RetrogeneDB ID:

retro_btau_961

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:21:52763490..52765141(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000006363
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MOXD1
Ensembl ID:ENSBTAG00000019460
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_btau_961
TTCCGCCTCAAGGTGCAGACCGCCGGCTACGTGGGCTTCAGTTTCTTGTCCACCGGGGCCATGGCAGCGGCCGACATCAT
CATGGGTGGGGTGGCCCGTGGGCGGCCCTACCTCTAGGATTATTTTACAAATGCAAACAGAGAATTGAGAAAAGATGCTC
AGCAAGATTACCACCTAGAATATGCCATGGAAAATAGTACACACACAGTAATTGAATTTGCCAGAGAACTGCATACGTGT
GACATAAATGACAAGAGTATAATGGAGAACACGGTAAGGGTGATCTGGGCCTACCACCATGAAGATGTGGGAGAAGCAGG
TCCTAAGTACCATGAATCCAATCATGGTACCAAGAGTCTGCAGTTACTGAATCCTGAGAAAACCAGTATGTTGTCTACAG
CTGTACCATACTTTGACCTGGTCAATCAAGACGTTCCCATCCCAAACAAAGGTACAACATACTGGTGCCAACTGTTTAAG
ATTCCTAGGCTCCAGGAAAAGCATCATGTCATAAAGGTTGAGCCCGTGATTCAGAAAGGCCATGAGAGTCTGGTCCATCA
CATGCTGCTCTATCAGTGCAGCAGCAACTTCAGTGACAGTGTCCCGGACGACGGGCACGAGTGTTACCACCCTAACATGC
CCGATGCCTTCCTCACCTGTGAGACCGTCATTTTCCCCCTGGGCCATTGGTGGAGAGGCTTTTTCCTATCCACCTCATGT
TGGATTGTCCCTTGGCACTCCGTTAGATCCTCATTATGTGCTCCTGGAAGTCCATTATGACAATCCAACATATAAGGAAG
GCTTAATAGATAATTCTGGATTGAGATTATTTTATACGGCAGATATAAGGAAATACGATGCTGGGGTGATTGAGGCTGGC
CTCTGGGTAAGCCTCTTTCACACCATCCCTCCGGGCCTGCCCGACTTCCGGTCTGAGGGTCATTGCACCCTGGAATGCCT
GGAAGAGGCTTTGGAAGCTGAAAAGCCAAGTGGCATCCATGTTTTTGCTGTTCTGCTCCATGCTCACCTGGCAGGCAGAG
GCATCAGGCTGTGTCATTTTCACAAAGGGGAGGAAATGAGATTACTTGCTTATGATGACAATTTTGATTTCAATTTCCAG
GAGTTTCAGTACCTAAAAGAAGAACAAACAATCTTACCAGGAGATAATCTAATTACTGAGTGTCGGTACAACACAAAAGA
TAGAGCCCGGATGACTTGGGGAGGATTAAGCACCGGGAATGAAATGTGTCTCTCATACATTCTTTATTACCCAAGAATTA
ATCTTACTCGATGTGCAAGTATCCCAGACATCATGGAGCAACTTCAGTTCATTGGTGTTAAGGAGATCTACAGGCCAGTC
ACGACCTGGGCTTTCATTATCAAAAGCCCTAAGCAGTATAAAAACCTTTCTTTCATGGACGCAATGAACAAGTTTAAATG
GACTAAAAAGGAAGGTCTTGCTTTCAATAAGCTTGTCCTTAGCCTGCCGGTCAACGTGAGATGCTCCAAGACAGACAATG
CAGAGTGGTCGATTCAAGGCATGACAGCATTACCTCCAGATATAGAAAGACCATATCAAGCAGAGCCCTTGGTGTATGGA
GCTTCTTCCAGTTCTCTTCATGGAAATGTCTGTCTCGAGCTGCTCCTAAGC

