RetrogeneDB ID:

retro_mmul_460

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:1:215415476..215417363(+)
Located in intron of:ENSMMUG00000005669
Retrocopy
information
Ensembl ID:ENSMMUG00000031161
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CHM
Ensembl ID:ENSMMUG00000016776
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_460
ATGGCGGACAGTCTTCCCACAGAGTTTGATGTGGTTATAATAGGGACAGGTTTGCCCGAATCCATCCTTGCAGCTGCATG
TTCAAGAATTGGTCAGAGGGTTCTGCATATTGATTCAAGAAGTTACTATGGAGGCAACTGGGCTAGTTTCAGCTTTTCAG
GATTGCTAACCTGGTTGAAGGAGCATCAGCAAAACAATGACATTGGGGAAGAAAGTACTGTTGAATGGCAGGACCTGATC
CATGAAACAGAAGAAGCCATCTCTCTTCGCAAGAAGGATGAAACTATCCAACACACAGAAGCTTTTTGTTATGCCAGTCA
GGATATGGAGGACAATGTTGAAGAGGTTGGTGCTCTGCAGAAAAATCCTTCTTCAGGGGTGTCTAGTACCTTCACTGAAG
TTCTGGATTCCGCAGGCTTGCCTGAAGACAGCCAGTCATCAAATTTTAATAGCGATGAAATGTCTGCCAAACACACTCAG
AAAAGTGATAGAGAGATTTCACTAGAAGTAACTGATGTAGAGGAATCAGTGGAGAAGGAAAAGTATTGTGGAGATAAAAC
TTGTATGCACACAGTTTCAGATAAAGATGGAAATAAAGATGAAAGCAAATCTACAGTAGAAGATAATGCCAATCAACCAA
TTAGAAATAGGATTACTTACCTTCAAATAGTTAAAGAAGGGAGGAGGTTTAATATTGATTTGGTATCAAAACTGCTATAT
TCTCAAGGATTGCTAATTGATCTTTTAATCAAATCAGATGTTAGTCGTTATGTAGAATTCAAAAATGTCACTAGGATTCT
TGCATTTCGGGAAGGAAAGGTAGAACAAGTGCCTTGTTCCAGAGCAGATGTCTTTAATAGCAAGGAACTCACCATGGTTG
AAAAGAGGATGCTAATGAAATTTCTCACATTTTGTTTAGAGTATGAACAACATCCTGATGAATACCAAGCTTTCAGGCAG
TGTTCATTTTCAGAATACTTAAAAACTAAAAAACTAACTCCCAACCTTCAACATTTTGTACTGCACTCAATTGCAATGAC
ATCAGAATCATCTTGCACTACAATAGATGGCCTTAACGCAATTAAAAACTTCCTTCAGTGTCTCGGACGGTTTGGCAACA
CTCCCTTTTTATTTCCCTTGTATGGCCAAGGAGAAATTCCCCAATGTTTCTGTAGGATGTGCGCAGTTTTTGGTGGAATC
TATTGTCTTCGTCATAAAGTACAATGCTTTGTAGTCGACAAAGAATCTGGACGATGTAAAGCAATTATAGATCACTTTGG
TCAAAGAATAAATGCTAAATATTTTATTGTGGAAGACAGTTACCTTTCTGAGGAAACATGCTCAAATGTGCAGTATAAGC
AGATCTCTAGGGCAGTACTCATTACAGATCAGTCTATACTAAAGACAGATTCAGATCAGCAGACTTCCATTCTGATAGTT
CCTCCAGCAGAGCCAGGAGCTTGTGCTGTACGGGTCACTGAATTATGTTCTTCAACCATGACATGCATGAAGGACACCTA
TCTGGTACATTTGACATGTTCATCTTCTAAAACAGCAAGAGAAGACTTAGAATCAGTGGTGAAGAAATTATTCACTCCAT
ATACTGAAACAGAAATAAACAAGGAAGAACTTACAAAGCCAAGACTCTTGTGGGCTCTTTATTTTAATATGAGAGATTCC
TCGGGAATCAGCAGAAGCTCATATAATGGCTTGCCTTCCAATGTTTATGTCTGCTCTGGGCCTGACTGTGGCCTGGGAAA
TGAGCATGCCGTCAAGCAAGCTGAAACACTTTTCCAGGAGATCTTTCCAACTGAAGAATTCTGCCCTCCACCTCCAAATC
CAGAAGACATTATTTTTGATGGCGATGATAAGCAGCCAGAGTCTTCT

