RetrogeneDB - Retrocopy retro_ocun

						
>retro_ocun_1836
CCGAGGCGTCAAAATGGGAGCTGCGCGTGCAGCTCTGTCACCGCCCACTCTGGGGGTGGGGCGATTTCCCTTGGGTGCGC

ACGCAGCTTTCTGGGAGCCTCTCATGGCGTCCGTCACAGAATTCTAGTTAGTCTGCGGACCCCAGAGGCCGCTCTCCGGC

CCGCGCCCTGAACCCCCTTTCTCCACAGGCGCCCCCGAACCGGGGCCCTCGGACCCCAGGGCTCAGGAGGTGCGCGGAGC

GCAGAGCAGGGGACACTGCATCAGTTCACGACTCCTTTCTGACTCCTCCCAGATGTGCCCCAGACGTTCTCCTTTCAGAA

ATCCCCTCAGGGTCCCTTTCACGTCCTCCAGACACTGCCCTCTCACACCCAGCCCTTCCTCGAGGGGCCCCACACTGACC

CCGCCCAGCTGGATCCAGTCGGGCGCTCCCAGGT

ORF - retro_ocun_1836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	57.43 %
Parental protein coverage:	59.66 %
Number of stop codons detected:	2
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalPRRQKGSCARSSGTAHSGGGT-DFRWMRAQ----LSGRAVMASLTSADPGGRSPARALDPLSPQAPPHRG
		PRRQ.GSCA.SS.TAHSGGG..DF.W.R.Q....LS.R....S..SADP.GRSPARAL.PLSPQAPP.RG
RetrocopyPRRQNGSCACSSVTAHSGGGA<DFPWVRTQLSGSLSWRPSQNSS*SADPRGRSPARALNPLSPQAPPNRG
ParentalPRTPGLRRWAR-SAERGHC-SRHSPFLTPPRGAQASSSQKAPQGLLSRP--TAAGPSRRCRGAFRSPRPT
		PRTPGLRR.A.....RGHC.S.H..FLTPPR.A........P.G.LSRP..TA.......RGA...PRP.
RetrocopyPRTPGLRRCAE<AQSRGHC>SVHDSFLTPPRCAPDVLLSEIPSGSLSRPPDTALSHPALPRGAPH*PRPA
ParentalSTTGQAEG
		.......G
RetrocopyGSSRALPG

							

							Legend:
							
								*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

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 - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_1836 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1836 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_1836 has 0 orthologous retrocopies within eutheria group .

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 ,

	RetrogeneDB ID:	retro_ocun_1836
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	GL019224:122..556(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SWI5
	Ensembl ID:	ENSOCUG00000005318
	Aliases:	None
	Description:	SWI5 recombination repair homolog (yeast) [Source:HGNC Symbol;Acc:31412]

Parental	PRRQKGSCARSSGTAHSGGGT-DFRWMRAQ----LSGRAVMASLTSADPGGRSPARALDPLSPQAPPHRG
	PRRQ.GSCA.SS.TAHSGGG..DF.W.R.Q....LS.R....S..SADP.GRSPARAL.PLSPQAPP.RG
Retrocopy	PRRQNGSCACSSVTAHSGGGA<DFPWVRTQLSGSLSWRPSQNSS*SADPRGRSPARALNPLSPQAPPNRG

Parental	PRTPGLRRWAR-SAERGHC-SRHSPFLTPPRGAQASSSQKAPQGLLSRP--TAAGPSRRCRGAFRSPRPT
	PRTPGLRR.A.....RGHC.S.H..FLTPPR.A........P.G.LSRP..TA.......RGA...PRP.
Retrocopy	PRTPGLRRCAE<AQSRGHC>SVHDSFLTPPRCAPDVLLSEIPSGSLSRPPDTALSHPALPRGAPH*PRPA

Parental	STTGQAEG
	.......G
Retrocopy	GSSRALPG

*	Stop codon
>	Forward frameshift by one nucleotide
<	Reverse frameshift by one nucleotide

RetrogeneDB ID:

retro_ocun_1836