ORF - retro_btau_961 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.37 %
Parental protein coverage: 89.58 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFRLEVRTAGYVGFGFSSTGAMAAADIVVGGVARGRPYLQDYFTNANRELRKDAQQDYHLEYAMENSTHTV
FRL.V.TAGYVGF.F.STGAMAAADI..GGVARGRPYL.DYFTNANRELRKDAQQDYHLEYAMENSTHTV
RetrocopyFRLKVQTAGYVGFSFLSTGAMAAADIIMGGVARGRPYL*DYFTNANRELRKDAQQDYHLEYAMENSTHTV
ParentalIEFTRELHTCDINDKSISESTVRVIWAYHHEDVGEAGPKYHESNRGTKSLRLLNPEKTSMLSTAIPYFDL
IEF.RELHTCDINDKSI.E.TVRVIWAYHHEDVGEAGPKYHESN.GTKSL.LLNPEKTSMLSTA.PYFDL
RetrocopyIEFARELHTCDINDKSIMENTVRVIWAYHHEDVGEAGPKYHESNHGTKSLQLLNPEKTSMLSTAVPYFDL
ParentalVNQDVSIPNKGTTYWCQMFKIPMLQEKHHVIKVEPVIQKGHESLVHHILLYQCSSNFSDSVLDDGHECYH
VNQDV.IPNKGTTYWCQ.FKIP.LQEKHHVIKVEPVIQKGHESLVHH.LLYQCSSNFSDSV.DDGHECYH
RetrocopyVNQDVPIPNKGTTYWCQLFKIPRLQEKHHVIKVEPVIQKGHESLVHHMLLYQCSSNFSDSVPDDGHECYH
ParentalPNMPDAFLTCETVIFA-WAIGGEGFSYPPHVGLSLGTPLDPHYVLLEVHYDNPTYKEGLIDNSGLRLFYT
PNMPDAFLTCETVIF..WAIGGE.FSYPPHVGLSLGTPLDPHYVLLEVHYDNPTYKEGLIDNSGLRLFYT
RetrocopyPNMPDAFLTCETVIFP>WAIGGEAFSYPPHVGLSLGTPLDPHYVLLEVHYDNPTYKEGLIDNSGLRLFYT
ParentalADIRKYDAGVIEAGLWVSLFHTIPPGLPDFRSEGHCTLECLEEALEAEKPSGIHVFAVLLHAHLAGRGIR
ADIRKYDAGVIEAGLWVSLFHTIPPGLPDFRSEGHCTLECLEEALEAEKPSGIHVFAVLLHAHLAGRGIR
RetrocopyADIRKYDAGVIEAGLWVSLFHTIPPGLPDFRSEGHCTLECLEEALEAEKPSGIHVFAVLLHAHLAGRGIR
ParentalLRHFRKGEEMRLLAYDDDFDFNFQEFQYLKEEQTILPGDNLITECRYNTKDRARMTWGGLSTRNEMCLSY
L.HF.KGEEMRLLAYDD.FDFNFQEFQYLKEEQTILPGDNLITECRYNTKDRARMTWGGLST.NEMCLSY
RetrocopyLCHFHKGEEMRLLAYDDNFDFNFQEFQYLKEEQTILPGDNLITECRYNTKDRARMTWGGLSTGNEMCLSY
ParentalLLYYPRINLTRCASIPDIMEQLQFIGVKEIYRPVTTWPFIIKSPKQYRNLSFMDAMNKFKWTKKEGLAFN
.LYYPRINLTRCASIPDIMEQLQFIGVKEIYRPVTTW.FIIKSPKQY.NLSFMDAMNKFKWTKKEGLAFN
RetrocopyILYYPRINLTRCASIPDIMEQLQFIGVKEIYRPVTTWAFIIKSPKQYKNLSFMDAMNKFKWTKKEGLAFN
ParentalKLVLSLPVNVRCSKTDNAEWSIQGMTALPPDIERPYQAEPLVCGASSTSLRGNVCLELLLS
KLVLSLPVNVRCSKTDNAEWSIQGMTALPPDIERPYQAEPLV.GASS.SL.GNVCLELLLS
RetrocopyKLVLSLPVNVRCSKTDNAEWSIQGMTALPPDIERPYQAEPLVYGASSSSLHGNVCLELLLS

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 36 .91 RPM
ERP005899_muscle 0 .00 RPM 2 .43 RPM
SRP017611_brain 0 .05 RPM 7 .22 RPM
SRP017611_kidney 0 .06 RPM 20 .51 RPM
SRP017611_liver 0 .15 RPM 162 .87 RPM
SRP030211_testis 0 .09 RPM 3 .55 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_961 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_961 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_961 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 ENSBTAG00000019460 1 retrocopy
retro_btau_961 ,


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