ORF - retro_mmul_460 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.66 %
Parental protein coverage: 95.87 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMADTLPSEFDVIVIGTGLPESIIAAACSRSGRRVLHVDSRSYYGGNWASFSFSGLLSWLKEHQENSDIEN
MAD.LP.EFDV..IGTGLPESI.AAACSR.G.RVLH.DSRSYYGGNWASFSFSGLL.WLKEHQ.N.DI..
RetrocopyMADSLPTEFDVVIIGTGLPESILAAACSRIGQRVLHIDSRSYYGGNWASFSFSGLLTWLKEHQQNNDIGE
ParentalDSPV-WQDQILENEEAIALSRKDKTIQHVEVFCYASQDLHEDVEEAGALQKNHALVTSANSTEAADSSFL
.S.V.WQD.I.E.EEAI.L..KD.TIQH.E.FCYASQD....VEE.GALQKN.....S...TE..DS..L
RetrocopyESTVEWQDLIHETEEAISLRKKDETIQHTEAFCYASQDMEDNVEEVGALQKNPSSGVSSTFTEVLDSAGL
ParentalPMEDESLSTMNCEMLTEQTPSSDPENALEVNGAEVTGEKENHCDDKTCVPSTSAEDVS--ENVPIAEDTT
P....S......EM....T..SD.E..LEV...E...EKE..C.DKTC....S..D....E.....ED..
RetrocopyPEDSQSSNFNSDEMSAKHTQKSDREISLEVTDVEESVEKEKYCGDKTCMHTVSDKDGNKDESKSTVEDNA
ParentalEQPKKNRITYSQIIKEGRRFNIDLVSKLLYSRGLLIDLLIKSNVSRYAEFKNITRILAFREGRVEQVPCS
.QP..NRITY.QI.KEGRRFNIDLVSKLLYS.GLLIDLLIKS.VSRY.EFKN.TRILAFREG.VEQVPCS
RetrocopyNQPIRNRITYLQIVKEGRRFNIDLVSKLLYSQGLLIDLLIKSDVSRYVEFKNVTRILAFREGKVEQVPCS
ParentalRADVFNSKQLTMVEKRMLMKFLTFCMEYEKYPDEYKGYEDITFYEYLKTQKLTPNLQYIVLHSIAMTSET
RADVFNSK.LTMVEKRMLMKFLTFC.EYE..PDEY.......F.EYLKT.KLTPNLQ..VLHSIAMTSE.
RetrocopyRADVFNSKELTMVEKRMLMKFLTFCLEYEQHPDEYQAFRQCSFSEYLKTKKLTPNLQHFVLHSIAMTSES
ParentalASSTIDGLKATRNFLHCLGRYGNTPFLFPLYGQGELPQCFCRMCAVFGGIYCLRHSVQCLVVDKESRKCK
...TIDGL.A..NFL.CLGR.GNTPFLFPLYGQGE.PQCFCRMCAVFGGIYCLRH.VQC.VVDKES..CK
RetrocopySCTTIDGLNAIKNFLQCLGRFGNTPFLFPLYGQGEIPQCFCRMCAVFGGIYCLRHKVQCFVVDKESGRCK
ParentalAIIDQFGQRIISEHFLVEDSYFSENMCSRVQYRQISRAVLITDRSVLKTDSDQQISILTVPAEEPGMFAV
AIID.FGQRI....F.VEDSY.SE..CS.VQY.QISRAVLITD.S.LKTDSDQQ.SIL.VP..EPG..AV
RetrocopyAIIDHFGQRINAKYFIVEDSYLSEETCSNVQYKQISRAVLITDQSILKTDSDQQTSILIVPPAEPGACAV
ParentalRVIELCSSTMTCMKGTYLVHLTCTSSKTAREDLEPVVQKLFIPYTEMEIENEQVEKPRILWALYFNMRDS
RV.ELCSSTMTCMK.TYLVHLTC.SSKTAREDLE.VV.KLF.PYTE.EI..E...KPR.LWALYFNMRDS
RetrocopyRVTELCSSTMTCMKDTYLVHLTCSSSKTAREDLESVVKKLFTPYTETEINKEELTKPRLLWALYFNMRDS
ParentalSDISRSCYKDLPSNVYVCSGPDCGLGNDNAVKQAETLFQEICPSEDFCPPPPNPEDIVLDGDGLQPEAS
S.ISRS.Y..LPSNVYVCSGPDCGLGN..AVKQAETLFQEI.P.E.FCPPPPNPEDI..DGD..QPE.S
RetrocopySGISRSSYNGLPSNVYVCSGPDCGLGNEHAVKQAETLFQEIFPTEEFCPPPPNPEDIIFDGDDKQPESS

