RetrogeneDB ID:

retro_mmul_1418

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:2:18860725..18862943(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.1001
Ensembl ID:ENSMMUG00000006305
Aliases:None
Description:NEDD4-like E3 ubiquitin-protein ligase WWP1 [Source:RefSeq peptide;Acc:NP_001247726]


Retrocopy-Parental alignment summary:






>retro_mmul_1418
TTGAAACACAACAGAAAATTGGAAAGAGTCAAAGAATAATTGAAACTTTCCTTGGAAAACAAGAATGGCACAGCACAAAC
TGGTGAATTGATGGTTGTGCTTGATGGACTGGTGATTGAGCAAGAAAATATAACAAACTGTAACTCATCTCCAACCATAG
AAATACAGCAAAATGGTGATGCCTTACGTGAACATGGAGAGCCTTCAGCAAGGACAACTGCCAGGTTGGCTGTTGAAGGC
ACAAATGGAATAGATAATCATGTACCTACAAGCACTCTAGTGCAAAACTCATGTTGCTCGTATGTAGTTAATGGAGACAA
TATACCTTCATCTCCATCTCAGGTTGCTGCCAGACCCCAAAATACACCACCTCCAAAACCACTCACATCTGAGCCTGCCA
ATGACACTGTTAATAGAGAATCATCCTCATTTGCACCAACTGATAATGCTTCTGTCACGGGTATTCCAGTAGTGTCTGAA
GAAAATGCCTTGTCTCCAAATTGCACTAGTACTACCGTTGAAGATCCTCCAGTTCAAGAAATACTGACTTCCTCAGAAAA
CAATGAATGTATTCCTTCTACCAGTGCAGAATTGGGATCTGAATCTAGAAGTATATTAGACCCTGACACCTCTAATTCTG
GAAGTAGTTCTGCTTTTGAAGCAGCCAAATCAAGGCAGCCAGATGGGTGTATAGATCGTTTGTGACAGGAATCTGGGAAT
GCCAACACAGAAACGTTGCCATCAGGGTGGAAACAAAGAAAAGATCCTCATGGTAGAACCTATTATGTGGATCATAATAC
TCGAACTATCACATGGGAGAGACCACAACCTTTACCTTCAGGCTGGGAAAGAAGAGTTGATGATCATATAAGAGTTTATT
ATGTGGATCATAGCACCGGAACAACGTGGCAGCGGGCTACCATGGAATCCGTCCGAAATTCTGAACAGTGGCAATCTCAG
CGCAACCAGTTGTAGGGAGCTATGCAACAGTTTAACCAACGATACCTCTATTCAGCTTCAATGTTAGCTGCAGAAAATGA
CCCTTATGGACCTTTGCCACCAGGCTGGGAAAAAAGAGTGGATTCAACAGACAGGGTTTACTTTGTGACTCATAACACAA
AAACAACCCAGTGGGAAGATCCAAGAACTCAAGGCTTACAGAATGAAGAACTCCGCCAGAAGGCTGGGAAATTAGACATA
CTCATGAAGGTGTGAGGTACTTTGTTGATCATAATGCAAGAACAACAACATTCAAAGATCCTCGCAATGGGAAGTCATCT
GTAACTAAAGGTGGTCCACAAATTGCTTTTGAATGCAGCTTTAGATGGAAACTTGCTCACTTCTGTTATTTATGCCAGTC
TAATGCACTACCCAGTCATGTAAAGATCAATCTGTCCCAGCAGACGTTGTTTGAAGATTCCTTCCAGCAGCTTATGGCAT
TAAAACCCTATGACTTGAGGAGGCGCTTACATGTAATATTTAGAGGAGAAGAAGGACTTGATTATGGTGGTCTAGTGAGA
GAATAGTTTTTCTTGCTTTCGCATGAAGTTTTGAACCCAGTGTATTGCTCATTTGAGTATGCGGGGAAGAACAACTATTG
TCTGCAGATAAATCCAGCATCAGCCATTAATCCAGACCATCTTTCGTACTTCTGTTTCATTGGTAGTTTTATTGCCATGG
CACTATTTCATGGAAAGTTTATCAATACTGGTTTCTCTTTACCATTCTACAAGTGTATGTTAAGTAAAAAACTTACTATT
AAGGATTTGGAATCTATTGATACTGAATTTTATAGCTCCCTTATCTGGATAAGAGGTAGCAACATTGAAGAATGTGGCTT
AGAAATGTACTTTTCTGTTGACATGGAGATTTGGGGAACAGTTACTTCACATGACCTGAAGTTGGGAGTTTCCAATATTC
TGGTGACTGAGGAGAACAAAGATGAATATATTGGTTTAATGACAGAATGGCATTTTTCTCGAGGAGTACAAGAACAAACC
AAACTTTCCTTGATGGTTTTAATGAAGTTCTTCCTCATCAGTGGCTATAGTACTTCGATGAAAAAGAATTAGAGGTTACG
TTGTGTGGCATGCAGGACGCTGACTTGGCAGATCGGCAGAGAAATAATGTTTATCGACATTCCACAAGAAACAGCCAGCA
AATCATTTGGTTTTGGCAGTTCGTGAAAGAGACAGACAATGGAGTAAGAATGCTACTT

