RetrogeneDB ID:

retro_mmul_911

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:12:39884672..39885433(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LAMR1
Ensembl ID:ENSMMUG00000022965
Aliases:RPSA, LAMR1
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_911
ATGTCCAGAGCCCTTGATGTCCTGCCAATGAAGAAGGAGGACGTCCTCAAGTTCCTTTCAGCAGGAACCCGCTTTGGTGA
CACCAGCCTTGACTTCCAAATGGAACAGTACATCTATAAAATGAAAAGTGATGGCATCTACATCCTAAATCAGAAGAAGA
CCTGGGAGAGGTTTCTGCTGGCAGCTCGTGCCATTGTTGCCATTGAAAACCCTGCTGATGTCAGTGTCATATCCTCCAGA
AAAACTGGCCAGAAAGCCATGCTGATATTTGCTGCTGTCACTGGAGCCAGTCTTGTTGCTGGCTGCTTCACTCCTAGAAC
ATTCGCTAACCAGATCCAGGCGGCCTTCCAGGAGCCACGACTTCTGGTGGTTTCTGATCCCAGGGCTGATCACTAGCCCC
TCACAAAGGCATTTTATGTTAACCTACTTACCATTGCTTTGTGTCACACAGATTCTCCTCTGTGCTATGTGGACATTGTC
ATCCCATGCAACAACAAGGGAGCTCACTCAGGGGGTTTGACGTGGTGGATGCTGGCCTGGAAAGTCCTGCACATGCCTCG
CACCATTTCCCACAAACATCCGTGGAATGTCATGCCTCATCTCTACTTCTACAGAGATCCTGAAGAGATGGAAAAAGACC
AGGCTGCTGCTGAAAAGGCTATGACCAAGGAGGAATTTCAGGGTGAACAGATGTGCCAGCTCCTGAGTTCTCCGCTACTC
AGCCTGAGGGTGCAGACTGGTCTGAATGCATGCAGGTGCCC

ORF - retro_mmul_911 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.73 %
Parental protein coverage: 86.44 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLLAARAIVAIEN
MS.ALDVL.MK.EDVLKFL.AGT..G.T.LDFQMEQYIYK.KSDGIYI.N.K.TWE..LLAARAIVAIEN
RetrocopyMSRALDVLPMKKEDVLKFLSAGTRFGDTSLDFQMEQYIYKMKSDGIYILNQKKTWERFLLAARAIVAIEN
ParentalPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAAFREPRLLVVTDPRADHQPLTEASYV
PADVSVISSR.TGQ.A.L.FAA.TGA...AG.FTP.TF.NQIQAAF.EPRLLVV.DPRADH.PLT.A.YV
RetrocopyPADVSVISSRKTGQKAMLIFAAVTGASLVAGCFTPRTFANQIQAAFQEPRLLVVSDPRADH*PLTKAFYV
ParentalNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRMRGTISREHPWEVMPDLYFYRDPEEI
NL.TIALC.TDSPL.YVDI.IPCNNKGAHS.GL.WWMLA..VL.M..TIS..HPW.VMP.LYFYRDPEE.
RetrocopyNLLTIALCHTDSPLCYVDIVIPCNNKGAHSGGLTWWMLAWKVLHMPRTISHKHPWNVMPHLYFYRDPEEM
ParentalEKEEQAAAEKAVTKEEFQGE-WTAPAPEFTATQPEVADWSEGVQVP
EK..QAAAEKA.TKEEFQGE....PAPEF.ATQPE.ADWSE..QVP
RetrocopyEK-DQAAAEKAMTKEEFQGE<TDVPAPEFSATQPEGADWSECMQVP

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 72 .05 RPM
SRP007412_brain_prefrontal_cortex 0 .00 RPM 252 .90 RPM
SRP007412_cerebellum 0 .00 RPM 39 .58 RPM
SRP007412_heart 0 .00 RPM 64 .60 RPM
SRP007412_kidney 0 .00 RPM 55 .05 RPM
SRP007412_liver 0 .00 RPM 133 .79 RPM
SRP007412_testis 0 .00 RPM 29 .89 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_911 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_911 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_911 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1729

Parental genes homology:
Parental genes homology involve 27 parental genes, and 379 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000041831 retrocopy
Ailuropoda melanoleuca ENSAMEG0000000896213 retrocopies
Bos taurus ENSBTAG0000000975719 retrocopies
Canis familiaris ENSCAFG0000000510127 retrocopies
Callithrix jacchus ENSCJAG0000000967515 retrocopies
Dasypus novemcinctus ENSDNOG0000000404827 retrocopies
Dipodomys ordii ENSDORG000000082671 retrocopy
Equus caballus ENSECAG000000130625 retrocopies
Echinops telfairi ENSETEG000000181604 retrocopies
Felis catus ENSFCAG0000000273922 retrocopies
Homo sapiens ENSG000001680282 retrocopies
Loxodonta africana ENSLAFG000000320095 retrocopies
Macropus eugenii ENSMEUG0000000816914 retrocopies
Microcebus murinus ENSMICG0000000451832 retrocopies
Macaca mulatta ENSMMUG000000079302 retrocopies
Macaca mulatta ENSMMUG00000022965 19 retrocopies
Monodelphis domestica ENSMODG000000109672 retrocopies
Mustela putorius furoENSMPUG0000000246321 retrocopies
Mus musculus ENSMUSG000000325181 retrocopy
Ochotona princeps ENSOPRG0000000450516 retrocopies
Pan troglodytes ENSPTRG000000228411 retrocopy
Pteropus vampyrus ENSPVAG0000000779419 retrocopies
Rattus norvegicus ENSRNOG0000001864527 retrocopies
Sarcophilus harrisii ENSSHAG000000068962 retrocopies
Tupaia belangeri ENSTBEG0000001594654 retrocopies
Tursiops truncatus ENSTTRG0000001449624 retrocopies
Vicugna pacos ENSVPAG000000123074 retrocopies



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