RetrogeneDB ID:

retro_mmul_1273

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:17:337161..337932(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.1802
Ensembl ID:ENSMMUG00000009693
Aliases:None
Description:succinyl-CoA ligase [Source:RefSeq peptide;Acc:NP_001248050]


Retrocopy-Parental alignment summary:






>retro_mmul_1273
CAGGCACTTCAATTAACTTCCAGAAGATGGCAGACCCTCCAGGAACACCACAGTGAGAAACTGATGTCTGACAACAGAGT
GAGAGTTCAAATATTCCTTGTAGCAGACACTGTGAATGAAGCACTTGAGGTTGCCAAGAGACTAAAAGCAAAATAAATTG
TTTTAATTAAAAGCCCAGATCTTAGCCGGAGGAAAAGGAAAGGGTGTCTTCAATTGTGGTTTGAAAGGAGGTATTCACTT
AACAAAAGAACCTAAAGTTGTGGGAAAGCTGGCTAAACATGATTGGGTATGTTTGGGGCAATAAACCAAACTCCAAAAGA
AGATGTGAAAGTTAATAAGCTGATGGTTACTGAAACCTTGGACACTTCCAGAAAAACTTACCTGGTGATTCTGATGGACA
GGTCCTGCCATGGCCCCATGCTGGTGGGCAGGCCCCAGGGGCCATTGACATTGAGGAGGTGGATGCTTCAAACTCAGAAT
TTATTTTTAAGGAGCAAATTTTTCAAGGGATAAAGGACAGCCGAGTTCAGAGTTGAGCAGATGGCAGAAAATCTAGGCTT
CCTTGGGTCTTTGAAAAATCAGGTTGCAGATCAAATTAAGAAACTGTATAATCTCTTCCTAAAAATTGATGCTACTCAGG
TGATAGTGAATCCCTCTGGTGAAATTTGAGAAAGACAAGTTGTCTGCTTTAATGCCAACGTAAACTTTCATGACAATGCA
GGATTCTGACAACAGGACATATCTGCTAGGGATGACAAATCGGAGAATGAG

ORF - retro_mmul_1273 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.42 %
Parental protein coverage: 59.26 %
Number of stop codons detected: 7
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalQAAQLTSRRWLNLQEYQSKKLMSDNGVRVQRFFVADTANEALEAAKRLNAKEIVL-KAQILAGGRGKGVF
QA.QLTSRRW..LQE..S.KLMSDN.VRVQ.F.VADT.NEALE.AKRL.AK.IVL.K...L.....KG..
RetrocopyQALQLTSRRWQTLQEHHSEKLMSDNRVRVQIFLVADTVNEALEVAKRLKAK*IVLIKSPDLSRRKRKGCL
ParentalNSGLKGGVHLTKDPNVVGQLAKQMIGYNLATKQTPKEGVKVNKVMVAEALDISRETYLAILMDRSCNGPV
.........L.K.....G.......G...A..QTPKE.VKVNK.MV.E.LD.SR.TYL.ILMDRSC.GP.
RetrocopyQLWFERRYSLNKRT*SCGKAG*T*LGMFGAINQTPKEDVKVNKLMVTETLDTSRKTYLVILMDRSCHGPM
ParentalLVGSPQGGVDIEEVAASNPELIFKEQIDIFEGIKDSQAQRMAENLGFVGPLKSQAADQITKLYNLFLKID
LVG.PQG.............L...................MAENLGF.G.LK.Q.ADQI.KLYNLFLKID
RetrocopyLVGRPQGPLTLRRWMLQTQNLFLRSKFFKG*RTAEFRVEQMAENLGFLGSLKNQVADQIKKLYNLFLKID
ParentalATQVEVNPFGETPEGQVVCFDAKINFDDNAEFRQKDIFAMDDKSENE
ATQV.VNP.GE..E.QVVCF.A..NF.DNA.F.Q.DI.A.DDKSENE
RetrocopyATQVIVNPSGEI*ERQVVCFNANVNFHDNAGF*QQDISARDDKSENE

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 11 .32 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 8 .49 RPM
SRP007412_cerebellum 0 .00 RPM 8 .33 RPM
SRP007412_heart 0 .00 RPM 72 .43 RPM
SRP007412_kidney 0 .00 RPM 181 .10 RPM
SRP007412_liver 0 .00 RPM 111 .31 RPM
SRP007412_testis 0 .08 RPM 12 .06 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1273 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1273 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1273 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001723401 retrocopy
Gorilla gorilla ENSGGOG000000274381 retrocopy
Myotis lucifugus ENSMLUG000000172941 retrocopy
Macaca mulatta ENSMMUG000000075391 retrocopy
Macaca mulatta ENSMMUG00000009693 2 retrocopies
retro_mmul_1273 , retro_mmul_1995,
Mus musculus ENSMUSG000000618381 retrocopy
Nomascus leucogenys ENSNLEG000000075531 retrocopy
Otolemur garnettii ENSOGAG000000061901 retrocopy
Pongo abelii ENSPPYG000000137351 retrocopy
Pteropus vampyrus ENSPVAG000000045541 retrocopy



Copyright © RetrogeneDB 2014-2017