RetrogeneDB ID:

retro_btau_442

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:11:49070192..49071859(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSBTAG00000039981
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:DNAJC11
Ensembl ID:ENSBTAG00000011217
Aliases:None
Description:DnaJ homolog subfamily C member 11 [Source:UniProtKB/Swiss-Prot;Acc:Q2NL21]


Retrocopy-Parental alignment summary:






>retro_btau_442
ATGGCGACGGCCTTGAGCAAGGAGGAGCTGGACAATGAAGACTATTACTCGTTGCTGAACGTGCGCAGGGAGGCCTCTTG
CGAAGAGCCAAAAGCGGCCTACCGGCGGCTGTGCATGCTTTACCACCCCGACAAGCACAGAGACCCAGGGCTCAAATCGC
AGGCCGAGCGGCTGTTTAACCTCATTCACCAGGCTTATGAAGTGTTCAGTGACCCCCAGACCAGGGCCATCTATGACATC
TATGGCAAGAGAGGACTGGAGATGGAAGGCTGGGAGGTTGTGGAAAGGAGGAGAACGCCAGCTGAGATCAGAGAAGAGTT
TGAGCGGCTGCAGCGCGAGAGGGAGGAGAGCAGGCTGCAGCAGCGCACCAACCCCAAGGGGACCATCAGTGTTGGCACTG
ACGCCACTGACCTTTTTGATCGCTATGAGGAGGAGTACGAGGATGTGTCCGGAAGTGGCTTTCCACAGATTGAAGTTAAC
AAGATGCACATATCACAGTCCATTGTGGCACCCCAACAGCTTCAGACACAGCCATCCTCTCTGGAAGCCTCTCAACCCAG
AATGGGAATGGAGGGGGTTCCATTAACTTTGCGCTCAGACGAGTCACTTCTGTGAAGGGCTGGGGAGAGTTAGAATTTGG
AGCTGGGGATCTGCAGGGGCCTTTATTTGGCCTGAAGCTGTTCCGTAATCTCACACCAAGATGCTTTGTGATGACACACT
GTGCCCTGCAGTTTTCATCCCACGGCATCCAGCCGGGCCTCACCACTGTCCTGGCCCGGAACCTGGACAAGAATACGGTG
GGCTACCTGCAGTGGCGCTGGGGCGTCCAGTCAGCCATGAACACCAGCATCGTCCGGGACACCAAGACCAGCCACTTCAC
TGTGGGCCCGCAGCTTGGAATCCCTCACTCCTTCGCACTCATCAGCTATCAGCACGAATTCCAGGATGACGACCAGACCC
GAGTGAAGGGGTCCCTGAAGGCCAGCTTCTTCGGGACGGTGATGGAAGCAGAGAGGAAGATCTCCAGGCACAGTGTCCTC
GGGGCGGCTGTCAGCGTTGGAGTCCCACAGGCCGTTTCCCTCAAAATCAAGTTAAATAGGGCCAGTCAGACCTACTTCTT
CCCTATCTACCTGACAGACCAGCTGCTGCCCAGCGCCGTGTTCTACGCCACCGAGGGGCCGCTCCTGCTGTACTTCGCTC
TGCACCGCCTGGTCATCAGACCCTACCTCAGGGCTCAGAAGGAGAAGGAACTGGAGAAGCAAAGGGAAAGCACAGCCACC
GACATCCTGCAGAAGAAACCAGAGGCAGAAGCTGCCGTTTGGTTGATGCAGGAATCTGTCCGAAGAATAATCGAGGTCGA
AGAGTCCAGAATGGGGCTCATCATCATCAATGCCTGGTATGGAAAATTTGTCAATGACAAGAGCAAGAAGAGCGAGAAGG
TGAAGGTGATCGATGTGACCGTGCCCCTGCAGTGTCTGATGAAGGACTCCAAGCTCATCCTCACCGAGGCCTCCAAGGCT
GGGCTGCCCAGCTTCTACGACCCGTGTGTGGGTGAAGAGAACCTGAAAGTGCTTTACCAGTTCCGCGGGGTCCTTCATCA
GGTGATGGTGCTCGACAGCGAGGCACTCAGGATACCAAAGCAGTCTCACAGAATTGATACTGATGGA

