RetrogeneDB ID:

retro_pabe_3783

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:81776394..81776749(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:POMP
Ensembl ID:ENSPPYG00000005247
Aliases:None
Description:Proteasome maturation protein [Source:UniProtKB/Swiss-Prot;Acc:Q5R9L9]


Retrocopy-Parental alignment summary:






>retro_pabe_3783
ATGGATGCCAGAAGACCTGGATCTCAGCTAAAGGGCAGTGTTCCAGCTACTGAACTTTCAGCAAGTGAATCTCTCGAAAG
TCATAATCTTCAGAAAGTGTTTTTTGTGTGTGTGAAAAATGAAATTTTAGCTAGTCATCCTCTTGAATTTTCAGAAGAGA
ATTTCCAATGCAACCAAGATAAAATGAATATTTCCACAGTGAGAAACATTCAGTGGTTATTTGCCCCACTAAAATTATAA
ATCGAAATTTAAGGCAGTGCAGCAGGTTCAATGTCTTCCATTTCTTTTGAGCTCAAACCTTTCACTGGATATTTTGAGGG
GTAATGAAGAGACTACCAGATTTGAAGCTATTCTT

ORF - retro_pabe_3783 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.59 %
Parental protein coverage: 83.57 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMNARGLGSELKDSIPVTELSASGPFESHDLLRKGFSCVKNELLPSHPLELSEKNFQLNQDKMNF-TLRNI
M.AR..GS.LK.S.P.TELSAS...ESH.L....F.CVKNE.L.SHPLE.SE.NFQ.NQDKMN..T.RNI
RetrocopyMDARRPGSQLKGSVPATELSASESLESHNLQKVFFVCVKNEILASHPLEFSEENFQCNQDKMNISTVRNI
ParentalQGLFAPLKLQME-FKAVQQVQRLPFLSSSNLSLDVLRGNDETIGFEDIL
Q.LFAPLKL..E.FKAVQQVQ.LPFL.SSNLSLD.LRGN.ET..FE.IL
RetrocopyQWLFAPLKL*IE>FKAVQQVQCLPFLLSSNLSLDILRGNEETTRFEAIL

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_prefrontal_cortex 0 .00 RPM 33 .45 RPM
SRP007412_cerebellum 0 .00 RPM 35 .75 RPM
SRP007412_heart 0 .00 RPM 36 .85 RPM
SRP007412_kidney 0 .00 RPM 39 .91 RPM
SRP007412_liver 0 .00 RPM 39 .38 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3783 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3783 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3783 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4866
Gorilla gorilla retro_ggor_3038
Macaca mulatta retro_mmul_2603
Callithrix jacchus retro_cjac_4191

Parental genes homology:
Parental genes homology involve 34 parental genes, and 100 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000096711 retrocopy
Ailuropoda melanoleuca ENSAMEG000000089611 retrocopy
Bos taurus ENSBTAG000000140243 retrocopies
Choloepus hoffmanni ENSCHOG0000001280712 retrocopies
Callithrix jacchus ENSCJAG000000194733 retrocopies
Cavia porcellus ENSCPOG000000017103 retrocopies
Dasypus novemcinctus ENSDNOG000000088484 retrocopies
Equus caballus ENSECAG000000119511 retrocopy
Echinops telfairi ENSETEG000000124482 retrocopies
Felis catus ENSFCAG000000082355 retrocopies
Homo sapiens ENSG000001329632 retrocopies
Gorilla gorilla ENSGGOG000000153162 retrocopies
Loxodonta africana ENSLAFG000000036651 retrocopy
Macropus eugenii ENSMEUG000000154162 retrocopies
Myotis lucifugus ENSMLUG000000103221 retrocopy
Macaca mulatta ENSMMUG000000000972 retrocopies
Mustela putorius furoENSMPUG000000046903 retrocopies
Mus musculus ENSMUSG000000296493 retrocopies
Nomascus leucogenys ENSNLEG000000005723 retrocopies
Oryctolagus cuniculus ENSOCUG000000101371 retrocopy
Otolemur garnettii ENSOGAG000000060441 retrocopy
Ochotona princeps ENSOPRG000000165172 retrocopies
Procavia capensis ENSPCAG000000096801 retrocopy
Pongo abelii ENSPPYG00000005247 1 retrocopy
retro_pabe_3783 ,
Pan troglodytes ENSPTRG000000057451 retrocopy
Pteropus vampyrus ENSPVAG000000000323 retrocopies
Rattus norvegicus ENSRNOG000000484702 retrocopies
Rattus norvegicus ENSRNOG000000492294 retrocopies
Sorex araneus ENSSARG000000011345 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000136872 retrocopies
Tupaia belangeri ENSTBEG0000001214913 retrocopies
Tarsius syrichta ENSTSYG000000051214 retrocopies
Tursiops truncatus ENSTTRG000000129244 retrocopies
Vicugna pacos ENSVPAG000000013152 retrocopies



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