RetrogeneDB ID:

retro_mmul_1709

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:3:108183772..108184725(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.13619
Ensembl ID:ENSMMUG00000011423
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_1709
AGAACCTGCAGTGTAATGACAACAGTTAAGTCCAGGCCATTTTGGGAAAAGCAAGGGAAGATACTGCTGAAAGGTCGCAG
GCTCCTTATAGACGCTCTCAAGGCTGGAGCTGTGCCAACAGTTTTCTTCTCTAGCCATCTATAATACATAAAGAAGCTGC
TCATCGATAAGCCGAAGGGTGTCAGCCTCATTAAGATGAAATTCGAGGACATGAGGGATTGGTCCAACCTAGTAATGCCA
CAAAAATAATGGGGATTTTTGCCAAACCTGACCATGTTAACATGACATATCCAAAGACTCAGCTTTAGCACTCACTGCCT
TTGTTATTGATTTGTGACAATCTCTGTGACCCTGGGAATCTGGGGACAATTCTGAGATCTCCAGCTGGGGCGGGCTGCAG
CAAAGTGTTAGTCATTTTGAAATGTGTGGATGCCTAGGAGCCCAAAGTGCTACGGGTGGTTATGGGTGTACTTTTCCCGG
TGCCCATTATCAGTAGTCTGAAAACAAAAACAGTGGCAAATTACCTGCCCCCTGACACCCAGGTCTGTTTGGCTGACAAC
CGAAGCCTTTATGCTGAGGCTCAGATGTCTAATAAAGACAGTGACTATGGCTGGGTGTGTGATTGGCGATTCCTGAAGTT
TCACAAGTACGAAGAAAAGGAAGGTCTAGAAACTGGAGCCAGTAAAGGTTTGCTACCTGTTATTGAGGTTCAGAGTTATG
GCTTCGACTGGACAGAGGCACCAGCAGCTGCAGTGGTTGGCAGCGAGACCTACGGCATGAACCTGGATTCTCTGTAGTTG
GCCGAGAGCCCTGGGGGCAACAGGCTGCTGATCCCTGTTGCACCTGGTGTGGACAGCCTCAACTCAGCCATGGCTGCACG
CATCCCGCTTTTTGAAGGGAAAAGACAACTGTGGGTGAGGGCGGAACACTTGAGCAGGGACAGGAGTTACCAC

ORF - retro_mmul_1709 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.04 %
Parental protein coverage: 75.71 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalRLSSVMTIVKSRPFREKQGKILLEGRRLITDALKAGAVPKMFFFSRLEYLKELPVDKLKGVSLIKVKFED
R..SVMT.VKSRPF.EKQGKILL.GRRL..DALKAGAVP..FF.S.L.Y.K.L..DK.KGVSLIK.KFED
RetrocopyRTCSVMTTVKSRPFWEKQGKILLKGRRLLIDALKAGAVPTVFFSSHL*YIKKLLIDKPKGVSLIKMKFED
ParentalIKDWSNLVTPQG-IMGIFAKPDHVKMAYPKTQLQHSLPLSLICDNLRDPGNLGTILRSAAGAGCSKVLLT
..DWSNLV.PQ..IMGIFAKPDHV.M.YPKTQL.HSLPL.LICDNL.DPGNLGTILRS.AGAGCSKVL..
RetrocopyMRDWSNLVMPQK<IMGIFAKPDHVNMTYPKTQL*HSLPLLLICDNLCDPGNLGTILRSPAGAGCSKVLVI
ParentalKGCVDPWEPKVLRAGMGAHFQVPIINNLEWETVPNYLPPDTRVYVADNCGLYAQAQMSNKASDHGWVSNQ
..CVD..EPKVLR..MG..F.VPII..L...TV.NYLPPDT.V..ADN..LYA.AQMSNK.SD.GWV...
RetrocopyLKCVDA*EPKVLRVVMGVLFPVPIISSLKTKTVANYLPPDTQVCLADNRSLYAEAQMSNKDSDYGWVCDW
ParentalRLLKFQKYEEEEDVETGASQDWLPDVEVQSYDSDWTEAPAAVVIGGETDGVSVESLQLAESTGGKRLLIP
R.LKF.KYEE.E..ETGAS...LP..EVQSY..DWTEAPAA.V.G.ET.G....SL.LAES.GG.RLLIP
RetrocopyRFLKFHKYEEKEGLETGASKGLLPVIEVQSYGFDWTEAPAAAVVGSETYGMNLDSL*LAESPGGNRLLIP
ParentalVVPGVDSLNSAMAASILLFEGKRQLRGRAEHLSRDRSHH
V.PGVDSLNSAMAA.I.LFEGKRQL..RAEHLSRDRS.H
RetrocopyVAPGVDSLNSAMAARIPLFEGKRQLWVRAEHLSRDRSYH

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 0 .00 RPM 5 .15 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 18 .25 RPM
SRP007412_cerebellum 0 .00 RPM 6 .52 RPM
SRP007412_heart 0 .00 RPM 5 .71 RPM
SRP007412_kidney 0 .00 RPM 6 .57 RPM
SRP007412_liver 0 .00 RPM 8 .95 RPM
SRP007412_testis 0 .08 RPM 11 .16 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1709 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1709 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1709 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3704
Gorilla gorilla retro_ggor_2505
Pongo abelii retro_pabe_3149
Callithrix jacchus retro_cjac_3130

Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000217011 retrocopy
Homo sapiens ENSG000001718611 retrocopy
Gorilla gorilla ENSGGOG000000155181 retrocopy
Macaca mulatta ENSMMUG00000011423 1 retrocopy
retro_mmul_1709 ,
Nomascus leucogenys ENSNLEG000000005701 retrocopy
Pongo abelii ENSPPYG000000077621 retrocopy



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