ORF - retro_btau_442 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.75 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMATALSEEELDNEDYYSLLNVRREASCEELKAAYRRLCMLYHPDKHRDPELKSQAERLFNLVHQAYEVLS
MATALS.EELDNEDYYSLLNVRREASCEE.KAAYRRLCMLYHPDKHRDP.LKSQAERLFNL.HQAYEV.S
RetrocopyMATALSKEELDNEDYYSLLNVRREASCEEPKAAYRRLCMLYHPDKHRDPGLKSQAERLFNLIHQAYEVFS
ParentalDPQTRAIYDIYGKRGLEMEGWEVVERRRTPAEIREEFERLQREREERRLQQRTNPKGTISVGIDATDLFD
DPQTRAIYDIYGKRGLEMEGWEVVERRRTPAEIREEFERLQREREE.RLQQRTNPKGTISVG.DATDLFD
RetrocopyDPQTRAIYDIYGKRGLEMEGWEVVERRRTPAEIREEFERLQREREESRLQQRTNPKGTISVGTDATDLFD
ParentalRYEEEYEDVSGSGFPQIEINKMHISQSIEAPL-TASDTAILSGSLSTQNGNGGGSINFALRRVTSAKGWG
RYEEEYEDVSGSGFPQIE.NKMHISQSI.AP..TASDTAILSGSLSTQNGNGGGSINFALRRVTS.KGWG
RetrocopyRYEEEYEDVSGSGFPQIEVNKMHISQSIVAPQ<TASDTAILSGSLSTQNGNGGGSINFALRRVTSVKGWG
ParentalELEFGAGDLQGPLFGLKLFRNLTPRCFVTTHCALQFSSRGIRPGLTTVLARNLDKNTVGYLQWRWGVQSA
ELEFGAGDLQGPLFGLKLFRNLTPRCFV.THCALQFSS.GI.PGLTTVLARNLDKNTVGYLQWRWGVQSA
RetrocopyELEFGAGDLQGPLFGLKLFRNLTPRCFVMTHCALQFSSHGIQPGLTTVLARNLDKNTVGYLQWRWGVQSA
ParentalMNTSIVRDTKTSHFTVALQLGIPHSFALISYQHKFQDDDQTRVKGSLKAGFFGTVVEYGAERKISRHSVL
MNTSIVRDTKTSHFTV..QLGIPHSFALISYQH.FQDDDQTRVKGSLKA.FFGTV.E..AERKISRHSVL
RetrocopyMNTSIVRDTKTSHFTVGPQLGIPHSFALISYQHEFQDDDQTRVKGSLKASFFGTVME--AERKISRHSVL
ParentalGAAVSIGVPQGVSLKIKLNRASQTYFFPIHLTDQLLPSAVFYATAGPLVLYFALHRLVIRPYLRAQKEKE
GAAVS.GVPQ.VSLKIKLNRASQTYFFPI.LTDQLLPSAVFYAT.GPL.LYFALHRLVIRPYLRAQKEKE
RetrocopyGAAVSVGVPQAVSLKIKLNRASQTYFFPIYLTDQLLPSAVFYATEGPLLLYFALHRLVIRPYLRAQKEKE
ParentalLEKQRESTATDILQKKQEAEAAVRLMQESVRRIIEAEESRMGLIIVNAWYGKFVNDKSKKSEKVKVIDVT
LEKQRESTATDILQKK.EAEAAV.LMQESVRRIIE.EESRMGLII.NAWYGKFVNDKSKKSEKVKVIDVT
RetrocopyLEKQRESTATDILQKKPEAEAAVWLMQESVRRIIEVEESRMGLIIINAWYGKFVNDKSKKSEKVKVIDVT
ParentalVPLQCLVKDSKLILTEASKAGLPGFYDPCVGEEKNLKVLYQFRGVLHQVMALDSEALRIPKQSHRIDTDG
VPLQCL.KDSKLILTEASKAGLP.FYDPCVGEE.NLKVLYQFRGVLHQVM.LDSEALRIPKQSHRIDTDG
RetrocopyVPLQCLMKDSKLILTEASKAGLPSFYDPCVGEE-NLKVLYQFRGVLHQVMVLDSEALRIPKQSHRIDTDG

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 15 .79 RPM
ERP005899_muscle 0 .00 RPM 63 .35 RPM
SRP017611_brain 0 .14 RPM 43 .26 RPM
SRP017611_kidney 0 .12 RPM 66 .44 RPM
SRP017611_liver 0 .00 RPM 33 .00 RPM
SRP030211_testis 1 .24 RPM 23 .81 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_442 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_442 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_442 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 ENSBTAG00000011217 1 retrocopy
retro_btau_442 ,


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