RetrogeneDB ID:

retro_mmul_238

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:X:25306300..25308772(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000016657
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.2609
Ensembl ID:ENSMMUG00000007001
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_238
ATGGCAGACCTGAAGTACGGTGTAAAAGTCTATGTCCTGAACGAAGACCAGGAATGGAACAATCTAGGCACCGGTCAGGT
CTCATCCACCTACGACGAGCAGTTCCAGGGCATGTGTCTGCTTGTTCGGTCAGATTCAGATGGGTCAGTCATCCTGCGGT
CACAGATACCTCCAGACAGGCCCTATCGGAAACATGAAGAGACACTAATTGTTTGGTATGAAGCTGAGAACCATGGTTTG
GTGCTGAATTTCCAGGACCCAGCCGGCTGCCAGGATATTTGGAAAGAAATTTGTCAAGTTCAAGGTAAGGATCCGTCTGT
CCAAATCACACAGAACATTTCAGATGAACCAGAAGAAGACTTTGATGAAATGTCAGTAATTGGTAATACGGTTGTGCTGC
CTGACTGTGAACTCAATACACTTGATCAAATTGCTAACATAGTTAACTCAGTTCTCGCCTCACCTATCCGTAGGGAAAGA
CTGGCTCTGATCTTGAAAAATGAGGCTTATATTCAAAAACTACTGCAACTGTTCCACACTTGTGAAAACCTAGAGAACAC
TGAAGGTTTATACCGTTTGCATGAAATTATTAAGGGAATTTTATCCCTCAACAAGTCATGTCTGTTTGAGATAATGTTTT
CTGACGAGTGTATCATGGATGTGGTGGGATGCCTTGAGTATGATCCTGCTTTGGATCAGCCAAAAAGGCATAGGGACTTC
TTGACCAATGATGCAAAGTTCAAGGAAGTTATACCAATAACTAACTCTGAACTTAGGCAAAAAATACATCAGACATACAG
AGTACAGTACATTCATGACATTCTTTTGCCTGTGCCTTCCATATTTGAAGACAATTTTCTTTCTACACTTACAACGTTTA
TTTTATCCAACAAGGCTGAGATAGTAAGCATGCTGCAGAAAGATCACAAATTTTTGTATGAAGTTTTTGCACAGTTAAAG
GATGAGACTACACATGATGATAGACGGTGTGAATTGCTAATTTTTTTCAAGGAATTATGTTCATTTTCTCAGGCATTACA
GCCTCAAAGCAAAGATGCACTATTAGAAACATTGACACAGTTGGGAATTCTTCCTGTTCTTAAAATCATAATGATCAGGG
ATGATTTGCAAGTGAGGTCAGCTGCTGCAGTTATATGTGCTTATCTAGTGGAGTACAGTCCATCCAGGATCCGAGAATTT
ATAATTTCAGAATCCCAGGTGTGCAAAGATAGTGACCTTTTCATTAATGTAATAATTAAACAAATGATCTGTGATACTGA
TCCTGAGTTAGGAGGTGCCGTTCATTTGATGGTAGTTCTCCATACTCTACTTGATCCACGCAACATGCTGACAACACCTG
AGAAAAGTGAAAGAAGTGAATTCCTACATTTCTTCTACAAACATTGCATGCATAAATTTACAGCACCACTTTTGGCCGCC
ACCTCAGAACACAACTGTGAGGAGGATGATATAGTTGGATATGACAAAAACAAAAATTGCCCCAATAATAATCAAACAGC
ACAACTGCTTGCTTTGATTTTGGAGCTACTTACATTTTGTATACAACATCATACATACTACATAAGAAACTATATCTTGA
ACAAAGACTTGCTAAGAAAGGCCTTGATATTGACGAATTCAAAGCATACTCACCTGATTTTGTGTGCTCTTCGCTTTATG
AGAAGGATGATCAGCCTTAATGATGAAATTTATAATAATTACATCATCAAGGGAAATCATTTTGAGCCAGTTGTAAATGC
TCTTCTAGATAATGGAACTCGGTATAATATGTTGAATTCAGCTATTCTTGAGCTATTTGAATACATAAGAGTGGAAAATA
TCAAGTCTCTTGTTTCACATATAGTTGAAAAGTTTTATAACACACTTGAATCGATTGAATATGTTCAGACATTCAAAGGA
TTGAAGATTAAATATGAAAAAGAGAGAGACAGACAAAGTCAAATACAGAAGAATTTACATTCTGTACTGCAAAATATGGT
AGTTTGCACAGGTACCATAGAAGAAATGGAGCTGAAAGAAGAAATATGTTTTATGGAAGATGCAGAAGAAGCAGTTATGC
CACCACTGGAAGATGATGATGAATTTATCGAGACTAAAAGAACCCAAGAAGGAGAAGCAGTTATGCCACCACTGGAAGAT
GATGATGAATTTATGGAGACTAAAAGAACCCAAGAAGGAGAAGCAGTTATGCTACCACTGGAAGATGACGATGAATTTAT
GGAGACTAAAAGAACCCAAGAACATGAAGACAAAGTAGACTCTCCCAAAAGAACATCTTCTGGTGATTTCAAATTCTCTT
CATCTTATTCTGCTTGTGCTGCTATTGGAACAGGTAGCCCAAGTGGTAGCAGTGTGGTTCGTTTAGTGGATCATCCAGAT
GATGAAGAAGAAAAACAAGAAGATAAAGAAGATGAAACATCCCCCAAGAAGAAACCTCGTCCTAGCTCCTAA

