RetrogeneDB - Retrocopy retro_btau

                        
>retro_btau_1125
TGGGCAGCACGGGTACGAGCAGTGGGAGGCGATCAAGACTCCAGCATCTTCCCTGGCTGCATCAACAAGGCTGAGGTCTT

TGAAGACCAGGTAAACGGACGCCTCAAGAAGGGACTGGCGGAAGGTAAGGACTATGTGCTGCTCCCAATGGCTGCTCAGC

GTTACCTGGTCAACTGGTATGTTCTAGAGCACGACCCGCCCCGCATGGAACGCAAGGTCGTGGAACTGCCCAGCGTCCAC

GAGGTTGAAGAACTGGTGCTTGTCCAGCTCAGTGATACGGACACAACGCCACGTCTCATCTCAGCCCCGCAGATTCTAGT

GACCTCGTTTTTGCGCACCGCTTGAGAGCAGTTTCCGGGGCACCCCAGGAAGAGACCCGGCTGTGGCTCAAGAACACGGA

GGGCCCTTTTGAGAGGTTGTGCGACGCCTGCGTCACAGTGCTTGACGCCCGCTCTCGAGACTGAGCAGGTGGTCGTCATG

GAGACCCGAAACAAGGATGGCGCCTGGCCCAGTGCGCGGCCACAGGCCACGAGCGGAGCGTCGGAGGAGGGTGAGGACTT

CCAAGGCCAGCCGGGCATCTGTGGTCTCACCAACCTGGGCAACACGTGCTTCATGAACTCGGCCCTGCAGTGCCTCAGCA

ACGTGCCACAGCTCACCGAGTACTTCCTCCAAAACCGCTACCTAGAGGAGCTCAACCTCAGCAACCCGCTGGGCATGAAG

GGGGAGATTGCAGAGGCCTATGCCGACCTGGTGAAGCAGGCGTGGTCCGGCCACCACCGCTCCATCGTGCCCTACGTGTT

CAAGACCAAGGTCAGCCACTTTGCGTCCCAGTTCCTGGGCTACCAGCTGCATGACTCACAGGAGCTGCTGTCGTTCCTCC

TGGATGGACTTCACGAGGACCTCAATCGGGTCAAGAAGAAGGAATACGTGAAGCTGTGCGACGCTGCTGGGAGGCCCGAT

CAGGAGGTGGCTCAGGAGGCCTGGCAGAACCACAAACGGTGGAACGATTCTGTGATTGTGGACACTTTCCATGGCCTCTT

CAAGTCCACCTTGGTGTGCCCTGAGTGTGGCAATGTGTCTGTGACCTTCGACCCCTTCTGCTACCTCAGTGTCCCACTGC

CTGTGAGCCACAAGAGGGTCATGGAGATTTTCTTTGTCTCCATGGACCCCCGCCGCAAGCCCGAGCAACACCAGCTCCTG

GTCCCCAAGAAAGGCAAGATCTCGGATCTGTGTGTGGCTCTGGCCAAACACACCGGTGTCTCTCCAGAAAGGATGATGGT

GGCGGATGTCTTCAGTCACCGCTTCTATAAGATCTACCAAGTGGAGGAGTCTCTGAGCAGCATCTTGGACCGAGACGATA

TCTTCATATACGAGGTATCAGGCAGGGCGGCCGGTGGGGAGAACTCCAGAGAGGACGTTGTGCTTCCTGTCTACCTGCGG

GAGCGCACCCCAGCCCGGGACTACAAGGGTTCCTACTATGGCCTGATGCTCTTCGGGCACCCGCTTCTGGTGTCGGTGCC

CCGGGACCGGCTCTCGTGGGACGCCCTGTATCACATCCTGCTGTACCGCCTCTCACGCTACGTGACCAGACCCAGCTGGG

ATGATGAGGAAGATGGGGATGAGAAAGACCTGGAGGGTAAGGACAGCCTCCCTCAGCCTGGACATGGGTCTGGGGGCAGC

TCCCAAGACCCTGGGCTGGAGCAGGCTGGGTCCAGCTCTGGAGTCGTGAGCGGTAGTCCGGGCCCTGTGGACACCTCTCC

TGGGCCATCTCACTGGCCCCAGAGGGTGCGGCACAAGCACCTCTTCACCCTGCAAAGGGTTAATTCCAATGGGACCAGTG

ACCGCTCGACCTTCAACGAGGATACCCAGGCGCAGCCGTACATTGCCATTGACTGGGAGCCAGAGATGAAGAAGCGTTAC

TATGACGAGGTGGAGGCTGAGGGCTACGTGAAGCACAACTGTGTCGGGTACATGCTGAAGAAGGCCCCAGTGCAGCTTCA

GGAATGCATCGAGCTCTTCACCACTGTTGAGACCCTGGAGAAGGAAAACCCCTGGTACTGCCCCACTTGCAAGCAGCACC

AGCCGGCCACCAAGAAGCTGGACTTGTGGATGCTACCAGAGACACTCATTATCCACCTGAAGCGCTTTTCCTACACCACT

TCCTCCCGCGAAAAGCTGGACACCCTTGTGGAGTTTCCTATCCGGGACCTGGACTTCTCTGAGTTTGTCATCAAGCCGCA

GGACAACTTAGCTCCGGAGCTCTACAAATATGACCTCATCGCGGTTTCCAACCATTATGGGGGCCTGCGGGATGGACACT

ACACGACGTTTGCCTGCAACAAGGACAGCGGCCAGTGGCACTACTTCGATGACAACAGCGTCTTGCCTGTGACGGAGAAT

CAGATTGAGTCCAAGGCAGCCTATGTCCTCTTCTACCAGCGCCAGGATGTGGCACGCCGTCTACAACCCCAGGCTGGCTC

ATTGAACCCCCCGGCATCCTCTGCCTGCGATGCACCACCTAAGTCGGGGTTCATGGATGTAAAC

ORF - retro_btau_1125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	85.63 %
Parental protein coverage:	93.41 %
Number of stop codons detected:	1
Number of frameshifts detected:	4

Retrocopy - Parental Gene Alignment:

