RetrogeneDB ID:

retro_mmul_1401

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:19:44153574..44155941(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSMMUG00000006820
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_1401
TCCACAGTCAGGCTTTCATCTCTCATCCTCTTCTAGGCAGTACTTTGGATACAGAAAAAGGGTACAGAAATGAAAGGAAT
GGTAGAGAAGATGAGGCTTCGCGTGATGGATCAGCTGCCGCCCATCCAAGCAATGGTCCACACAGGTTCCTACCACATGT
TAATTGCTTACTGTGGTGACATGCGCCTAAGGCTTTTTGGAGATCACCATCAAGGGTTCAGATGTCTGGGTACAGTGCCC
TGTCATTTCTCCACCAGCTGCCTCTTCTATGATCCAGCAACTGAGTTGCTGCTATGTGGTACCCTGGGGGCTGTGGTTAC
CTGGTTTATCTTACCAAATGGCAGGAGCATCGAGATGGCTCAAATAGTCCCTATGGCTAATCATGAGCTTGTACAGGGAT
TTTCCCTGAATGGCCCCCAGGGATCCCTGTTGGCTCTGTGTGAGGATACAGTGAGGGTCTTCATTCACCGGGGTCAGGGC
CAGCTGGAAGAAGTGAAGAAGTTCACGCCTGTCGCCAGTGGCTCTTCCATCACTTGCTCCTTTACTTGTGTCTCTCAGGG
CAATTTCTACGCTGGAAACACGGCTGGAGAGATCCACGCTTGGGGTTTAGACCAGGGTAACTTCCTCCACAGCTTTCAAG
CCCATTCCTCATCAGTGATATGTATCCATAGCCGGCCAGAGATCCACACCTTACTAACAGCAGGCAGTGAAGGCACAGTG
AGGGAATGGAATCTCACTTATGGGAACTTGCTGCGGCAGCTGAATGTTGACGAGGATCTTCAGAGACTGCAGTTTATTGA
TAATACCACTTTTTTCTGCCAGACCACCTACAGTTTTTCATTGCATCACCTGCCCTACTTTTATAGCCTCTTCAATGTCT
GTGGTTCTGCTCCCCAGCAGGTGCAGCGGGTCTGCTGCGGCCATAACTGGACTCGGATTCTATGTGCCACTGAGGATGGT
TTATTGCGCTTCTTATCTCCAGTAACAGGGGATCTCCTGGTTATCACCTGGCCTCTACTTGTTATGGATAAGGCTTTGGC
TTGGGCCTATGACTCAGAGAGAGAGGAGCTCTTTGTGGCATTAGGCAGTTCAGAGGTGCTGGTGTTTGATGCAACACGCT
CTCCTTGTACAGTCAAGTATCTTGTGTGCACTTCAGCAGACGGTAAGGATAGAGTAAGATGCTTGGCTTATGGGAGGTCC
CATCTGCAAAAAGGCCTAGGAGGATTGATGTTCTGTGGGCATGAGAGTGGCATTGTGAGAATCCTTTCCCACTACAGTCG
TGCCCGAATAGAGAAGACTGTTCACTCTGGGGCAGTATTGGCATTGTCTACCCTGGAAGGCCTTCAGGAAAATGCCTTGC
TCTGTTCCTATGGCATGGATAACATCATACACTTGACAGAGGCCGTGCTTCAGGTGAACAAGGTAGTCCTTCAGCCTGTC
AGCAAAATCCTCTGTGGCTGCCCCCTAAAACATGTGATACTCTTGCCAGGTTCTGTGGGTGCCATCACTGAAAGCTACTG
CTGGCGTCTCTGGCACTATGAAGGCTCTCTGACATCTTCAGAATCAAAACAGAGCTTTGTGTGGAGAGAGACAAAATGCC
TGCATGAGTGTGACATCACTTCATTTGATGTCTGCCTTCCCCTGAAACTTTTTGTCACAGGTGGCATTGATGGCTCAGTC
CGGATCTGGGACTTCCACGGTAGACTTGTAACCGAGATCGACTCAGCCCTGCATTTTGGCCCACTCTGCTTTGCCAATAA
TCGAGGTGACCTGTTGTTGACTTTCAACCAGAGTATCTACATAGTATCTTGCTTAAAGCTTCTCCCTCCAGCTCAGCTGG
TTCACCTGCGTATCCTAAAAAATGCAGATGAAATACAAGAAGTCCCTAAACCCTTCCTTCCTAGCTTCTTCTTTATGTTT
GAAACAGTATTTGTACCCAGATTTGTCTACCTTGGAAGAGGGCGGCAGGAATTACAGGGGCTAGAGACCCTTGTCAACAA
ACGGTTCATTGCCTTCGACAATACTGTGCCTCATGTTGTAGAAGAAGAGAGAAGCATGTCCCTTGTGATTCAAAAGACCA
AATTTCCTTTGTTTGAGGCTAAGGATATTGATTTCTCTACTCTTGATTCCAAGCATAATCGTCCCCGACATGAGGTTCCT
GCTCAGTTGCAGCTGGCTGGCTGGGATGGATTCAATGCCTACCAAATGCTACGGTGCTTCTTTGGTCAAGGGCGGCAATG
GCCCTTTGCTCCCGATGGCTACATCCCTAACTCAGTGATCCGTGCCCGCCTTTGGCCTGAGGGTACCCCAGTCTTCCTAT
GCTGTGATCTGTATTCATCCTACCAAGTTAAGGACTGGGACTTGTCA

