RetrogeneDB - Retrocopy retro_ocun

						
>retro_ocun_538
CCTAGCCCAGTCCCAGTATCCGACAAGAATGCCACCAGCGACTCCGAGGAAGATGCAGACTTGGAAGTTCTGATTCCTAG

CATATTTGATAGACGAGCATCAGTCTGTGCTGAGGTGTATACCCCTGACGAAGAGGAAGAAGATAGAGACCCAAGGGTGA

TTCATCCTAAAACTTATGACTAGTGATGCAGACTTCAAGAACCTTGCAAAGATAGTCTCCTTTTCAAAAATCATGATCAG

AAATAACTTTCTCAAGTTCTTGATGCCATGTTTGAAAGGATAGTCTAATTGATGAACATGTCATTGATCAAGGAGATGAT

GGAGACGATTTTATGTCATAGAAAGGGGAACCTATGACATGTTGGTAACAAGAGATAAGCAAACATGCTCTTTTGGTCAG

TATGATAATCATGGCAGTTTTGGAGAGCTAGCCCTGATGTACAATACCCCAAGAGCTATTACCACTGCTGCTAATTCTGA

AGGCTTCCTTTGGGGACTGGACCAGGTGACTTTTAGAAGAAATATAGTGAAAAACAATGCAAAAAAGAAGATGTTTGAAT

CATTTATTGAGTCTGTCCCCTCCTTAAGTCACTACAGGTGTCGGAATGAATGAAGACTGTAGATGTCATTGGAGAGAAGG

TCTATAAGGATGGAGAATGCATAATTGCTCAGGTGAAAATGCTGATAGCATTTATATCACAGAATCTGGGGATGTGAGCA

TCTTGATTAAAAGCAAGATTAAATCAAACAAGGATGGTGGGAACCAGGAAGTTGAGATTGCCCACTGCCATAAGGGGCTG

TACTTTGGAGAGCTTGCACTAGTCACCAACAAACTCAGAGCTACTTTGGCTTATGCAGTTGGAGATGTCAAATGCTTAGT

TATGGATGTGCCAGCATTTGAGAGGCTTCTAGGGCCCTGCAAGGACATCATGAAGAGAAACATCTCACACTAGAAGAAAC

AGCTGGTAAGATATTTGGCTCCAACATGGATCTAATTGACCCTGGGCAA

ORF - retro_ocun_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	82.56 %
Parental protein coverage:	84.54 %
Number of stop codons detected:	5
Number of frameshifts detected	5

Retrocopy - Parental Gene Alignment:

									ParentalPSPVPVADENADSDSEEDADLEVPIPSRFNRRVSVCAEAYNPDEEEEDTDPRVIHPKTDEQRCRLQESCK
		PSPVPV.D.NA.SDSEEDADLEV.IPS.F.RR.SVCAE.Y.PDEEEED.DPRVIHPKT....CRLQE.CK
RetrocopyPSPVPVSDKNATSDSEEDADLEVLIPSIFDRRASVCAEVYTPDEEEEDRDPRVIHPKTYD**CRLQEPCK
ParentalDILLFKNLDQEQLSQVLDAMFERIV-KVDEHVIDQGDDGDNF-YVIERGTYDILVTRDNQTRSVGQYDNH
		D.LLFKN.DQ..LSQVLDAMFERIV...DEHVIDQGDDGD.F.YVIERGTYD.LVTRD.QT.S.GQYDNH
RetrocopyDSLLFKNHDQK*LSQVLDAMFERIV<LIDEHVIDQGDDGDDF<YVIERGTYDMLVTRDKQTCSFGQYDNH
ParentalGSFGELALMYNTPRAATIVATSEGSLWGLDRVTFRRIIVKNNAKKRKMFESFIESVP-LLKSLEVSERMK
		GSFGELALMYNTPRA.T..A.SEG.LWGLD.VTFRR.IVKNNAKK.KMFESFIESVP.LLKSL.VSE.MK
RetrocopyGSFGELALMYNTPRAITTAANSEGFLWGLDQVTFRRNIVKNNAKK-KMFESFIESVP<LLKSLQVSE*MK
ParentalIVDVIGEKVYKDGERIITQ-GEKADSFYIIESGEVSILIKSKTKSNKDGGNQEVEIARCHKGQYFGELAL
		.VDVIGEKVYKDGE.II.Q.GE.ADS.YI.ESG.VSILIKSK.KSNKDGGNQEVEIA.CHKG.YFGELAL
RetrocopyTVDVIGEKVYKDGECIIAQ<GENADSIYITESGDVSILIKSKIKSNKDGGNQEVEIAHCHKGLYFGELAL
ParentalVTNKPRAASAYAVGDVKCLVMDVQAFERLLGPCMDIMKRNISHYEEQLV-KIFGSSMDLIDPGQ
		VTNK.RA..AYAVGDVKCLVMDV.AFERLLGPC.DIMKRNISH...QLV.KIFGS.MDLIDPGQ
RetrocopyVTNKLRATLAYAVGDVKCLVMDVPAFERLLGPCKDIMKRNISH*KKQLV<KIFGSNMDLIDPGQ

