RetrogeneDB ID:

retro_mmul_98

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:6:174753655..174755227(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000008440
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.8244
Ensembl ID:ENSMMUG00000000858
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_98
ATGGGATCGTCGAGCAGCCGGGTGCTGCGCCAGCCGAGGCGAGCCCTTGCCCAGCAGGAGCAGGGTGCCAGGGCGGGGGG
CTTGGCCGGGAGGCCGGACCCTGGAGACCCTGCGGCGGGCTACGGCTTCTGTTACTGCCCGGGCAGTCACAAGAGCAGCG
GGGCCTTCCGCTACTGTCGCCCTGACTCGGAGAGAGACGAGGATGAGGAGGAGAGGGACGAGCAGCAGCCTCTCCTCCAC
ATCCCTGCAAGGAAAAAATTAAGGAGTACATCCAAATATATTTATCAAACATTATTTTTGAATGGTGAAGACAGTGACAT
TAAGATTTGTGCTCTAGGAGAAGAATGGCGATTACACAAAATATATTTATGTCAGTCTGGCTACTTTTCTAGTATGTTCA
GTGGTTCTTGGAAAGAATCCAGCATGAATATTATTGAACTGGAGATTCCTGACCAGAACATTGATGTAGAAGCGCTGCAG
GTTGCGTTTGGTTCACTGTATCGAGATGACGTGCTGATAAAGCCCAGTCGAGTTGTTGCCATTTTGGCAGCTGCTTGTAT
GCTGCAGTTGGATGGTTTAATACAGCAGTGTGGGGAGACGATGAAGGAGACAATTACTGTGAAAACTGTATGTGGCTATT
ACACATCAGTAGGGACCTATGGATTAGATTCCGTAAAGAAAAAGTGCCTTGAATGGCTTCTAAACAATTTGATGACTCAC
CAGAATGTTAAACTTTTTAAAGAACTCAGTATAAATGTCATGAAACAGCTCATTGGTTCATCTAACTTATTTGTGATGCA
AGTGGAGATGGATGTATACACCGCTCTAAAAAAGTGGATGTTTCTTCAACTTGTGCCTTCTTGGAATGGATCTTTAAAAC
AGCTTTTGACAGAAACAGATGTCTGGTTTTCCAAACAGAGAAAAGATTTTGAAGATATGGCCTTTCTTGAAACTGAACAA
GGAAAACCATTTGTATCAGTATTCAGACATTTAAGGTTACAATATATTATCAGTGACCTGGCTTCTGCAAGAATTATTGA
ACAAGATGCTATAGTACCTGCAGAATGGCTGTCTTCTGTGTATAAACAGCAGTGGTTTGCTATGCTGCGGGCCGAACAAG
ACAGTGAGGTAGGGCCTCAAGAAATCGATAAAGAAGAACTGGAGGGAAATAGCATGAGGTGTGGTAGAAAGCTTGCCAAA
GACGGTGAATACTGCTGGTGTTGGACGGGTTTTAACTTCGGCTTTGACCTACTTGTAACTTACACCAATCGATGCGTCAT
TTTCAAACGCAATACACTGAATCAGCCATGTAGCGGGTCTGTCAGTTTACAGCCTCAAAGGAGCATAGCATTTAGATTAC
GTTTGGCTTCTTTTGATAGTAGTGGAAAACTAATATGTAGTAGAACAACTGGCTATCAAATACTTATACTTAAAAAGGAT
CAGGAACAAGTGGTGATGAATTTGGACAGCAGGTTTCTGACCTTCCCTTTATATATCTGCTGTAACTTCTTGTATATATC
GCCAGAGAAAAGAATTGAAAATAATCATCACCCAGAAAATCCAGAAAACTGA

