RetrogeneDB - Retrocopy retro_btau

						
>retro_btau_710
CCCAAACCCCGACTCAAATCAGGTGGAGGGTTTGGGCCGGATGCTGGGTCAGGGACCACAGTGCCCCCCGGATGCCTCCC

TGTCCCTCGGGCCGCTTTTGACGCCTCAGCTCGTGAAGAGGAGGAGGAAAACCCGACGATGAAGGTGAAGGTGAGGAGGG

GGAAGCGGCAGCTTGGAGGCCACCCCCCAGATGGGCTCAGCTGGGGGCGTCCCAGGGGCCTCGCCCTCCCCGCCCTACTT

ATCGGAAAACCTGTTTGCAGCGCCGACCTCACAGAGCTGTGAGTCTTCCGGATGCTGCTGTACTCAGAGAAGCACCTCGA

TGCCACTCCACTGCAAGCTTTGGGGTGCCACCGGGGCCGGCGGGGGAACCTCACACACCCCAAGGGCCACCTTTCACCCC

GGGAAGGGGCTGCGACGCCACAGGTGCCCTCCCCCTGCTGTCGTTTTGACTTCCCCGCGGGGACCACCTCCTCCCCCGCC

CGGTCTGCTAGGTGCTCTCATGGCTGAGGAGGGGGTGACAGGGTCTCCACCAGAGCCCTCTCGGGCCCCCGTGGAGGAAG

GTGGATTAAGCTGGACTCCAGTGTCTCCTCTGGGCCCTGACCTGGGTCTCGTCTCCTGGACTCTGCCCAGCGGCTTTGGG

GGAACCACCTGGGCCGCAAGGAGAGTGAAGTCTGGCACCCTGTGAGGCCAGCATCCTCATCAGCAGTGCGTGAAGGGCTG

GGGACTGCGTGGCCCAGGAGCTCTTCCAGGCCCGGACATGGGCGCTGTAGGAGAGGCCGAGCAGCCTGGGGGAAGCTGGG

CAGGACAGCACCCCAAGGGAGAAGCTTGTCTGCTGTGTGCAGAGCATCTCGGATGAATTCCTTCAGACAGATGGCAGCCT

CGTCCTCCTCAGCACAGGTGAGGGCATGGAGCAACCGGAGGACATTTCCTGCCAGAATTGTCTGTACCGTCCAGGAAGGG

CTTGGGGCGGCGATGGAGCCAGCCATACCCGCGGATGCCAGGCAATGCCCAGCTGAGGGGCCTCCCGTCACCCATAAGGG

CATGTGCCCACCACAGGTGGCTCGGGGACTCTG

ORF - retro_btau_710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	68.92 %
Parental protein coverage:	62.54 %
Number of stop codons detected:	3
Number of frameshifts detected	11

Retrocopy - Parental Gene Alignment:

									ParentalPKPRLKSGGGFGPDPGSGTTVPTRRLPVPRPSFDASASEEEEE-EEDDEDEDEEEEVAAWRLPPRWGQLG
		PKPRLKSGGGFGPD.GSGTTVP...LPVPR..FDASA.EEEEE...DDE.E.EE.E.AAWR.PPRW.QLG
RetrocopyPKPRLKSGGGFGPDAGSGTTVPPGCLPVPRAAFDASAREEEEE<KPDDEGEGEEGEAAAWRPPPRWAQLG
ParentalASQRPRPPRPTHRKTCSQRRRRA-MRAFRMLLYS-KSTSLTFHWKLWGR-HRGRRRNLAHPKNHLSPREG
		ASQ.PRPPRPT.RKTC.QRR.......FRMLLYS..STS...H.KLWG..HRGRR.NL.HPK.HLSPREG
RetrocopyASQGPRPPRPTYRKTCLQRRPHR>L*VFRMLLYS>RSTSMPLHCKLWGA<HRGRRGNLTHPKGHLSPREG
ParentalAVTPQVPSPCCRFD-SPRGPPPPRLSLLGALMAEDGVRGSPPVPSGAPMEEDGLRWTPKSPLGPDSGLLS
		A.TPQVPSPCCRFD.SPRGPPPP...LLGALMAE.GV.GSPP.PS.AP.EE.GL.WTP.SPLGPD.GL.S
RetrocopyAATPQVPSPCCRFD>SPRGPPPPPPGLLGALMAEEGVTGSPPEPSRAPVEEGGLSWTPVSPLGPDLGLVS
ParentalCTLPNGFGG-PLGPEGERSLAPPDASILISNVCSIGDHVAQELFQ-GSDVGTAEEAERP-GEKAGQHSPL
		.TLP.GFGG.P.GP.GE.SLAP..ASILIS.....GD.VAQELFQ.G.D.G...EAE.P.GE.AGQ.S..
RetrocopyWTLPSGFGG>PPGPQGE*SLAPCEASILISSA*RAGDCVAQELFQ<GPDMGAVGEAEQP>GE-AGQDSTP
ParentalREEHVTCVQSILDEFLQTYGSLIPLSTDEVVEKLEDI-FQQEFSAPSRKGLVLQLIQSYQRMPGNAMVRG
		RE..V.CVQSI.DEFLQT.GSL..LST.E..E..EDI.F..E.S.PSRKGL.....Q.Y.RMPGNA..RG
RetrocopyREKLVCCVQSISDEFLQTDGSLVLLSTGEGMEQPEDI<FLPELSVPSRKGLGRRWSQPYPRMPGNAQLRG
ParentalF-RVTYK-RHVLTMDDLGTL
		...VT.K..HV.T....GTL
RetrocopyL<PVTHK<GHVPTTGGSGTL