							

							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	57 .78 RPM
SRP017611_kidney	0 .00 RPM	121 .02 RPM
SRP017611_liver	0 .00 RPM	67 .44 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_538 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_538 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_538 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003255	1 retrocopy	retro_cjac_1807,
Monodelphis domestica	ENSMODG00000013392	1 retrocopy	retro_mdom_97,
Oryctolagus cuniculus	ENSOCUG00000012426	1 retrocopy	retro_ocun_538 ,
Oryctolagus cuniculus	ENSOCUG00000012747	1 retrocopy	retro_ocun_1288,
Otolemur garnettii	ENSOGAG00000006822	1 retrocopy	retro_ogar_2423,

	RetrogeneDB ID:	retro_ocun_538
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	12:137186011..137187020(+)
	Located in intron of:	ENSOCUG00000006898
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PRKAR2A
	Ensembl ID:	ENSOCUG00000012426
	Aliases:	None
	Description:	protein kinase, cAMP-dependent, regulatory, type II, alpha [Source:HGNC Symbol;Acc:9391]

Parental	PSPVPVADENADSDSEEDADLEVPIPSRFNRRVSVCAEAYNPDEEEEDTDPRVIHPKTDEQRCRLQESCK
	PSPVPV.D.NA.SDSEEDADLEV.IPS.F.RR.SVCAE.Y.PDEEEED.DPRVIHPKT....CRLQE.CK
Retrocopy	PSPVPVSDKNATSDSEEDADLEVLIPSIFDRRASVCAEVYTPDEEEEDRDPRVIHPKTYD**CRLQEPCK

Parental	DILLFKNLDQEQLSQVLDAMFERIV-KVDEHVIDQGDDGDNF-YVIERGTYDILVTRDNQTRSVGQYDNH
	D.LLFKN.DQ..LSQVLDAMFERIV...DEHVIDQGDDGD.F.YVIERGTYD.LVTRD.QT.S.GQYDNH
Retrocopy	DSLLFKNHDQK*LSQVLDAMFERIV<LIDEHVIDQGDDGDDF<YVIERGTYDMLVTRDKQTCSFGQYDNH

Parental	GSFGELALMYNTPRAATIVATSEGSLWGLDRVTFRRIIVKNNAKKRKMFESFIESVP-LLKSLEVSERMK
	GSFGELALMYNTPRA.T..A.SEG.LWGLD.VTFRR.IVKNNAKK.KMFESFIESVP.LLKSL.VSE.MK
Retrocopy	GSFGELALMYNTPRAITTAANSEGFLWGLDQVTFRRNIVKNNAKK-KMFESFIESVP<LLKSLQVSE*MK

Parental	IVDVIGEKVYKDGERIITQ-GEKADSFYIIESGEVSILIKSKTKSNKDGGNQEVEIARCHKGQYFGELAL
	.VDVIGEKVYKDGE.II.Q.GE.ADS.YI.ESG.VSILIKSK.KSNKDGGNQEVEIA.CHKG.YFGELAL
Retrocopy	TVDVIGEKVYKDGECIIAQ<GENADSIYITESGDVSILIKSKIKSNKDGGNQEVEIAHCHKGLYFGELAL

Parental	VTNKPRAASAYAVGDVKCLVMDVQAFERLLGPCMDIMKRNISHYEEQLV-KIFGSSMDLIDPGQ
	VTNK.RA..AYAVGDVKCLVMDV.AFERLLGPC.DIMKRNISH...QLV.KIFGS.MDLIDPGQ
Retrocopy	VTNKLRATLAYAVGDVKCLVMDVPAFERLLGPCKDIMKRNISH*KKQLV<KIFGSNMDLIDPGQ

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

RetrogeneDB ID:

retro_ocun_538