ORF - retro_mmul_1418 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.77 %
Parental protein coverage: 80.37 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLIHNRKLERVKEQLKLSLENKNGIAQTGELTVVLDGLVIEQENITNCSSSPTIEIQQNGDALHENGEPSA
L.HNRKLERVKE.LKLSLENKNG.AQTGEL.VVLDGLVIEQENITNC.SSPTIEIQQNGDAL.E.GEPSA
RetrocopyLKHNRKLERVKE*LKLSLENKNGTAQTGELMVVLDGLVIEQENITNCNSSPTIEIQQNGDALREHGEPSA
ParentalRTTARLAVEGTNGIDNHVPTSTLVQNSCCSYVVNGDNTPSSPSQVAARPKNTPAPKPLTSEPADDTVNGE
RTTARLAVEGTNGIDNHVPTSTLVQNSCCSYVVNGDN.PSSPSQVAARP.NTP.PKPLTSEPA.DTVN.E
RetrocopyRTTARLAVEGTNGIDNHVPTSTLVQNSCCSYVVNGDNIPSSPSQVAARPQNTPPPKPLTSEPANDTVNRE
ParentalSSSFAPTDNASVTGTPVVSEENALSPNCTSTTVEDPPVQEILTSSENNECIPSTSAELGSEARSILEPDT
SSSFAPTDNASVTG.PVVSEENALSPNCTSTTVEDPPVQEILTSSENNECIPSTSAELGSE.RSIL.PDT
RetrocopySSSFAPTDNASVTGIPVVSEENALSPNCTSTTVEDPPVQEILTSSENNECIPSTSAELGSESRSILDPDT
ParentalSNSRSSSAFEAAKSRQPDGCVDPVRQQSGNANAETLPSGWEQRKDPHGRTYYVDHNTRTTTWERPQPLPP
SNS.SSSAFEAAKSRQPDGC.D...Q.SGNAN.ETLPSGW.QRKDPHGRTYYVDHNTRT.TWERPQPLP.
RetrocopySNSGSSSAFEAAKSRQPDGCIDRL*QESGNANTETLPSGWKQRKDPHGRTYYVDHNTRTITWERPQPLPS
ParentalGWERRVDDRGRVYYVDHNTRTTTWQRPTMESVRNFEQWQSQRNQLQGAMQQFNQRYLYSASMLAAENDPY
GWERRVDD..RVYYVDH.T..TTWQR.TMESVRN.EQWQSQRNQL.GAMQQFNQRYLYSASMLAAENDPY
RetrocopyGWERRVDDHIRVYYVDHST-GTTWQRATMESVRNSEQWQSQRNQL*GAMQQFNQRYLYSASMLAAENDPY
ParentalGPLPPGWEKRVDSTDRVYFVNHNTKTTQWEDPRTQGLQNEE-PLPEGWEIRYTREGVRYFVDHNTRTTTF
GPLPPGWEKRVDSTDRVYFV.HNTKTTQWEDPRTQGLQNEE...PEGWEIR.T.EGVRYFVDHN.RTTTF
RetrocopyGPLPPGWEKRVDSTDRVYFVTHNTKTTQWEDPRTQGLQNEE<TPPEGWEIRHTHEGVRYFVDHNARTTTF
ParentalKDPRNGKSSVTKGGPQIAYERSFRWKLAHFRYLCQSNALPSHVKINVSRQTLFEDSFQQIMALKPYDLRR
KDPRNGKSSVTKGGPQIA.E.SFRWKLAHF.YLCQSNALPSHVKIN.S.QTLFEDSFQQ.MALKPYDLRR
RetrocopyKDPRNGKSSVTKGGPQIAFECSFRWKLAHFCYLCQSNALPSHVKINLSQQTLFEDSFQQLMALKPYDLRR
ParentalRLYVIFRGEEGLDYGGLAREWFFLLSHEVLNPMYCLFEYAGKNNYCLQINPASTINPDHLSYFCFIGRFI