                                ParentalWEVYVR--GGNQDSSTFPGCINNAELFEDQVNWRLKKGLVEGEDYVLLPAAAWHYLVNWYGLEHGQPPIE
W...VR..GG.QDSS.FPGCIN.AE.FEDQVN.RLKKGL.EG.DYVLLP.AA..YLVNWY.LEH..P..E
RetrocopyWAARVRAVGGDQDSSIFPGCINKAEVFEDQVNGRLKKGLAEGKDYVLLPMAAQRYLVNWYVLEHDPPRME
ParentalRKVVELPSTHKVEVYSVELLLVRHSDMDTPH-TAQFSQTDSVDLV-LHTAREQF-LVSPQEETRLWIKNA
RKVVELPS.H.VE....EL.LV..SD.DT...T...S..DS.DLV.L.TA.EQF....PQEETRLW.KN.
RetrocopyRKVVELPSVHEVE----ELVLVQLSDTDTTP<TSHLSPADSSDLV>LRTA*EQF<SGAPQEETRLWLKNT
ParentalEGSFERLCNTRVTVLDA-ALKTGQVVVMETRNKDGTWPSAQPHDTRSTLEEEEDFQGQPGICGLTNLGNT
EG.FERLC...VTVLDA.AL.T.QVVVMETRNKDG.WPSA.P..T....EE.EDFQGQPGICGLTNLGNT
RetrocopyEGPFERLCDACVTVLDA>ALETEQVVVMETRNKDGAWPSARPQATSGASEEGEDFQGQPGICGLTNLGNT
ParentalCFMNSALQCLSNVPQLTEYFLKNRYLEELNFCNPLGMKGEIAQAYADLVKQAWSGHHRSIVPQVFKTKVG
CFMNSALQCLSNVPQLTEYFL.NRYLEELN..NPLGMKGEIA.AYADLVKQAWSGHHRSIVP.VFKTKV.
RetrocopyCFMNSALQCLSNVPQLTEYFLQNRYLEELNLSNPLGMKGEIAEAYADLVKQAWSGHHRSIVPYVFKTKVS
ParentalHFASQFLGYQQHDSQELLSFLLDGLHEDLNRIKKKEYVELCDAAGRPDQEVAQEAWQNHKRRNDSVIVDT
HFASQFLGYQ.HDSQELLSFLLDGLHEDLNR.KKKEYV.LCDAAGRPDQEVAQEAWQNHKR.NDSVIVDT
RetrocopyHFASQFLGYQLHDSQELLSFLLDGLHEDLNRVKKKEYVKLCDAAGRPDQEVAQEAWQNHKRWNDSVIVDT
ParentalFHGLFKSTLVCPDCGNVSVTFDPFCYLSVPLPVSHKRVMEVFFVSMDPRRKPEQHRLVVPKKGKISDLCV
FHGLFKSTLVCP.CGNVSVTFDPFCYLSVPLPVSHKRVME.FFVSMDPRRKPEQH.L.VPKKGKISDLCV
RetrocopyFHGLFKSTLVCPECGNVSVTFDPFCYLSVPLPVSHKRVMEIFFVSMDPRRKPEQHQLLVPKKGKISDLCV