ORF - retro_mmul_1401 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.9 %
Parental protein coverage: 58.28 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSLIVLSDRSQILAVVWMKSKTED---MIEKRIFSMTERLPPIQSMVHTGSFHILVVYCGDLILRLFGDHF
S...LS......AV.W...K......M.EK........LPPIQ.MVHTGS.H.L..YCGD..LRLFGDH.
RetrocopySTVRLSSLILF*AVLWIQKKGTEMKGMVEKMRLRVMDQLPPIQAMVHTGSYHMLIAYCGDMRLRLFGDHH
ParentalRAFKPLGKVHCRFNISCLCYDPEMKMLLSGVLGAVVTWVIERSGTGLHIAHMISMPGDELVQDIVLNGPN
..F..LG.V.C.F..SCL.YDP....LL.G.LGAVVTW.I...G.....A....M...ELVQ...LNGP.
RetrocopyQGFRCLGTVPCHFSTSCLFYDPATELLLCGTLGAVVTWFILPNGRSIEMAQIVPMANHELVQGFSLNGPQ
ParentalGSLLALCETVVRVLMRQGKGQLGEVKRFMSTSSGSSITCCFTCFDQGFLYAGNQAGEIQVWSLQQGHPLH
GSLLALCE..VRV....G.GQL.EVK.F....SGSSITC.FTC..QG..YAGN.AGEI..W.L.QG..LH
RetrocopyGSLLALCEDTVRVFIHRGQGQLEEVKKFTPVASGSSITCSFTCVSQGNFYAGNTAGEIHAWGLDQGNFLH
ParentalSFQAHHSGVICIRSRPEAHTLLTAGSDSLIKEWNLTSGSLLRRLELGEELYRLQFIDSITFFCQTAHSFS
SFQAH.S.VICI.SRPE.HTLLTAGS.....EWNLT.G.LLR.L...E.L.RLQFID..TFFCQT..SFS
RetrocopySFQAHSSSVICIHSRPEIHTLLTAGSEGTVREWNLTYGNLLRQLNVDEDLQRLQFIDNTTFFCQTTYSFS
ParentalLRRLPCFYSLFNVCGSAPQQLRRVYCGNNWFRILCTTEDGLLRFVSPITGDLLVITWPFSIVDRAVDWAY
L..LP.FYSLFNVCGSAPQQ..RV.CG.NW.RILC.TEDGLLRF.SP.TGDLLVITWP....D.A..WAY
RetrocopyLHHLPYFYSLFNVCGSAPQQVQRVCCGHNWTRILCATEDGLLRFLSPVTGDLLVITWPLLVMDKALAWAY
ParentalDPGKEELFVATGSSEVLVFDTTRCPCPAKYLLGTSPNSQDFVQCLAYGHFNLGRGLEGLIFSGHQSGVIR
D...EELFVA.GSSEVLVFD.TR.PC..KYL..TS....D.V.CLAYG...L..GL.GL.F.GH.SG..R
RetrocopyDSEREELFVALGSSEVLVFDATRSPCTVKYLVCTSADGKDRVRCLAYGRSHLQKGLGGLMFCGHESGIVR
ParentalVLSQHSCARLQKFMHFGAVLALSTLSGGIFGGEGNSLLCSYGMDDYVHLSEAVLDGVRVQLQPLASILSS
.LS..S.AR..K..H.GAVLALSTL.....G...N.LLCSYGMD...HL.EAVL....V.LQP...IL..
