RetrogeneDB ID:

retro_ptro_2383

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:6:118558513..118558973(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAP1B
Ensembl ID:ENSPTRG00000005197
Aliases:None
Description:Pan troglodytes RAP1B, member of RAS oncogene family (RAP1B), mRNA. [Source:RefSeq mRNA;Acc:NM_001098545]


Retrocopy-Parental alignment summary:






>retro_ptro_2383
ATGCTTGAGTATAAATTAGTCATTCTTGGCTCAGGAGCTGTTGGAAATTCTGCTTTGACTGTACAATTTGTACAAAGAAT
TTTGTTGAAAAACATGGTCCTACAATAAAAGATATTACAGAAAGCAAGTGGAAATAGATGCACAACTCTGTATGCTTGAC
ATATTGGATACTGCAGGAACAGAACAATTTACAGCAATAAAGGGTTTGTACGTAAAAAATGGACAAGGCTTGGTATTAGC
ATATACCATCCCAGCACAGTCCACATTTTATGATTTACAAGATCTGAGAGAACAGATTCTTTAAGTTAAAGACACTGATA
TTGTCCCAGTGATTGTTGGTAATAAGTGTGACTTGGAAGATAAAAGAGTTGTAGGGAAGGAACAAGGTCAAAATCTAGCA
AGACAATGGAACAACTGTGCATTCTTAGAATCTTCTGCAAAATAAAAAATAAATCTTAAT

ORF - retro_ptro_2383 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.62 %
Parental protein coverage: 84.24 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMREYKLVVLGSGGVGKSALTVQFVQGI-FVEKYDPTIEDS-YRKQVEVDAQQCMLEILDTAGTEQFTAMR
M.EYKLV.LGSG.VG.SALTVQFVQ.I.FVEK..PTI.D..YRKQVE.DAQ.CML.ILDTAGTEQFTA..
RetrocopyMLEYKLVILGSGAVGNSALTVQFVQRI<FVEKHGPTIKDI<YRKQVEIDAQLCMLDILDTAGTEQFTAIK
ParentalDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKCDLEDERVVGKEQGQNLARQW
.LY.KNGQG..L.Y.I.AQSTF.DLQDLREQIL.VKDTD.VP...VGNKCDLED.RVVGKEQGQNLARQW
RetrocopyGLYVKNGQGLVLAYTIPAQSTFYDLQDLREQIL*VKDTDIVP-VIVGNKCDLEDKRVVGKEQGQNLARQW
ParentalNNCAFLESSAKSKINVN
NNCAFLESSAK.KIN.N
RetrocopyNNCAFLESSAK*KINLN

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 19 .66 RPM
SRP007412_cerebellum 0 .00 RPM 18 .82 RPM
SRP007412_heart 0 .00 RPM 31 .92 RPM
SRP007412_kidney 0 .00 RPM 67 .97 RPM
SRP007412_liver 0 .00 RPM 50 .28 RPM
SRP007412_testis 0 .00 RPM 82 .09 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_2383 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_2383 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_2383 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_1863

Parental genes homology:
Parental genes homology involve 18 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000086371 retrocopy
Cavia porcellus ENSCPOG000000082724 retrocopies
Dasypus novemcinctus ENSDNOG0000001972418 retrocopies
Erinaceus europaeus ENSEEUG000000100521 retrocopy
Echinops telfairi ENSETEG000000002421 retrocopy
Gorilla gorilla ENSGGOG000000256491 retrocopy
Loxodonta africana ENSLAFG000000164601 retrocopy
Microcebus murinus ENSMICG000000131481 retrocopy
Macaca mulatta ENSMMUG000000114422 retrocopies
Oryctolagus cuniculus ENSOCUG000000295525 retrocopies
Otolemur garnettii ENSOGAG000000057462 retrocopies
Pongo abelii ENSPPYG000000047511 retrocopy
Pan troglodytes ENSPTRG000000011021 retrocopy
Pan troglodytes ENSPTRG00000005197 3 retrocopies
retro_ptro_1812, retro_ptro_2383 , retro_ptro_2877,
Pan troglodytes ENSPTRG000000191081 retrocopy
Rattus norvegicus ENSRNOG000000070484 retrocopies
Sus scrofa ENSSSCG000000211481 retrocopy
Sus scrofa ENSSSCG000000300142 retrocopies



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