RetrogeneDB ID: retro_ocun_1809

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: GL018978:359058..359494(-)
• 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_1809
CCGAGGCGTCAAAATGGGAGCTGCACATGCAGCTCTGTCACCGCCCACTCTGGGGGCGGGGCGATTTCCCTTGGGTGCGG
GCGCAGCTTTCTGGGAGCCTCTCATGGCGTCCGACACAGAATTCTAGTTAGTCTACGGACCCCAGAGGCCGCTCTCCGGC
CCGCGCCCTGGACCCCTTTTCTCCACAGGCGCCCCCGAACCGGGGCCCTCGGACCCCAGGGCTCAGGAGGTGGGCGCGGA
GCGCAGAGCAGGGGACACTGCATCAGTTCACGACCCCTTTCTGACTCCTCCCAGATGTGCCCCAGACGTTCTCCTTTCAG
AAATCCCCTCAGGGTCCCTTTCACGTCCTCCAGACACTGCCCTCTCACACCCAGCCCTTCCTCGAGGAGCCCCACGCTGA
CCCCGCCCAGCTGGATCCAGTCGGGCACGCCCAGGT

Alignment

ORF - retro_ocun_1809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.16 %
• Parental protein coverage: 59.66 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PRRQKGSCARSSGTAHSGGGT-DFRWMRAQLSG----RAVMASLTSADPGGRSPARALDPLSPQAPPHRG
          PRRQ.GSC..SS.TAHSGGG..DF.W.RAQLSG....R....S..S.DP.GRSPARALDP.SPQAPP.RG
Retrocopy PRRQNGSCTCSSVTAHSGGGA<DFPWVRAQLSGSLSWRPTQNSS*STDPRGRSPARALDPFSPQAPPNRG

Parental  PRTPGLRRWARSAE-RGHC-SRHSPFLTPPRGAQASSSQKAPQGLLSRP--TAAGPSRRCRGAFRSPRPT
          PRTPGLRRWARSAE.RGHC.S.H.PFLTPPR.A........P.G.LSRP..TA.......RGA.R.PRP.
Retrocopy PRTPGLRRWARSAE>RGHC>SVHDPFLTPPRCAPDVLLSEIPSGSLSRPPDTALSHPALPRGAPR*PRPA

Parental  STTGQAEG
          .......G
Retrocopy GSSRARPG

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_1809 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1809 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1809 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,