RetrocopyILSHYSRARIEKTVHSGAVLALSTLE----GLQENALLCSYGMDNIIHLTEAVLQVNKVVLQPVSKILCG
ParentalCHLTHLILLPKSVGAITETNCLRLWKFHDFM-SSGSQNGLKFIETLPLHLCAITSFDVCLSLSLFVTGSA
C.L.H.ILLP.SVGAITE..C.RLW.......SS.S.......ET..LH.C.ITSFDVCL.L.LFVTG..
RetrocopyCPLKHVILLPGSVGAITESYCWRLWHYEGSLTSSESKQSFVWRETKCLHECDITSFDVCLPLKLFVTGGI
ParentalDGSVRIWDFHGRLIAILDSSLHFGPLCFANDRGDLLVTFNQSLYLVSCLKLLPPALLTRLSFMSISDEVL
DGSVRIWDFHGRL....DS.LHFGPLCFAN.RGDLL.TFNQS.Y.VSCLKLLPPA.L..L......DE..
RetrocopyDGSVRIWDFHGRLVTEIDSALHFGPLCFANNRGDLLLTFNQSIYIVSCLKLLPPAQLVHLRILKNADEIQ
ParentalEIPKPFIPSFFFSFETMFVPKYIYLGKAQQKLVGLENLVNKRAIAFDHSVPHVIEEDEEGSPVLLRSSMH
E.PKPF.PSFFF.FET.FVP...YLG...Q.L.GLE.LVNKR.IAFD..VPHV.EE....S.V.......
RetrocopyEVPKPFLPSFFFMFETVFVPRFVYLGRGRQELQGLETLVNKRFIAFDNTVPHVVEEERSMSLVIQKTKFP
Parental-YSLQDMENWTQMSKRYQRHYVLPPQLQLTSWDGLNPYQILRYYFGHGREWLFAPDCYIPNSVIRARLWP
.....D....T..SK........P.QLQL..WDG.N.YQ.LR..FG.GR.W.FAPD.YIPNSVIRARLWP
RetrocopyLFEAKDIDFSTLDSKHNRPRHEVPAQLQLAGWDGFNAYQMLRCFFGQGRQWPFAPDGYIPNSVIRARLWP
ParentalEGTPIYLQCNLHAPQRELEWDRS
EGTP..L.C.L........WD.S
RetrocopyEGTPVFLCCDLYSSYQVKDWDLS

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 0 .00 RPM
SRP007412_brain_prefrontal_cortex 0 .48 RPM 0 .00 RPM
SRP007412_cerebellum 0 .26 RPM 0 .00 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .00 RPM
SRP007412_testis 19 .68 RPM 118 .02 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_1401 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1401 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1401 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Macaca mulatta ENSMMUG00000006820 1 retrocopy
retro_mmul_1401 ,


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