ORF - retro_mmul_238 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.37 %
Parental protein coverage: 81.64 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSDTRRRVKVYTLNEDRQWDDRGTGHVSSTYVEELKGMSLLVRAESDGSLLLESKINPNTAYQKQQDTLI
M.D....VKVY.LNED..W...GTG.VSSTY.E...GM.LLVR..SDGS..L.S.I.P...Y.K...TLI
RetrocopyMADLKYGVKVYVLNEDQEWNNLGTGQVSSTYDEQFQGMCLLVRSDSDGSVILRSQIPPDRPYRKHEETLI
ParentalVWSEAENYDLALSFQEKAGCDEIWEKICQVQGKDPSVEVTQDLIDESEEERFEEMPETSHLIDLPTCELN
VW.EAEN..L.L.FQ..AGC..IW..ICQVQGKDPSV..TQ...DE.EE..F.EM........LP.CELN
RetrocopyVWYEAENHGLVLNFQDPAGCQDIWKEICQVQGKDPSVQITQNISDEPEED-FDEMSVIGNTVVLPDCELN
ParentalKLEEIADLVTSVLSSPIRREKLALALENEGYIKKLLQLFQACENLENTEGLHHLYEIIRGILFLNKATLF
.L..IA..V.SVL.SPIRRE.LAL.L.NE.YI.KLLQLF..CENLENTEGL..L.EII.GIL.LNK..LF
RetrocopyTLDQIANIVNSVLASPIRRERLALILKNEAYIQKLLQLFHTCENLENTEGLYRLHEIIKGILSLNKSCLF
ParentalEVMFSDECIMDVVGCLEYDPALAQPKRHREFLTKTAKFKEVIPITDSELRQKIHQTYRVQYIQDIILPTP
E.MFSDECIMDVVGCLEYDPAL.QPKRHR.FLT..AKFKEVIPIT.SELRQKIHQTYRVQYI.DI.LP.P
RetrocopyEIMFSDECIMDVVGCLEYDPALDQPKRHRDFLTNDAKFKEVIPITNSELRQKIHQTYRVQYIHDILLPVP
ParentalSVFEENFLSTLTSFIFFNKVEIVSMLQEDEKFLSEVFAQLTDEATDDDKRRELVNFFKEFCAFSQTLQPQ
S.FE.NFLSTLT.FI..NK.EIVSMLQ.D.KFL.EVFAQL.DE.T.DD.R.EL..FFKE.C.FSQ.LQPQ
RetrocopySIFEDNFLSTLTTFILSNKAEIVSMLQKDHKFLYEVFAQLKDETTHDDRRCELLIFFKELCSFSQALQPQ
ParentalNRDAFFKTLAKLGILPALEIVMGMDDLQVRSAATDIFSYLVEFSPSMVREFVMQEAQQSDDDILLINVVI
..DA...TL..LGILP.L.I.M..DDLQVRSAA..I..YLVE.SPS..REF...E.Q...D..L.INV.I
RetrocopySKDALLETLTQLGILPVLKIIMIRDDLQVRSAAAVICAYLVEYSPSRIREFIISESQVCKDSDLFINVII
ParentalEQMICDTDPELGGAVQLMGLLRTLIDPENMLATTNKTEKSEFLNFFYNHCMHVLTAPLLTNTSKDKCEKD
.QMICDTDPELGGAV.LM..L.TL.DP.NML.T..K.E.SEFL.FFY.HCMH..TAPLL..TS...CE.D
RetrocopyKQMICDTDPELGGAVHLMVVLHTLLDPRNMLTTPEKSERSEFLHFFYKHCMHKFTAPLLAATSEHNCEED
ParentalNIVGSNKNNTICPDNYQTAQLLALILELLTFCVEHHTYHIKNYIMNKDLLRRVLVLMNSKHTFLALCALR
.IVG..KN...CP.N.QTAQLLALILELLTFC..HHTY.I.NYI.NKDLLR..L.L.NSKHT.L.LCALR
RetrocopyDIVGYDKNKN-CPNNNQTAQLLALILELLTFCIQHHTYYIRNYILNKDLLRKALILTNSKHTHLILCALR
ParentalFMRRIIGLKDEFYNRYITKGNLFEPVINALLDNGTRYNLLNSAVIELFEFIRVEDIKSLTAHIVENFYKA
FMRR.I.L.DE.YN.YI.KGN.FEPV.NALLDNGTRYN.LNSA..ELFE.IRVE.IKSL..HIVE.FY..
RetrocopyFMRRMISLNDEIYNNYIIKGNHFEPVVNALLDNGTRYNMLNSAILELFEYIRVENIKSLVSHIVEKFYNT
ParentalLESIEYVQTFKGLKTKYEQEKDRQNQKLNSVPSILRS
LESIEYVQTFKGLK.KYE.E.DRQ.Q......S.L..
RetrocopyLESIEYVQTFKGLKIKYEKERDRQSQIQKNLHSVLQN

