RetrogeneDB ID:

retro_mmul_1675

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:3:42854212..42856072(-)
Located in intron of:ENSMMUG00000011232
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.4761
Ensembl ID:ENSMMUG00000018610
Aliases:None
Description:poly(A) polymerase alpha [Source:RefSeq peptide;Acc:NP_001252826]


Retrocopy-Parental alignment summary:






>retro_mmul_1675
CCGGTGACAACCCAGGGACCACCGCAGCAGGCGCCGCTGCCGAAGTGCTACGGCATCTCCTCGCCTATCAGCCTAGCGGT
CCCCAAGGAGACGGACTGCCTTCTCACCCAGAGGCTAATAGAAACCCTCAGGCCCTTCGGGGTCTTTGAAGAGGAAGAGG
AACTGCAGCGCAGGATTTTAGTTTTGGAAAAATTAAATAATCTGGTAAAGGAATGGATACGCGAAATCAGTGAAAGCAAG
AGCCTTCCCCAGTCTGTAATTGAAAACGTTGGCGGAAAGATTTTTACGTTTGGCTCTTACAGATTAGGAGTACATACGAA
AGGTGCAGATATTGACGCCTTGTGCGTTGCACCAAGGCATGTGGATCGAAGCGACTTTTTTACCTCATTCTATGTTAAAC
TGAAACTACAGGAGGAAGTAAAAGATTTAAGGGCTGTTGAGGAGGCATTTGTGCCAGTTATCAAACTGTGTTTTGATGGG
ATAGAGATTGATATTTTATTTGCAAGATTAGCACTACAGACTATTCCAGAAGATTTGGACCTAAGAGATGACAGTCTGCT
TAAAAATTTAGACATTAGATGCATAAGAAGCCTTAACGGTTGCCGGGTAACCGATGAAATTTTACATCTAGTGCCAAACA
TTGACAACTTCAGGTTGACTCTAAGAGCCATCAAACTGTGGGCCAAGTGCCACAATATCTATTCCAATATATTAGGTTTC
CTCGGAGGTGTTTCCTGGGCCATGCTGGTAGCAAGAACTTGTCAGCTTTATCCAAATGCAGTAGCGTCAACTCTCGTGCG
GAAATTCTTCTTGGTATTTTCGGAATGGGAATGGCCAAACCCAGTGTTACTGAAAGAGCCTGAAGAACGGAATCTTAACT
TGCCTGTATGGGACCCAAGAGTAAATCCCAGTGATAGGTACCATCTTATGCCCATCATCACACCAGCATACCCACAGCAG
AACTCCACATACAACGTGTCTGTTTCAACCAGGATGGTCATGATTGAGGAGTTTAAACAGGGACTTGCTATCACACACGA
GATTTTGCTGAGTAAGGCTGAGTGGTCCAAACTCTTTGAAGCTCCAAGCTTCTTTCAGAAGTACAAGCATTATATTGTAC
TTCTGGCAAGTGCACCAACAGAAAAACAGCATTTAGAATGGGTGGGCTTGGTGGAATCAAAGATCCGAATCCTGGTTGGG
AGCTTGGAGAAGAATGAATTTATTACGCTGGCACATGTGAATCCACAGTCATTTCCAGCACCCAAAGAAAATCCTGATAT
GGAAGAATTTCGTACAATGTGGGTGATTGGTTTAGTGCTAAAAAAGCCAGAAAACTCTGAAATTCTCAGTATTGATCTCA
CCTATGATATCCAGTCTTTCACAGATACTGTTTATAGGCAAGCAATGAATAGTAAGATGTTTGAGATGGGTATGAAAATT
ACTGCAATGCATTTAAGAAGAAAGGAGCTTCACCAGCTGCTGCCTCATCGTGTGCTTCAGGACAAGAAAGCACACGCAAC
AGAAGGTAGAAGATTGACAGATCTGAACGACAGCAGCTTTGACTTGTCTGCAGGCTGTGAAAACAGCATGTCTGTGCCTT
CATCTACTAGCACTATGAAGACAGGCCCATTGATTAGCAGTTCTCAGGGTAGAAATAGTCCTGCCCTGGCTGTAATGACA
GCATCGATGGCTAACGTACAGGCTACTGAAATTTCCTTGCAACAGATGAATACCAGTGAAAGTTCAGGGGTTGCATTAAA
TGAAAGTATTCCTCACGCTGTCTCTCAGCCTGCCATTTCTCCATCACCAAAGGCCATGGTCGCCAGAGTTGTTTCTTCGA
CATGTCTCATAAGCCATCCA

