RetrogeneDB ID:

retro_mmul_202

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:X:124386330..124387722(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000015706
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DCAF12
Ensembl ID:ENSMMUG00000017458
Aliases:DCAF12, WDR40A
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_202
ATGGCCCAGCAGCAAACAGGTAGCAGGAAACGGAAAGCGCCCGCGGTCGAGGCGGGCGCCGGGAGCTCGTCCTCGCAGGG
CTTAGCGGCGGCGGACGGAGAGGGGCCTCTGCTACCCAAGAAGCAGAAGCGGCCGGCGACGCGTCGCAGGCTGGTGCACT
ATCTGAAGGGCCGGGAGGTAGGAGCGAGGGGCCCCGCCGGGCTCCAGGGCTTTGAGGGCGAGCTTCGGGGCTACGCGGTA
CAGAGGCTGCCCGAGCTGCTGACAGAGCGCCAGCTGGACCTGGGCACCCTCAACAAGGTGTTCGCGTCACAGTGGCTGAA
CGCCAGGCAGGTGGTGTGCGGCACCAAGTGTAACACGCTCTTCGTGGTGGACGTGCAGTCAGGCCACATCACGCGCATCC
CCCTCATGCGGGACAAGGAGGCCGGGCTGGCCCAGGCCCAACAGGGCTGCGGCATCCATGCCATCGAGCTGAATCCCTCC
AAGACGCTTCTGGCCACCGGCGGCGAAAACCCCAACAGCCTGGCCATCTACCAGCTGCCCACCCTGGACCCCCTGTGCCT
GGGCGACCGCCATGGCCACAAGGACTGGATCTTCGCCGTTGCCTGGCTGAGTGACACCGTAGCCGTGAGCGGCTCCCGCG
ACGGCACTGTGGCGCTGTGGCGGATGGACCCGGACATGTTCAATGGCAGCATTGCCTGGCACAGCGAGGTGGGTCTCCCC
GTATATGCCCACATCCGTCCGAAGGATGTGGAGGCCATACCCAGGGCCAGCACCAACCCCAGTAACCGCAAGGTGCGGGC
CCTGGCCTTCAGCGGCAAGAACCAGGAGCTGGGAGCGGTGTCCTTAGACGGCTACTTCCACCTGTGGAAAGCCAGGAGCA
CACTATCCAGGCTCCTGTCCATCAGGCTGCCCTACTGCCGAGAGAATGTGTGCCTGACCTACTGCGATGAGTTGTCCCTC
TACGCTGTGGGCTCCCAGTCCCACGTCTCCTTCCTGGATCCGCGCCAGCGCCAGCAGAACATCCGGCCCCTGTGCTCTCG
AGAAGGTGGCACAGGCGTGCGGTCTCTGAGCTTCTACCAGCACATCATCACTGTGGGCACCGGCCATGGCTCCCTGCTCT
TCTATGACATCCGGGCCCAGAAGTTCCTGGAGGAGAGAGCCTCTGCCAGTCTGGACTCTACGCCGGGGCCCGCAGGGAGG
AAGCTCAAGCTTGCCTGTGGCAGAGGCTGGCTCAACCAGGATGACGTCTGGGTGAACTACTTTGGTGGCATGGAAGAGTT
CCCCAATGCGCTCTACACCCACTGCTACAACTGGCCCGAGATGAAGCTCTTTGTGGCTGGGGGGCCTCTCCCTTCAGGAC
TCCATGGGAACTACGCAGGCCTCTGGAGTTAA

ORF - retro_mmul_202 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.18 %
Parental protein coverage: 85.43 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLHGYAAQQLPSLLKEREFHLGTLNKVFASQWLNHRQVVCGTKCNTLFVVDVQTSQITKIPILKDREPG-G
L.GYA.Q.LP.LL.ER...LGTLNKVFASQWLN.RQVVCGTKCNTLFVVDVQ...IT.IP...D.E.G..
RetrocopyLRGYAVQRLPELLTERQLDLGTLNKVFASQWLNARQVVCGTKCNTLFVVDVQSGHITRIPLMRDKEAGLA
ParentalVTQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRLPTLDPVCVGD-DGHKDWIFSIAWISDTMAVSGSRD
..QQGCGIHAIELNPS.TLLATGG.NPNSLAIY.LPTLDP.C.GD..GHKDWIF..AW.SDT.AVSGSRD
RetrocopyQAQQGCGIHAIELNPSKTLLATGGENPNSLAIYQLPTLDPLCLGDRHGHKDWIFAVAWLSDTVAVSGSRD
ParentalGSMGLWEVTDDVLTKSDARHSVSRVPVYAHITHKALKDIPKEDTNPDNCKVRALAFNSKNKELGAVSLDG
G...LW....D....S.A.HS....PVYAHI..K....IP...TNP.N.KVRALAF..KN.ELGAVSLDG
RetrocopyGTVALWRMDPDMFNGSIAWHSEVGLPVYAHIRPKDVEAIPRASTNPSNRKVRALAFSGKNQELGAVSLDG
ParentalYFHLWKAENTLSKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSRERGSGIR
YFHLWKA..TLS.LLS..LPYCRENVCL.Y..E.S.YAVGSQ.HVSFLDPRQ...N....CSRE.G.G.R
RetrocopyYFHLWKARSTLSRLLSIRLPYCRENVCLTYCDELSLYAVGSQSHVSFLDPRQRQQNIRPLCSREGGTGVR
ParentalSVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLSACYGSKPRLAGENLKLTTGKGWLNHDETWRNYFSDI
S.SFY.HIITVGTG.GSLLFYDIRAQ.FLEER.SA...S.P..AG..LKL..G.GWLN.D..W.NYF...
RetrocopySLSFYQHIITVGTGHGSLLFYDIRAQKFLEERASASLDSTPGPAGRKLKLACGRGWLNQDDVWVNYFGGM
ParentalDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
..FPNA.YTHCY.....KLFVAGGPLPSGLHGNYAGLWS
RetrocopyEEFPNALYTHCYNWPEMKLFVAGGPLPSGLHGNYAGLWS

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
SRP007412_brain 1 .01 RPM 14 .01 RPM
SRP007412_brain_prefrontal_cortex 5 .24 RPM 15 .95 RPM
SRP007412_cerebellum 0 .39 RPM 20 .86 RPM
SRP007412_heart 0 .00 RPM 11 .78 RPM
SRP007412_kidney 0 .00 RPM 27 .58 RPM
SRP007412_liver 0 .75 RPM 16 .15 RPM
SRP007412_testis 3 .20 RPM 161 .89 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_202 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_202 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_202 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 ENSBTAG000000215733 retrocopies
Equus caballus ENSECAG000000230642 retrocopies
Erinaceus europaeus ENSEEUG000000132791 retrocopy
Microcebus murinus ENSMICG000000058811 retrocopy
Macaca mulatta ENSMMUG00000017458 1 retrocopy
retro_mmul_202 ,
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



Copyright © RetrogeneDB 2014-2017