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 58 .71 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 39 .67 RPM
SRP007412_cerebellum 0 .00 RPM 71 .68 RPM
SRP007412_heart 0 .00 RPM 22 .67 RPM
SRP007412_kidney 0 .00 RPM 46 .48 RPM
SRP007412_liver 0 .00 RPM 16 .94 RPM
SRP007412_testis 6 .75 RPM 51 .45 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_238 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_238 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_238 has 7 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4799
Pan troglodytes retro_ptro_3191
Oryctolagus cuniculus retro_ocun_9
Bos taurus retro_btau_232
Sus scrofa retro_sscr_1187
Canis familiaris retro_cfam_226
Equus caballus retro_ecab_23
Parental genes homology:
Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000038431 retrocopy
retro_amel_48,
Bos taurus ENSBTAG000000005451 retrocopy
retro_btau_232,
Canis familiaris ENSCAFG000000028601 retrocopy
retro_cfam_226,
Equus caballus ENSECAG000000138191 retrocopy
retro_ecab_23,
Echinops telfairi ENSETEG000000024201 retrocopy
retro_etel_1699,
Felis catus ENSFCAG000000264571 retrocopy
retro_fcat_13,
Homo sapiens ENSG000001380411 retrocopy
retro_hsap_4799,
Loxodonta africana ENSLAFG000000178251 retrocopy
retro_lafr_791,
Myotis lucifugus ENSMLUG000000038751 retrocopy
retro_mluc_994,
Macaca mulatta ENSMMUG00000007001 1 retrocopy
retro_mmul_238 ,
Mustela putorius furoENSMPUG000000024351 retrocopy
retro_mputfur_92,
Nomascus leucogenys ENSNLEG000000093381 retrocopy
retro_nleu_1112,
Oryctolagus cuniculus ENSOCUG000000068801 retrocopy
retro_ocun_9,
Otolemur garnettii ENSOGAG000000098371 retrocopy
retro_ogar_140,
Pan troglodytes ENSPTRG000000119331 retrocopy
retro_ptro_3191,
Sus scrofa ENSSSCG000000083981 retrocopy
retro_sscr_1187,
Ictidomys tridecemlineatus ENSSTOG000000062761 retrocopy
retro_itri_63,
Tursiops truncatus ENSTTRG000000000271 retrocopy
retro_ttru_1397,


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