RetrogeneDB ID:

retro_mmul_1964

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:5:100165430..100165965(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMMUG00000006011
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.4339
Ensembl ID:ENSMMUG00000021075
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_mmul_1964
TCTGTATGTGAAACTTGCCTACTGATCAGTTACACAACCAATGCATTTCCTGGAGAATATATCCCTACTGTCTTTGACAA
TTATTCTGCCAATGTTATGGTAGATAGAAAACCAGTGAATCTGGGCTCATGGGATACAGCTGCTCAAGAAGATTATGACA
GATCATGCCGCCTATCCTATCCTCAAACAGATGTGTTCTTAATTTGCTTTTCCCTTGTGAGTCCTGCATCATTTGAAAAT
GTCCGTGCAAAGTGGTATCCTGAGGTGCGGCACCACCGTCCCAACACTCCCATCATCCTAGTGGGAACTAAACTTGAACT
TAGGGATGATAAAGACACGATCGAGAAACTGAAGAAGAAGCTGACTCCCATCACCTATCTGCAGGGTCTAGCTATAGCTA
AGGAGACTGGTGCTGTAAAATACCTGGAGTGCTTGGCGTTCACACAGTGAGGCCTCAACAGTGTTAGACGAAGAGATTCA
AGCAGTCCTCTGCCCACCTCCCGTGAAGAAGAGGAAGAGAAAATGCTTGCTGTTG

ORF - retro_mmul_1964 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.87 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPLSYPQTDVFLICF
.V..TCLLISYTTNAFPGEYIPTVFDNYSANVMVD.KPVNLG.WDTA.QEDYDR...LSYPQTDVFLICF
RetrocopySVCETCLLISYTTNAFPGEYIPTVFDNYSANVMVDRKPVNLGSWDTAAQEDYDRSCRLSYPQTDVFLICF
ParentalSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYPQGLAMAKEIGAV
SLVSPASFENVRAKWYPEVRHH.PNTPIILVGTKL.LRDDKDTIEKLK.KKLTPITY.QGLA.AKE.GAV
RetrocopySLVSPASFENVRAKWYPEVRHHRPNTPIILVGTKLELRDDKDTIEKLK-KKLTPITYLQGLAIAKETGAV
ParentalKYLECSALTQRGLKTV-FDEAIRAVLCPPPVKKRKRKCLLL
KYLEC.A.TQ.GL..V...E.......PP.VKKRKRKCLLL
RetrocopyKYLECLAFTQ*GLNSV>DEEIQAVLCPPP-VKKRKRKCLLL

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 250 .10 RPM
SRP007412_brain_prefrontal_cortex 0 .16 RPM 187 .62 RPM
SRP007412_cerebellum 0 .13 RPM 177 .26 RPM
SRP007412_heart 0 .00 RPM 88 .62 RPM
SRP007412_kidney 0 .00 RPM 125 .94 RPM
SRP007412_liver 0 .00 RPM 73 .03 RPM
SRP007412_testis 0 .08 RPM 39 .58 RPM
Macaca mulatta was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_mmul_1964 retrocopy.
Macaca mulatta was not studied using FANTOM5 data.
retro_mmul_1964 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_1964 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3072
Gorilla gorilla retro_ggor_2110
Pongo abelii retro_pabe_2546

Parental genes homology:
Parental genes homology involve 10 parental genes, and 29 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000092332 retrocopies
Canis familiaris ENSCAFG000000157161 retrocopy
Gorilla gorilla ENSGGOG000000267332 retrocopies
Macaca mulatta ENSMMUG000000188542 retrocopies
Macaca mulatta ENSMMUG00000021075 4 retrocopies
Macaca mulatta ENSMMUG000000220098 retrocopies
Oryctolagus cuniculus ENSOCUG000000099561 retrocopy
Pan troglodytes ENSPTRG000000189104 retrocopies
Tupaia belangeri ENSTBEG000000072724 retrocopies
Xenopus tropicalis ENSXETG000000275931 retrocopy



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