RetrogeneDB ID:

retro_pabe_3225

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:7_random:8706770..8707072(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPPYG00000017272
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_3225
GCTGCACTTCAACAAGGAAAGTTTCCTCCTACTCCATTCTCTGCCTCTCCCCAGCAGGGGCGATGATCCCACCTCCCCCG
AAGTCTCCCGGCTCCTCTTTGCCCTGGTATGATGCCTGCACCTCCTATAAGGGGCCCTCCCATGATGTCAGTGATGGGTT
CTCCTCCTCCTGGGATGATGCCAGTGGGACCTGCTCCTGGAATGAGACTGCCATGGGAGGTCACATGCCAATGTTGCCTA
GGCCCCCAGTGATGGAACCTCCTACCTGCTCCGTGATGATGCCTGCTGAGCCCAGAATGACT

ORF - retro_pabe_3225 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.08 %
Parental protein coverage: 96.19 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalAAFQQGKIPPTPFSAPP-PAGAMIPPPP-SLPGPPRPGMMPAPHMGGPPMMPMMGPPPPGMMPVGPAPGM
AA.QQGK.PPTPFSA.P.PAGAMIPPPP.SLP.P..PGMMPAP...GPPMM..MG.PPPGMMPVGPAPGM
RetrocopyAALQQGKFPPTPFSASP<PAGAMIPPPP>SLPAPLCPGMMPAPPIRGPPMMSVMGSPPPGMMPVGPAPGM
ParentalRPP-MGGHMPMMPGPPMMRPPARPMMVPTRPGMT
R.P.MGGHMPM.P.PP.M.PP....M.P..P.MT
RetrocopyRLP<MGGHMPMLPRPPVMEPPTCSVMMPAEPRMT

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 12 .88 RPM
SRP007412_cerebellum 0 .00 RPM 9 .73 RPM
SRP007412_heart 0 .00 RPM 8 .46 RPM
SRP007412_kidney 0 .00 RPM 17 .04 RPM
SRP007412_liver 0 .00 RPM 13 .46 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3225 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3225 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3225 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 121 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000009637 retrocopies
Bos taurus ENSBTAG000000245491 retrocopy
Canis familiaris ENSCAFG000000012313 retrocopies
Felis catus ENSFCAG0000000587612 retrocopies
Homo sapiens ENSG000001245626 retrocopies
Loxodonta africana ENSLAFG000000135342 retrocopies
Myotis lucifugus ENSMLUG000000024888 retrocopies
Monodelphis domestica ENSMODG000000139041 retrocopy
Mustela putorius furoENSMPUG000000032107 retrocopies
Mus musculus ENSMUSG0000002421721 retrocopies
Oryctolagus cuniculus ENSOCUG000000266683 retrocopies
Otolemur garnettii ENSOGAG000000087559 retrocopies
Procavia capensis ENSPCAG000000168851 retrocopy
Pongo abelii ENSPPYG00000017272 4 retrocopies
Pongo abelii ENSPPYG000000299023 retrocopies
Pteropus vampyrus ENSPVAG000000155971 retrocopy
Rattus norvegicus ENSRNOG0000000049330 retrocopies
Sarcophilus harrisii ENSSHAG000000009451 retrocopy
Sus scrofa ENSSSCG000000015311 retrocopy



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