ORF - retro_mmul_1675 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.33 %
Parental protein coverage: 83.49 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalPVTTQGSQQTQPPQKHYGITSPISLAAPKETDCILTQKLIETLKPFGVFEEEEELQRRILILGKLNNLVK
PVTTQG..Q..P..K.YGI.SPISLA.PKETDC.LTQ.LIETL.PFGVFEEEEELQRRIL.L.KLNNLVK
RetrocopyPVTTQGPPQQAPLPKCYGISSPISLAVPKETDCLLTQRLIETLRPFGVFEEEEELQRRILVLEKLNNLVK
ParentalEWIREISESKNLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYDKLKLQEEV
EWIREISESK.LPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFY.KLKLQEEV
RetrocopyEWIREISESKSLPQSVIENVGGKIFTFGSYRLGVHTKGADIDALCVAPRHVDRSDFFTSFYVKLKLQEEV
ParentalKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
KDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
RetrocopyKDLRAVEEAFVPVIKLCFDGIEIDILFARLALQTIPEDLDLRDDSLLKNLDIRCIRSLNGCRVTDEILHL
ParentalVPNIDNFRLTLRAIKLWAKRHNIYSNILGFLGGVSWAMLVARTCQLYPNAIASTLVHKFFLVFSKWEWPN
VPNIDNFRLTLRAIKLWAK.HNIYSNILGFLGGVSWAMLVARTCQLYPNA.ASTLV.KFFLVFS.WEWPN
RetrocopyVPNIDNFRLTLRAIKLWAKCHNIYSNILGFLGGVSWAMLVARTCQLYPNAVASTLVRKFFLVFSEWEWPN
ParentalPVLLKQPEECNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMVEEFKQGLAITDEILL
PVLLK.PEE.NLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVM.EEFKQGLAIT.EILL
RetrocopyPVLLKEPEERNLNLPVWDPRVNPSDRYHLMPIITPAYPQQNSTYNVSVSTRMVMIEEFKQGLAITHEILL
ParentalSKAEWSKLFEAPNFFQKYKHYIVLLASAPTEKQRLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
SKAEWSKLFEAP.FFQKYKHYIVLLASAPTEKQ.LEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
RetrocopySKAEWSKLFEAPSFFQKYKHYIVLLASAPTEKQHLEWVGLVESKIRILVGSLEKNEFITLAHVNPQSFPA
ParentalPKENPDKEEFRTMWVIGLVFKKTENSENLSVDLTYDIQSFTDTVYRQAINSKMFEVDMKIAAMHVKRKQL
PKENPD.EEFRTMWVIGLV.KK.ENSE.LS.DLTYDIQSFTDTVYRQA.NSKMFE..MKI.AMH..RK.L
RetrocopyPKENPDMEEFRTMWVIGLVLKKPENSEILSIDLTYDIQSFTDTVYRQAMNSKMFEMGMKITAMHLRRKEL
ParentalHQLLPNHVLQKKKKHSTEGVKLTALNDSSLDLSMDSDNSMSVPSPTSATKTSPLNSSGSSQGRNSPAPAV
HQLLP..VLQ.KK.H.TEG..LT.LNDSS.DLS....NSMSVPS.TS..KT.PL.S..SSQGRNSPA.AV
RetrocopyHQLLPHRVLQDKKAHATEGRRLTDLNDSSFDLSAGCENSMSVPSSTSTMKTGPLIS--SSQGRNSPALAV
ParentalTAASVTNIQATEVSVPQVNSSESSGGTSSESIPQTATQPAISPPPKPTVSRVVSSTRLVNPP
..AS..N.QATE.S..Q.N.SESSG....ESIP....QPAISP.PK..V.RVVSST.L...P
RetrocopyMTASMANVQATEISLQQMNTSESSGVALNESIPHAVSQPAISPSPKAMVARVVSSTCLISHP

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 .11 RPM 61 .07 RPM
SRP007412_brain_prefrontal_cortex 0 .08 RPM 50 .77 RPM
SRP007412_cerebellum 1 .36 RPM 66 .06 RPM
SRP007412_heart 0 .18 RPM 43 .22 RPM
SRP007412_kidney 0 .23 RPM 74 .65 RPM
SRP007412_liver 0 .00 RPM 21 .93 RPM
SRP007412_testis 159 .71 RPM 215 .91 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_1675 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1675 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1675 has 9 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_30
Pan troglodytes retro_ptro_2595
Gorilla gorilla retro_ggor_202
Pongo abelii retro_pabe_3113
Callithrix jacchus retro_cjac_1763
Mus musculus retro_mmus_37
Rattus norvegicus retro_rnor_863
Bos taurus retro_btau_1078
Canis familiaris retro_cfam_1783
Parental genes homology:
Parental genes homology involve 17 parental genes, and 19 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000141421 retrocopy
retro_amel_517,
Bos taurus ENSBTAG000000040541 retrocopy
retro_btau_1078,
Canis familiaris ENSCAFG000000177831 retrocopy
retro_cfam_1783,
Callithrix jacchus ENSCJAG000000065122 retrocopies
retro_cjac_1763, retro_cjac_543,
Homo sapiens ENSG000000900601 retrocopy
retro_hsap_30,
Gorilla gorilla ENSGGOG000000062871 retrocopy
retro_ggor_202,
Myotis lucifugus ENSMLUG000000109221 retrocopy
retro_mluc_1396,
Macaca mulatta ENSMMUG00000018610 1 retrocopy
retro_mmul_1675 ,
Monodelphis domestica ENSMODG000000128872 retrocopies
retro_mdom_1714, retro_mdom_1916,
Mustela putorius furoENSMPUG000000030541 retrocopy
retro_mputfur_1375,
Mus musculus ENSMUSG000000211111 retrocopy
retro_mmus_37,
Nomascus leucogenys ENSNLEG000000006251 retrocopy
retro_nleu_2771,
Otolemur garnettii ENSOGAG000000046111 retrocopy
retro_ogar_987,
Pongo abelii ENSPPYG000000061281 retrocopy
retro_pabe_3113,
Pan troglodytes ENSPTRG000000067041 retrocopy
retro_ptro_2595,
Pteropus vampyrus ENSPVAG000000139251 retrocopy
retro_pvam_360,
Vicugna pacos ENSVPAG000000064641 retrocopy
retro_vpac_378,


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