ParentalALAKHTGISPERMMVADVFSHRFYKIYQLEESLSSILDRDDIFIYEVSGRAAIGENSREDVVLPIYLRER
ALAKHTG.SPERMMVADVFSHRFYKIYQ.EESLSSILDRDDIFIYEVSGRAA.GENSREDVVLP.YLRER
RetrocopyALAKHTGVSPERMMVADVFSHRFYKIYQVEESLSSILDRDDIFIYEVSGRAAGGENSREDVVLPVYLRER
ParentalTPARDYNSSYYGLMLFGHPLLVSVPRDRLSWDALYHILLYRLSRYVTRPSSDDEDDGDEKDLEDKDRLPK
TPARDY..SYYGLMLFGHPLLVSVPRDRLSWDALYHILLYRLSRYVTRPS.DDE.DGDEKDLE.KD.LP.
RetrocopyTPARDYKGSYYGLMLFGHPLLVSVPRDRLSWDALYHILLYRLSRYVTRPSWDDEEDGDEKDLEGKDSLPQ
ParentalPGRVTAGSSQDPGLEQAGPSSRVVSRSRAPVDNSPGPSHWPQRARRKHLFTLHTVNSNGTSDRSTFNEDT
PG....GSSQDPGLEQAG.SS.VVS.S..PVD.SPGPSHWPQR.R.KHLFTL..VNSNGTSDRSTFNEDT
RetrocopyPGHGSGGSSQDPGLEQAGSSSGVVSGSPGPVDTSPGPSHWPQRVRHKHLFTLQRVNSNGTSDRSTFNEDT
ParentalHAQPYIAIDWEPEMKKRYYDEVEAEGYVKHDCVGYVLKKAPVQLQECIELFTTVETLEKENPWYCPTCKQ
.AQPYIAIDWEPEMKKRYYDEVEAEGYVKH.CVGY.LKKAPVQLQECIELFTTVETLEKENPWYCPTCKQ
RetrocopyQAQPYIAIDWEPEMKKRYYDEVEAEGYVKHNCVGYMLKKAPVQLQECIELFTTVETLEKENPWYCPTCKQ
ParentalHQLATKKLDLWMLPETLIIHLKRFSYTKFSREKLDTLVEFPIRDLDFSEFVIKPQNDSSRELYKYDLIAV
HQ.ATKKLDLWMLPETLIIHLKRFSYT..SREKLDTLVEFPIRDLDFSEFVIKPQ.....ELYKYDLIAV
RetrocopyHQPATKKLDLWMLPETLIIHLKRFSYTTSSREKLDTLVEFPIRDLDFSEFVIKPQDNLAPELYKYDLIAV
ParentalSNHYGGLRDGHYTTFACNKDSGQWHYFDDSSVSPVTENQIESKAAYVLFYQRQDVARRLQTQASSSKPPA
SNHYGGLRDGHYTTFACNKDSGQWHYFDD.SV.PVTENQIESKAAYVLFYQRQDVARRLQ.QA.S..PPA
RetrocopySNHYGGLRDGHYTTFACNKDSGQWHYFDDNSVLPVTENQIESKAAYVLFYQRQDVARRLQPQAGSLNPPA
ParentalSSACGAPPKSEFVDVN
SSAC.APPKS.F.DVN
RetrocopySSACDAPPKSGFMDVN

