RetrogeneDB ID:

retro_mmul_2227

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:7:55241284..55242912(-)
Located in intron of:ENSMMUG00000011045
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TYRO3
Ensembl ID:ENSMMUG00000013803
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_2227
ATGGCGCTGAGGCGGAGCATGGGGCGGCCAGGTCTCCCGCTGCTGCGGCCGCCGCTGGGGCTGCCATTGGCAGCTCTGGC
TTCTCTGCTGCTGCAGGTCTGGGGCTGCAGGTCCGAAGCTCAACAGAGCCCTGGTGAAGCTGACAGTGGCTCAGGGGCAG
CTGGTGAAGCTCAACTGCAGCATGGAGGGGATGGAGGAGCCTGACATCCAGCTGGTGAAGGATGGGCCTGTGATCCAGAA
CTTGGACCAGTTGTACACCCCAGTCAGCAAGCAGCACTGGATCGACTTCCTCAGCCTGAAGTCAGTGGAGCGCTCTGACG
CGGCCAGTACTGGTGCCAGGTGGAGAATGGGGGCAAAACCAAGATCTCCCAGCCAATGTGGCTCATGGTAGAAGGTGTGC
CACTTTTCGCAGTGGAGCCAAAAGATCTGGCAGTGCCACCCAATGCCCCTTTCCAACTGTCTTGCAAGGCTGTGGGTCCC
CCTGAAGCTGTTACCATTGTCTGGTGGAGAGAAACTATCAAGACCGGGAGACCCGCTCCCTCTCCATCTGTTTTAAATGT
AACAGGGGTGACCCAGAGCACCCATGTTTTCCTGTGAAGCTCACAACCTAAAATGCCTGGCCTCTTCTCGCATAGCCACT
GTTCACCTTCAAGCACTGCCTGCAGCCCCCTTCATCATCACCGTGACAAAGCTTTCCAGCAGCAACATTAGTGTGGCCTG
GATGCCAAGTGCTGATGGCTGAGCCCTGCTATAGTCCCGTACAGTTCAGGTAACACAGGCCCCAGGAGGCTGGGAAAGTC
CTGGCTGTTGTGGTCCCTGTGGCCCCCTTTACCTGCCTGCTCCGGGAGCTGGTGCCTGCCATCAGCTACAGCCTCAGGGT
GCACTGTGCCAATGCCTTGGGGCCCTCTCCCTATGCTGACTGGGTGCCCTTTCAGACCAAGGGTCTGGCCGCAGCCAGCA
CTCCCCAAAATCCCCATGCCATCTGCACAGATTCAGGCCTCATCTTGGAGTGGGAAGAAGTGATCCCCAAGGGCCCTTTG
GAAGGCCCCCTGGGACCCTGTAAACTGTCCTGGGTTCAAGACAGTGGAACCCAGGATGAGCTGACAGTGGAAGGGAGCAG
GACCAATTTGACAGGCTGGGATACCCAAAAGAACCTGATCATACGTGTGTGCGTCTCCAGTGCAGTTGGCTGTGGACCGT
GGAGTCAGCCACTGGTGGTCTCTTCTCATGACCATGCAGGCCAGCAGGGCCGTCCTCACAGCCGCACATCCTGGGTACCT
GTGGTCCTTGGTGTGCTAACGGCCCTGGTGATGGCTGCTGCCCTGGCCCTCATCCTGCTTCGAAAGAGACGGAAAGAGAC
ACGGTTTGGGCAAGGCTTTGACTGTGTCATGGCCCGGGGAGAGCCATCTGTTTACTTCCGGGCAGCCCAGTCCTTCAATC
GAGAAAGGCCCGAGTGCATCGAGGCCGCATTGGACAGCTTGAGCATCAACAGTGGACTAAAGGAAAAACAAGGATGTGCT
CAGCCCAGAGCAGCAGTTCACCCTGGCCAGATGTTGGGCAAAGGAGAGTGTGGTTCAGTGCGGTAGGCCCAGCTGAAGCA
GGAGGATGGCTCCTTTGTGAAAGATGCT