							

							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
ERP005899_liver	0 .00 RPM	4 .97 RPM
ERP005899_muscle	0 .00 RPM	20 .27 RPM
SRP017611_brain	0 .14 RPM	25 .35 RPM
SRP017611_kidney	0 .06 RPM	29 .70 RPM
SRP017611_liver	0 .00 RPM	16 .99 RPM
SRP030211_testis	0 .02 RPM	50 .10 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_710 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_710 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_btau_710 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000131	1 retrocopy	retro_btau_710 ,
Echinops telfairi	ENSETEG00000006699	2 retrocopies	retro_etel_1251, retro_etel_545,
Mus musculus	ENSMUSG00000005204	1 retrocopy	retro_mmus_1196,

	RetrogeneDB ID:	retro_btau_710
Retrocopy location	Organism:	*Cow (Bos taurus)*
	Coordinates:	18:63167291..63168364(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SENP3
	Ensembl ID:	ENSBTAG00000000131
	Aliases:	None
	Description:	sentrin-specific protease 3 [Source:RefSeq peptide;Acc:NP_001178303]

Parental	PKPRLKSGGGFGPDPGSGTTVPTRRLPVPRPSFDASASEEEEE-EEDDEDEDEEEEVAAWRLPPRWGQLG
	PKPRLKSGGGFGPD.GSGTTVP...LPVPR..FDASA.EEEEE...DDE.E.EE.E.AAWR.PPRW.QLG
Retrocopy	PKPRLKSGGGFGPDAGSGTTVPPGCLPVPRAAFDASAREEEEE<KPDDEGEGEEGEAAAWRPPPRWAQLG

Parental	ASQRPRPPRPTHRKTCSQRRRRA-MRAFRMLLYS-KSTSLTFHWKLWGR-HRGRRRNLAHPKNHLSPREG
	ASQ.PRPPRPT.RKTC.QRR.......FRMLLYS..STS...H.KLWG..HRGRR.NL.HPK.HLSPREG
Retrocopy	ASQGPRPPRPTYRKTCLQRRPHR>L*VFRMLLYS>RSTSMPLHCKLWGA<HRGRRGNLTHPKGHLSPREG

Parental	AVTPQVPSPCCRFD-SPRGPPPPRLSLLGALMAEDGVRGSPPVPSGAPMEEDGLRWTPKSPLGPDSGLLS
	A.TPQVPSPCCRFD.SPRGPPPP...LLGALMAE.GV.GSPP.PS.AP.EE.GL.WTP.SPLGPD.GL.S
Retrocopy	AATPQVPSPCCRFD>SPRGPPPPPPGLLGALMAEEGVTGSPPEPSRAPVEEGGLSWTPVSPLGPDLGLVS

Parental	CTLPNGFGG-PLGPEGERSLAPPDASILISNVCSIGDHVAQELFQ-GSDVGTAEEAERP-GEKAGQHSPL
	.TLP.GFGG.P.GP.GE.SLAP..ASILIS.....GD.VAQELFQ.G.D.G...EAE.P.GE.AGQ.S..
Retrocopy	WTLPSGFGG>PPGPQGESLAPCEASILISSARAGDCVAQELFQ<GPDMGAVGEAEQP>GE-AGQDSTP

Parental	REEHVTCVQSILDEFLQTYGSLIPLSTDEVVEKLEDI-FQQEFSAPSRKGLVLQLIQSYQRMPGNAMVRG
	RE..V.CVQSI.DEFLQT.GSL..LST.E..E..EDI.F..E.S.PSRKGL.....Q.Y.RMPGNA..RG
Retrocopy	REKLVCCVQSISDEFLQTDGSLVLLSTGEGMEQPEDI<FLPELSVPSRKGLGRRWSQPYPRMPGNAQLRG

Parental	F-RVTYK-RHVLTMDDLGTL
	...VT.K..HV.T....GTL
Retrocopy	L<PVTHK<GHVPTTGGSGTL

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

RetrogeneDB ID:

retro_btau_710