                            

                            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 .07 RPM	26 .96 RPM
ERP005899_muscle	0 .00 RPM	45 .29 RPM
SRP017611_brain	0 .23 RPM	120 .46 RPM
SRP017611_kidney	0 .06 RPM	82 .57 RPM
SRP017611_liver	0 .00 RPM	40 .55 RPM
SRP030211_testis	90 .62 RPM	66 .05 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

2 EST(s) were mapped to retro_btau_1125 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DY177259	24803490	24803816	100	326	0	326
EV611672	24802274	24802948	99.6	674	0	673

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_1125 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_btau_1125 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016772	1 retrocopy	retro_btau_1125 ,

	RetrogeneDB ID:	retro_btau_1125
Retrocopy location	Organism:	*Cow (Bos taurus)*
	Coordinates:	27:24801790..24804334(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSBTAG00000006562
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	USP11
	Ensembl ID:	ENSBTAG00000016772
	Aliases:	None
	Description:	ubiquitin carboxyl-terminal hydrolase 11 [Source:RefSeq peptide;Acc:NP_001073777]

Parental	WEVYVR--GGNQDSSTFPGCINNAELFEDQVNWRLKKGLVEGEDYVLLPAAAWHYLVNWYGLEHGQPPIE
	W...VR..GG.QDSS.FPGCIN.AE.FEDQVN.RLKKGL.EG.DYVLLP.AA..YLVNWY.LEH..P..E
Retrocopy	WAARVRAVGGDQDSSIFPGCINKAEVFEDQVNGRLKKGLAEGKDYVLLPMAAQRYLVNWYVLEHDPPRME

Parental	RKVVELPSTHKVEVYSVELLLVRHSDMDTPH-TAQFSQTDSVDLV-LHTAREQF-LVSPQEETRLWIKNA
	RKVVELPS.H.VE....EL.LV..SD.DT...T...S..DS.DLV.L.TA.EQF....PQEETRLW.KN.
Retrocopy	RKVVELPSVHEVE----ELVLVQLSDTDTTP<TSHLSPADSSDLV>LRTA*EQF<SGAPQEETRLWLKNT

Parental	EGSFERLCNTRVTVLDA-ALKTGQVVVMETRNKDGTWPSAQPHDTRSTLEEEEDFQGQPGICGLTNLGNT
	EG.FERLC...VTVLDA.AL.T.QVVVMETRNKDG.WPSA.P..T....EE.EDFQGQPGICGLTNLGNT
Retrocopy	EGPFERLCDACVTVLDA>ALETEQVVVMETRNKDGAWPSARPQATSGASEEGEDFQGQPGICGLTNLGNT

Parental	CFMNSALQCLSNVPQLTEYFLKNRYLEELNFCNPLGMKGEIAQAYADLVKQAWSGHHRSIVPQVFKTKVG
	CFMNSALQCLSNVPQLTEYFL.NRYLEELN..NPLGMKGEIA.AYADLVKQAWSGHHRSIVP.VFKTKV.
Retrocopy	CFMNSALQCLSNVPQLTEYFLQNRYLEELNLSNPLGMKGEIAEAYADLVKQAWSGHHRSIVPYVFKTKVS

Parental	HFASQFLGYQQHDSQELLSFLLDGLHEDLNRIKKKEYVELCDAAGRPDQEVAQEAWQNHKRRNDSVIVDT
	HFASQFLGYQ.HDSQELLSFLLDGLHEDLNR.KKKEYV.LCDAAGRPDQEVAQEAWQNHKR.NDSVIVDT
Retrocopy	HFASQFLGYQLHDSQELLSFLLDGLHEDLNRVKKKEYVKLCDAAGRPDQEVAQEAWQNHKRWNDSVIVDT