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
SRP007412_brain 15 .69 RPM 17 .82 RPM
SRP007412_brain_prefrontal_cortex 13 .80 RPM 15 .63 RPM
SRP007412_cerebellum 2 .65 RPM 17 .63 RPM
SRP007412_heart 0 .59 RPM 3 .77 RPM
SRP007412_kidney 1 .53 RPM 11 .97 RPM
SRP007412_liver 0 .20 RPM 1 .78 RPM
SRP007412_testis 5 .43 RPM 1 .73 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_460 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_460 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_460 has 10 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_56
Pan troglodytes retro_ptro_400
Gorilla gorilla retro_ggor_488
Pongo abelii retro_pabe_215
Mus musculus retro_mmus_284
Rattus norvegicus retro_rnor_981
Oryctolagus cuniculus retro_ocun_893
Bos taurus retro_btau_227
Canis familiaris retro_cfam_1873
Equus caballus retro_ecab_36
Parental genes homology:
Parental genes homology involve 21 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000101901 retrocopy
retro_amel_733,
Bos taurus ENSBTAG000000095981 retrocopy
retro_btau_227,
Canis familiaris ENSCAFG000000174061 retrocopy
retro_cfam_1873,
Equus caballus ENSECAG000000192011 retrocopy
retro_ecab_36,
Felis catus ENSFCAG000000306521 retrocopy
retro_fcat_1744,
Homo sapiens ENSG000001884191 retrocopy
retro_hsap_56,
Gorilla gorilla ENSGGOG000000229121 retrocopy
retro_ggor_488,
Loxodonta africana ENSLAFG000000005231 retrocopy
retro_lafr_441,
Myotis lucifugus ENSMLUG000000112861 retrocopy
retro_mluc_138,
Macaca mulatta ENSMMUG00000016776 1 retrocopy
retro_mmul_460 ,
Monodelphis domestica ENSMODG000000143641 retrocopy
retro_mdom_1776,
Mustela putorius furoENSMPUG000000011941 retrocopy
retro_mputfur_831,
Mus musculus ENSMUSG000000255311 retrocopy
retro_mmus_284,
Nomascus leucogenys ENSNLEG000000027621 retrocopy
retro_nleu_120,
Oryctolagus cuniculus ENSOCUG000000128191 retrocopy
retro_ocun_893,
Pongo abelii ENSPPYG000000205201 retrocopy
retro_pabe_215,
Pan troglodytes ENSPTRG000000220711 retrocopy
retro_ptro_400,
Rattus norvegicus ENSRNOG000000001611 retrocopy
retro_rnor_981,
Sarcophilus harrisii ENSSHAG000000175681 retrocopy
retro_shar_127,
Ictidomys tridecemlineatus ENSSTOG000000221111 retrocopy
retro_itri_870,
Vicugna pacos ENSVPAG000000019631 retrocopy
retro_vpac_231,


Copyright © RetrogeneDB 2014-2017