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






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 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

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_1795 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

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
retro_amel_73,
Bos taurus ENSBTAG00000021573 3 retrocopies
retro_btau_1794, retro_btau_1795 , retro_btau_1796,
Equus caballus ENSECAG000000230642 retrocopies
retro_ecab_1128, retro_ecab_1129,
Erinaceus europaeus ENSEEUG000000132791 retrocopy
retro_eeur_403,
Microcebus murinus ENSMICG000000058811 retrocopy
retro_mmur_14,
Macaca mulatta ENSMMUG000000174581 retrocopy
retro_mmul_202,
Nomascus leucogenys ENSNLEG000000049961 retrocopy
retro_nleu_6,
Otolemur garnettii ENSOGAG000000157991 retrocopy
retro_ogar_237,
Ochotona princeps ENSOPRG000000012812 retrocopies
retro_opri_1178, retro_opri_470,
Pongo abelii ENSPPYG000000191271 retrocopy
retro_pabe_64,
Pteropus vampyrus ENSPVAG000000086541 retrocopy
retro_pvam_16,
Sus scrofa ENSSSCG000000109861 retrocopy
retro_sscr_17,
Ictidomys tridecemlineatus ENSSTOG000000069041 retrocopy
retro_itri_168,
Tarsius syrichta ENSTSYG000000143941 retrocopy
retro_tsyr_1965,
Tursiops truncatus ENSTTRG000000105911 retrocopy
retro_ttru_8,


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