Parental	FHGLFKSTLVCPDCGNVSVTFDPFCYLSVPLPVSHKRVMEVFFVSMDPRRKPEQHRLVVPKKGKISDLCV
	FHGLFKSTLVCP.CGNVSVTFDPFCYLSVPLPVSHKRVME.FFVSMDPRRKPEQH.L.VPKKGKISDLCV
Retrocopy	FHGLFKSTLVCPECGNVSVTFDPFCYLSVPLPVSHKRVMEIFFVSMDPRRKPEQHQLLVPKKGKISDLCV

Parental	ALAKHTGISPERMMVADVFSHRFYKIYQLEESLSSILDRDDIFIYEVSGRAAIGENSREDVVLPIYLRER
	ALAKHTG.SPERMMVADVFSHRFYKIYQ.EESLSSILDRDDIFIYEVSGRAA.GENSREDVVLP.YLRER
Retrocopy	ALAKHTGVSPERMMVADVFSHRFYKIYQVEESLSSILDRDDIFIYEVSGRAAGGENSREDVVLPVYLRER

Parental	TPARDYNSSYYGLMLFGHPLLVSVPRDRLSWDALYHILLYRLSRYVTRPSSDDEDDGDEKDLEDKDRLPK
	TPARDY..SYYGLMLFGHPLLVSVPRDRLSWDALYHILLYRLSRYVTRPS.DDE.DGDEKDLE.KD.LP.
Retrocopy	TPARDYKGSYYGLMLFGHPLLVSVPRDRLSWDALYHILLYRLSRYVTRPSWDDEEDGDEKDLEGKDSLPQ

Parental	PGRVTAGSSQDPGLEQAGPSSRVVSRSRAPVDNSPGPSHWPQRARRKHLFTLHTVNSNGTSDRSTFNEDT
	PG....GSSQDPGLEQAG.SS.VVS.S..PVD.SPGPSHWPQR.R.KHLFTL..VNSNGTSDRSTFNEDT
Retrocopy	PGHGSGGSSQDPGLEQAGSSSGVVSGSPGPVDTSPGPSHWPQRVRHKHLFTLQRVNSNGTSDRSTFNEDT

Parental	HAQPYIAIDWEPEMKKRYYDEVEAEGYVKHDCVGYVLKKAPVQLQECIELFTTVETLEKENPWYCPTCKQ
	.AQPYIAIDWEPEMKKRYYDEVEAEGYVKH.CVGY.LKKAPVQLQECIELFTTVETLEKENPWYCPTCKQ
Retrocopy	QAQPYIAIDWEPEMKKRYYDEVEAEGYVKHNCVGYMLKKAPVQLQECIELFTTVETLEKENPWYCPTCKQ

Parental	HQLATKKLDLWMLPETLIIHLKRFSYTKFSREKLDTLVEFPIRDLDFSEFVIKPQNDSSRELYKYDLIAV
	HQ.ATKKLDLWMLPETLIIHLKRFSYT..SREKLDTLVEFPIRDLDFSEFVIKPQ.....ELYKYDLIAV
Retrocopy	HQPATKKLDLWMLPETLIIHLKRFSYTTSSREKLDTLVEFPIRDLDFSEFVIKPQDNLAPELYKYDLIAV

Parental	SNHYGGLRDGHYTTFACNKDSGQWHYFDDSSVSPVTENQIESKAAYVLFYQRQDVARRLQTQASSSKPPA
	SNHYGGLRDGHYTTFACNKDSGQWHYFDD.SV.PVTENQIESKAAYVLFYQRQDVARRLQ.QA.S..PPA
Retrocopy	SNHYGGLRDGHYTTFACNKDSGQWHYFDDNSVLPVTENQIESKAAYVLFYQRQDVARRLQPQAGSLNPPA

Parental	SSACGAPPKSEFVDVN
	SSAC.APPKS.F.DVN
Retrocopy	SSACDAPPKSGFMDVN

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

RetrogeneDB ID:

retro_btau_1125