ORF - retro_mmul_2227 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.9 %
Parental protein coverage: 61.98 %
Number of stop codons detected: 3
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMALRRSMGRPGLPPLLLPPPPRLGLLLAALASLLLPE-SAAAGLKLMGAPVKLTVSQGQPVKLNCSVEGM
MALRRSMGRPGLP..LL.PP..LGL.L.A....LL...S.AAG.KL..A.VKLTV.QGQ.VKLNCS.EGM
RetrocopyMALRRSMGRPGLP--LLRPP--LGLPL-AALASLLLQ>SGAAGPKLNRALVKLTVAQGQLVKLNCSMEGM
ParentalEEPDIQWVKDGAVVQNLDQLYIPVSEQHWIGFLTARLLKSAERSDA-GRYWCQVEDGGETEISQPVWLTV
EEPDIQ.VKDG.V.QNLDQLY.PVS.QHWI.FL....LKS.ERSDA.G.YWCQVE.GG.T.ISQP.WL.V
RetrocopyEEPDIQLVKDGPVIQNLDQLYTPVSKQHWIDFLS---LKSVERSDA<GQYWCQVENGGKTKISQPMWLMV
ParentalEGVPFFTVEPKDLAVPPNAPFQLSCEAVGPPEPVTIVWWRGTTKIGGPAPSPSVLNVTGVTQST-MFSCE
EGVP.F.VEPKDLAVPPNAPFQLSC.AVGPPE.VTIVWWR.T.K.G.PAPSPSVLNVTGVTQST.MFSCE
RetrocopyEGVPLFAVEPKDLAVPPNAPFQLSCKAVGPPEAVTIVWWRETIKTGRPAPSPSVLNVTGVTQST>MFSCE
ParentalAHNLKGLASSRTATVHLQALPAAPFNVTVTKLSSSNASVAWMPGADGRALLQSCTVQVTQAPGGWE-VLA
AHNLK.LASSR.ATVHLQALPAAPF..TVTKLSSSN.SVAWMP.ADG.ALL.S.TVQVTQAPGGWE.VLA
RetrocopyAHNLKCLASSRIATVHLQALPAAPFIITVTKLSSSNISVAWMPSADG*ALL*SRTVQVTQAPGGWE>VLA
ParentalVVVPVPPFTCLLRDLVPATNYSLRVRCANALGPSPYADWVPFQTKGLAPASAPQNLHAIRTDSGLILEWE
VVVPV.PFTCLLR.LVPA..YSLRV.CANALGPSPYADWVPFQTKGLA.AS.PQN.HAI.TDSGLILEWE
RetrocopyVVVPVAPFTCLLRELVPAISYSLRVHCANALGPSPYADWVPFQTKGLAAASTPQNPHAICTDSGLILEWE
ParentalEVIPEGPLEGPLGPYKLSWVQDNGTQDELTVEGTRANLTGWDPQKDLIVRVCVSNAVGCGPWSQPLVVSS
EVIP.GPLEGPLGP.KLSWVQD.GTQDELTVEG.R.NLTGWD.QK.LI.RVCVS.AVGCGPWSQPLVVSS
RetrocopyEVIPKGPLEGPLGPCKLSWVQDSGTQDELTVEGSRTNLTGWDTQKNLIIRVCVSSAVGCGPWSQPLVVSS
ParentalHDHAGQQGPPHSRTSWVPVVLGVLTALVTAAALALILLRKRRKETRFGQAFDSVMARGEPAVHFRAARSF
HDHAGQQG.PHSRTSWVPVVLGVLTALV.AAALALILLRKRRKETRFGQ.FD.VMARGEP.V.FRAA.SF
RetrocopyHDHAGQQGRPHSRTSWVPVVLGVLTALVMAAALALILLRKRRKETRFGQGFDCVMARGEPSVYFRAAQSF
ParentalNRERPERIEATLDSLGISDELKEKLEDVLIPEQQFTLGRMLGKGEFGSVREAQLKQEDGSFVKVA
NRERPE.IEA.LDSL.I...LKEK......P......G.MLGKGE.GSVR.AQLKQEDGSFVK.A
RetrocopyNRERPECIEAALDSLSINSGLKEK-QGCAQPRAAVHPGQMLGKGECGSVR*AQLKQEDGSFVKDA

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 51 .99 RPM
SRP007412_brain_prefrontal_cortex 0 .56 RPM 159 .77 RPM
SRP007412_cerebellum 0 .06 RPM 36 .29 RPM
SRP007412_heart 0 .18 RPM 1 .35 RPM
SRP007412_kidney 0 .12 RPM 6 .81 RPM
SRP007412_liver 0 .16 RPM 0 .67 RPM
SRP007412_testis 0 .00 RPM 13 .76 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_2227 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_2227 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_2227 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000924451 retrocopy
retro_hsap_1598,
Macaca mulatta ENSMMUG00000013803 1 retrocopy
retro_mmul_2227 ,




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