ORF - retro_mmul_98 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.61 %
Parental protein coverage: 99.81 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGSLSSRVLRQPRRALAQQAQGARAGGSARRPDTGDDAAGHGFCYCPGSHKRKRSSGAFCYCHPDSETDE
MGS.SSRVLRQPRRALAQQ.QGARAGG.A.RPD.GD.AAG.GFCYCPGSHK...SSGAF.YC.PDSE.DE
RetrocopyMGSSSSRVLRQPRRALAQQEQGARAGGLAGRPDPGDPAAGYGFCYCPGSHK---SSGAFRYCRPDSERDE
ParentalDEEEGDEQQRLLNTPRRKKLKSTSKYIYQTLFLNGENSDIKICALGEEWSLHKIYLCQSGYFSSMFSGSW
DEEE.DEQQ.LL..P.RKKL.STSKYIYQTLFLNGE.SDIKICALGEEW.LHKIYLCQSGYFSSMFSGSW
RetrocopyDEEERDEQQPLLHIPARKKLRSTSKYIYQTLFLNGEDSDIKICALGEEWRLHKIYLCQSGYFSSMFSGSW
ParentalKESSMNIIELEIPDQNIDVEALQVAFGSLYRDDVLIKPSRVVAILAAACLLQLDGLIQQCGETMKETINV
KESSMNIIELEIPDQNIDVEALQVAFGSLYRDDVLIKPSRVVAILAAAC.LQLDGLIQQCGETMKETI.V
RetrocopyKESSMNIIELEIPDQNIDVEALQVAFGSLYRDDVLIKPSRVVAILAAACMLQLDGLIQQCGETMKETITV
ParentalKTVCGYYTSAGTYGLDSVKKKCLEWLLNNLMTHQNVELFKELSINVMKQLIGSSNLFVMQVEMDIYTALK
KTVCGYYTS.GTYGLDSVKKKCLEWLLNNLMTHQNV.LFKELSINVMKQLIGSSNLFVMQVEMD.YTALK
RetrocopyKTVCGYYTSVGTYGLDSVKKKCLEWLLNNLMTHQNVKLFKELSINVMKQLIGSSNLFVMQVEMDVYTALK
ParentalKWMFLQLVPSWNGSLKQLLTETDVWFSKQRKDFEGMAFLETEQGKPFVSVFRHLRLQYIISDLASARIIE
KWMFLQLVPSWNGSLKQLLTETDVWFSKQRKDFE.MAFLETEQGKPFVSVFRHLRLQYIISDLASARIIE
RetrocopyKWMFLQLVPSWNGSLKQLLTETDVWFSKQRKDFEDMAFLETEQGKPFVSVFRHLRLQYIISDLASARIIE
ParentalQDAIVPSEWLSSVYKQQWFAMLRAEQDSEVGPQEINKEELEGNSMRCGRKLAKDGEYCWRWTGFNFGFDL
QDAIVP.EWLSSVYKQQWFAMLRAEQDSEVGPQEI.KEELEGNSMRCGRKLAKDGEYCW.WTGFNFGFDL
RetrocopyQDAIVPAEWLSSVYKQQWFAMLRAEQDSEVGPQEIDKEELEGNSMRCGRKLAKDGEYCWCWTGFNFGFDL
ParentalLVTYTNRYIIFKRNTLNQPCSGSVSLQPRRSIAFRLRLASFDSSGKLICSRTTGYQILTLEKDQEQVVMN
LVTYTNR..IFKRNTLNQPCSGSVSLQP.RSIAFRLRLASFDSSGKLICSRTTGYQIL.L.KDQEQVVMN
RetrocopyLVTYTNRCVIFKRNTLNQPCSGSVSLQPQRSIAFRLRLASFDSSGKLICSRTTGYQILILKKDQEQVVMN
ParentalLDSRLLIFPLYICCNFLYISPEKK
LDSR.L.FPLYICCNFLYISPEK.
RetrocopyLDSRFLTFPLYICCNFLYISPEKR

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 0 .34 RPM 8 .63 RPM
SRP007412_brain_prefrontal_cortex 0 .48 RPM 3 .97 RPM
SRP007412_cerebellum 0 .26 RPM 12 .27 RPM
SRP007412_heart 0 .06 RPM 3 .77 RPM
SRP007412_kidney 0 .00 RPM 8 .80 RPM
SRP007412_liver 0 .00 RPM 4 .28 RPM
SRP007412_testis 19 .22 RPM 80 .48 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_98 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_98 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_98 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3407
Pan troglodytes retro_ptro_2314
Pongo abelii retro_pabe_209
Parental genes homology:
Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000161161 retrocopy
retro_amel_1915,
Choloepus hoffmanni ENSCHOG000000123062 retrocopies
retro_chof_1562, retro_chof_802,
Equus caballus ENSECAG000000168132 retrocopies
retro_ecab_1109, retro_ecab_899,
Homo sapiens ENSG000000873381 retrocopy
retro_hsap_3407,
Loxodonta africana ENSLAFG000000025653 retrocopies
retro_lafr_220, retro_lafr_592, retro_lafr_98,
Myotis lucifugus ENSMLUG000000091832 retrocopies
retro_mluc_1521, retro_mluc_31,
Macaca mulatta ENSMMUG00000000858 1 retrocopy
retro_mmul_98 ,
Mus musculus ENSMUSG000000011571 retrocopy
retro_mmus_3665,
Nomascus leucogenys ENSNLEG000000101321 retrocopy
retro_nleu_2993,
Oryctolagus cuniculus ENSOCUG000000158082 retrocopies
retro_ocun_112, retro_ocun_160,
Otolemur garnettii ENSOGAG000000084081 retrocopy
retro_ogar_151,
Pongo abelii ENSPPYG000000123341 retrocopy
retro_pabe_209,
Pan troglodytes ENSPTRG000000120211 retrocopy
retro_ptro_2314,
Pteropus vampyrus ENSPVAG000000012423 retrocopies
retro_pvam_1259, retro_pvam_370, retro_pvam_816,
Sorex araneus ENSSARG000000046511 retrocopy
retro_sara_425,
Sus scrofa ENSSSCG000000083351 retrocopy
retro_sscr_62,
Ictidomys tridecemlineatus ENSSTOG000000007141 retrocopy
retro_itri_59,
Tursiops truncatus ENSTTRG000000074933 retrocopies
retro_ttru_1039, retro_ttru_1647, retro_ttru_1648,
Vicugna pacos ENSVPAG000000017561 retrocopy
retro_vpac_617,




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