RetrogeneDB ID:

retro_btau_1795

Retrocopy
location
Organism:Cow (Bos taurus)
Coordinates:X:10451920..10453102(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DCAF12
Ensembl ID:ENSBTAG00000021573
Aliases:DCAF12, WDR40A
Description:DDB1- and CUL4-associated factor 12 [Source:UniProtKB/Swiss-Prot;Acc:Q3MHH0]


Retrocopy-Parental alignment summary:






>retro_btau_1795
TCAGGCTTCGATAGCGAGCTGCATGGCTTCGCGGTGCGGAAGCTGCCAGAGCTGCTGCGGGAGCGCGAACTGTCCTTGGG
CACCGTGGACAAGGTGTTCGCGTCGCAGTGGCTGAACGCCAGGCAGGTGGTGTGCGGTACCAAGTGCAACACGCTCTTCG
TGGTGGACGTGCGGTCCAGCCAGGTAACGCGCATCCCCCTCATACGGGATCGTGGGCACCCGCCGGCCCGCGCCCAGCCG
GGCTGCGGCATCCATGCGGTCCAGCTGAATCCCTCCAAGACGCTGCTGGCCACCGGGGGCGAGAACCCCAACAGCCTGGC
CGTCTACTGGTTGCCAACGCTGGATCCCTTGTGCCTGGGCGACCATGGCCACAAAGACTGGATCTTCGCCATCGCCTGGA
TGAGCGACACGGTGGTGGTGAGCGGCTCCCGCGACGGCACCTTGGGCATCTGGAAGATAGACCCCGACGTATTCCGGAGC
AGCATCGCCTGGCGCAATCCTGCAGAGCTCTCCGTGTATGCCCACATCCGTCCCGCGGAAGTGGAGGATGTCCGCAGGGC
CGCCACCAACCCACGTAACTGCAAGGTCGGTGCTGTGGCCTTCAGCGCCAAGAGGCAGGAGCTGGGAGCCGTGACCATGG
ATGGCTACTTCCACCTGTGGAAAGCCCAGAATACCCTGTCCAAGCTGTTGTACATCAGGCTGCCTTACTGCAGAGAGAAC
GTGTGCCTGACCTACTGCGATGAGTTGTCCCTGTACGCGGTAGGCTCCCAGTCCCATGTCTCTTTCCTGGACCTGCGCCA
GGGTCACCAGAGCATCCGGTACCTGTGCTCCCGCGAGGGCGGCACGGGTGTGCGCTCTCTCAGCTTCTATGAGCACATCG
TCACCGTGGGCACTGGCCACGGCTCTCTGCTCTTCTATGACATCCGCGCGCAGAAGTTCCTGGAGGAGAAGGTCTCGGAC
AGCCAGCACTCCTCTCCGCGGCCCACAGGGCGGAGGTTCAGGCTGATTTGTGGCAGAGGCTGGCTCAACCAAGATGACCT
GCAGATGAACGACCTCAGTGCCTTGGACGAGTTGCCCAGTGCTCTCTACACCCATTGCTACAACTGGCCGGAGATGAAGC
TCTTCGTCGCTGGCGGCCCTCTTCCTTCAAGCCTCCGTGGGAACTATGCAGGCCTCTGGAGC

ORF - retro_btau_1795 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.94 %
Parental protein coverage: 86.75 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalTSYSRVLHGYAAQQLPSLLKEREFHLGTLNKVFASQWLNHRQVVCGTKCNTLFVVDVQTSQITKIPILKD
......LHG.A...LP.LL.ERE..LGT..KVFASQWLN.RQVVCGTKCNTLFVVDV..SQ.T.IP...D
RetrocopySGFDSELHGFAVRKLPELLRERELSLGTVDKVFASQWLNARQVVCGTKCNTLFVVDVRSSQVTRIPLIRD
ParentalR-EPGCVTQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRLPTLDPVCVGDDGHKDWIFSIAWISDTMAV
R..P....Q.GCGIHA..LNPS.TLLATGG.NPNSLA.Y.LPTLDP.C.GD.GHKDWIF.IAW.SDT..V
RetrocopyRGHPPARAQPGCGIHAVQLNPSKTLLATGGENPNSLAVYWLPTLDPLCLGDHGHKDWIFAIAWMSDTVVV
ParentalSGSRDGSMGLWEVTDDVLTKSDARHNVSRVPVYSHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGA
SGSRDG..G.W....DV...S.A..N.....VY.HI......D.....TNP.NCKV.A.AF..K..ELGA
RetrocopySGSRDGTLGIWKIDPDVFRSSIAWRNPAELSVYAHIRPAEVEDVRRAATNPRNCKVGAVAFSAKRQELGA
ParentalVSLDGYFHLWKTENTLSKLLSTKLPYCRENVCLAYGNEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSRER
V..DGYFHLWK..NTLSKLL...LPYCRENVCL.Y..E.S.YAVGSQ.HVSFLD.RQ........CSRE.
RetrocopyVTMDGYFHLWKAQNTLSKLLYIRLPYCRENVCLTYCDELSLYAVGSQSHVSFLDLRQGHQSIRYLCSREG
ParentalGSGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEEKLSACYGSKPKLAGENLKLTTGKGWLNHDETWRN
G.G.RS.SFYEHI.TVGTG.GSLLFYDIRAQ.FLEEK.S....S.P...G....L..G.GWLN.D....N
RetrocopyGTGVRSLSFYEHIVTVGTGHGSLLFYDIRAQKFLEEKVSDSQHSSPRPTGRRFRLICGRGWLNQDDLQMN
ParentalYFSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
..S..D..P.A.YTHCY.....KLFVAGGPLPS.L.GNYAGLWS
RetrocopyDLSALDELPSALYTHCYNWPEMKLFVAGGPLPSSLRGNYAGLWS

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






(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 39 .94 RPM
ERP005899_muscle 0 .00 RPM 58 .97 RPM
SRP017611_brain 0 .00 RPM 40 .29 RPM
SRP017611_kidney 0 .00 RPM 69 .64 RPM
SRP017611_liver 0 .00 RPM 41 .08 RPM
SRP030211_testis 4 .28 RPM 172 .39 RPM
Bos taurus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_btau_1795 retrocopy.
Bos taurus was not studied using FANTOM5 data.
retro_btau_1795 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_btau_1795 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003091 retrocopy
Bos taurus ENSBTAG00000021573 3 retrocopies
retro_btau_1794, retro_btau_1795 , retro_btau_1796,
Equus caballus ENSECAG000000230642 retrocopies
Erinaceus europaeus ENSEEUG000000132791 retrocopy
Microcebus murinus ENSMICG000000058811 retrocopy
Macaca mulatta ENSMMUG000000174581 retrocopy
Nomascus leucogenys ENSNLEG000000049961 retrocopy
Otolemur garnettii ENSOGAG000000157991 retrocopy
Ochotona princeps ENSOPRG000000012812 retrocopies
Pongo abelii ENSPPYG000000191271 retrocopy
Pteropus vampyrus ENSPVAG000000086541 retrocopy
Sus scrofa ENSSSCG000000109861 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000069041 retrocopy
Tarsius syrichta ENSTSYG000000143941 retrocopy
Tursiops truncatus ENSTTRG000000105911 retrocopy



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