RetrogeneDB ID:

retro_pabe_1405

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:16_random:2742626..2742970(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS26
Ensembl ID:ENSPPYG00000004642
Aliases:None
Description:ribosomal protein S26 [Source:HGNC Symbol;Acc:10414]


Retrocopy-Parental alignment summary:






>retro_pabe_1405
ATGACAAAGAAAAGAAAGGACAATGGTTGTGCCAAAAAGGGCTGCGGCCACGTGCAGCCTATTTGCTGCATGAACTGTGC
CTGATATGTGCCCAAGGACAAAGCCATTAGGAAATTCGTCATTCAAAACATAGTGGAGGCCACAGCAGTCGGCGACATTT
CTGAAGCGAGTGTCTTCGACGCCTATGTGCTTCCCAAGATGTATGTGAAGCTAAATTACTGTGTGAGTTGTGCAATTCAC
AACAAAGTAGTCAGGAATCGATCTTGTGAAGCCTGCAAGGACCGAACGCCCCAACCCGATTTAGACCTGTGGGTGCTGCC
CCACGACCCCTATCAAAGGTGATG

ORF - retro_pabe_1405 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.17 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMTKKRRNNGRAKKGRGHVQPIRCTNCARCVPKDKAIKKFVIRNIVEAAAVRDISEASVFDAYVLPKLYVK
MTKKR..NG.AKKG.GHVQPI.C.NCA..VPKDKAI.KFVI.NIVEA.AV.DISEASVFDAYVLPK.YVK
RetrocopyMTKKRKDNGCAKKGCGHVQPICCMNCA*YVPKDKAIRKFVIQNIVEATAVGDISEASVFDAYVLPKMYVK
ParentalLHYCVSCAIHSKVVRNRSREARKDRTP-PPRFRPAGAAPRPPPKPM
L.YCVSCAIH.KVVRNRS.EA.KDRTP.P.RFRP.GAAPRP..K.M
RetrocopyLNYCVSCAIHNKVVRNRSCEACKDRTP<PTRFRPVGAAPRPLSKVM

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 60 .38 RPM
SRP007412_cerebellum 0 .00 RPM 24 .69 RPM
SRP007412_heart 0 .00 RPM 60 .15 RPM
SRP007412_kidney 0 .00 RPM 128 .71 RPM
SRP007412_liver 0 .00 RPM 113 .01 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1405 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1405 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1405 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 16 parental genes, and 136 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000032607 retrocopies
Bos taurus ENSBTAG000000388963 retrocopies
Choloepus hoffmanni ENSCHOG0000000148910 retrocopies
Cavia porcellus ENSCPOG000000236306 retrocopies
Dipodomys ordii ENSDORG000000011512 retrocopies
Echinops telfairi ENSETEG0000000451035 retrocopies
Gorilla gorilla ENSGGOG000000115666 retrocopies
Loxodonta africana ENSLAFG000000133298 retrocopies
Myotis lucifugus ENSMLUG0000002996810 retrocopies
Mus musculus ENSMUSG000000253621 retrocopy
Pongo abelii ENSPPYG00000004642 16 retrocopies
Pan troglodytes ENSPTRG000000050751 retrocopy
Rattus norvegicus ENSRNOG000000055171 retrocopy
Sus scrofa ENSSSCG000000003742 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001055912 retrocopies
Tursiops truncatus ENSTTRG0000001501216 retrocopies



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