPM	12.33 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1628 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1628 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1628 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008548	1 retrocopy	retro_chof_2692,
Mus musculus	ENSMUSG00000044627	2 retrocopies	retro_mmus_317, retro_mmus_980,
Oryctolagus cuniculus	ENSOCUG00000005318	4 retrocopies	retro_ocun_1628 , retro_ocun_1809, retro_ocun_1826, retro_ocun_1836,