RL.VIFRGEEGLDYGGL.RE.FFLLSHEVLNP.YC.FEYAGKNNYCLQINPAS.INPDHLSYFCFIG.FI
RetrocopyRLHVIFRGEEGLDYGGLVRE*FFLLSHEVLNPVYCSFEYAGKNNYCLQINPASAINPDHLSYFCFIGSFI
ParentalAMALFHGKFIDTGFSLPFYKRMLSKKLTIKDLESIDTEFYNSLIWIRDNNIEECGLEMYFSVDMEILGKV
AMALFHGKFI.TGFSLPFYK.MLSKKLTIKDLESIDTEFY.SLIWIR..NIEECGLEMYFSVDMEI.G.V
RetrocopyAMALFHGKFINTGFSLPFYKCMLSKKLTIKDLESIDTEFYSSLIWIRGSNIEECGLEMYFSVDMEIWGTV
ParentalTSHDLKLGGSNILVTEENKDEYIGLMTEWRFSRGVQEQTK-AFLDGFNEVVPLQWLQYFDEKELEVMLCG
TSHDLKLG.SNILVTEENKDEYIGLMTEW.FSRGVQEQTK..FLDGFNEV.P.QWL.YFDEKELEV.LCG
RetrocopyTSHDLKLGVSNILVTEENKDEYIGLMTEWHFSRGVQEQTK<TFLDGFNEVLPHQWL*YFDEKELEVTLCG
ParentalMQEVDLADWQRNTVYRHYTRNSKQIIWFWQFVKETDNEVRMRL
MQ..DLAD.QRN.VYRH.TRNS.QIIWFWQFVKETDN.VRM.L
RetrocopyMQDADLADRQRNNVYRHSTRNSQQIIWFWQFVKETDNGVRMLL

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 .00 RPM 56 .14 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 47 .84 RPM
SRP007412_cerebellum 0 .00 RPM 48 .62 RPM
SRP007412_heart 0 .06 RPM 64 .36 RPM
SRP007412_kidney 0 .12 RPM 69 .60 RPM
SRP007412_liver 0 .04 RPM 43 .11 RPM
SRP007412_testis 0 .04 RPM 56 .99 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_1418 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1418 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1418 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2680
Pan troglodytes retro_ptro_1807
Pongo abelii retro_pabe_2299
Parental genes homology:
Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001231241 retrocopy
retro_hsap_2680,
Macaca mulatta ENSMMUG00000006305 1 retrocopy
retro_mmul_1418 ,
Mustela putorius furoENSMPUG000000108071 retrocopy
retro_mputfur_963,
Mus musculus ENSMUSG000000410581 retrocopy
retro_mmus_2017,
Nomascus leucogenys ENSNLEG000000015171 retrocopy
retro_nleu_1183,
Pongo abelii ENSPPYG000000187241 retrocopy
retro_pabe_2299,
Pan troglodytes ENSPTRG000000203951 retrocopy
retro_ptro_1807,




Copyright © RetrogeneDB 2014-2017