RetrogeneDB ID:

retro_pabe_2892

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:6:101696852..101697384(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PRDX2
Ensembl ID:ENSPPYG00000009607
Aliases:None
Description:Peroxiredoxin-2 [Source:UniProtKB/Swiss-Prot;Acc:Q5RC63]


Retrocopy-Parental alignment summary:






>retro_pabe_2892
ATGGATGGCGCTTTCAAAGAAGTGAAGCTGTAGGACTACAAAGAGAAGTACATGGTCCTCTTTTTCTACCTTCTGCACTT
CACTTTTGTGTGCCCTGCGGAGATCATCGCGTTCAGCAACCATGCCGAGGACTTCCGCGAGCTGGGCTGCGAAGTGCTGG
GCATCTCAGTGGACTCTCAGTTCACCCACCTGGCTTGGATCAACAACCGCCAGAGAGAGGGAGACTTGGGCCCCCTGAAC
ATCCCCCTGCTTGCTGAGGTGACCAGAGGCTTGTCTGAGGATTACGCCATGCCGAAAACAGATGCGGGCATTGCCTACAG
GGGCCGCTTTATCAATGATGGCAAGGGTGTCCTTCCCAGATCACTGTTAATGATTTGCCTGTGGGACGCTCTGTGGATGA
GGCTCTGCAGCTGGTCCAGGCCTTCCAGTACACAGAAGAGCATGCGGAAGTTTGTCCCACTGGCTGGAAGCCTGGCAGTG
ACACATTAAGCCCAACGTGGGTGACAGCAAGGAATATTTATCCGAACACAAT

ORF - retro_pabe_2892 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.11 %
Parental protein coverage: 89.9 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVDGAFKEVKLSDYKGKYVVLFFYPLDFTFVCPTEIIAFSNRAEDFHKLGCEVLGVSVDSQFTHLAWINTP
.DGAFKEVKL.DYK.KY.VLFFY.L.FTFVCP.EIIAFSN.AEDF..LGCEVLG.SVDSQFTHLAWIN..
RetrocopyMDGAFKEVKL*DYKEKYMVLFFYLLHFTFVCPAEIIAFSNHAEDFRELGCEVLGISVDSQFTHLAWINNR
ParentalRKEGGLGPLNIPLLADVTRRLSEDYGVLKTDEGIAYRGLFIIDGKGVL-RQITVNDLPVGRSVDEALRLV
..EG.LGPLNIPLLA.VTR.LSEDY...KTD.GIAYRG.FI.DGKGVL..QITVNDLPVGRSVDEAL.LV
RetrocopyQREGDLGPLNIPLLAEVTRGLSEDYAMPKTDAGIAYRGRFINDGKGVL<SQITVNDLPVGRSVDEALQLV
ParentalQAFQYTDEHGEVCPAGWKPGSDT-IKPNVDDSKEYFSKHN
QAFQYT.EH.EVCP.GWKPGSDT.IKPNV.DSKEY.S.HN
RetrocopyQAFQYTEEHAEVCPTGWKPGSDT<IKPNVGDSKEYLSEHN

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 125 .73 RPM
SRP007412_cerebellum 0 .00 RPM 85 .85 RPM
SRP007412_heart 0 .00 RPM 96 .96 RPM
SRP007412_kidney 0 .00 RPM 92 .78 RPM
SRP007412_liver 0 .00 RPM 47 .95 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2892 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2892 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2892 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 23 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000123073 retrocopies
Canis familiaris ENSCAFG000000171633 retrocopies
Ciona intestinalis ENSCING000000030021 retrocopy
Callithrix jacchus ENSCJAG000000048824 retrocopies
Dipodomys ordii ENSDORG000000090051 retrocopy
Felis catus ENSFCAG000000004731 retrocopy
Homo sapiens ENSG000001678153 retrocopies
Gorilla gorilla ENSGGOG000000250893 retrocopies
Macaca mulatta ENSMMUG000000056892 retrocopies
Monodelphis domestica ENSMODG000000069781 retrocopy
Mustela putorius furoENSMPUG000000045912 retrocopies
Mus musculus ENSMUSG000000051612 retrocopies
Nomascus leucogenys ENSNLEG000000128002 retrocopies
Otolemur garnettii ENSOGAG000000249982 retrocopies
Pongo abelii ENSPPYG000000014111 retrocopy
Pongo abelii ENSPPYG000000027001 retrocopy
Pongo abelii ENSPPYG00000009607 3 retrocopies
retro_pabe_2711, retro_pabe_2892 , retro_pabe_988,
Pan troglodytes ENSPTRG000000105413 retrocopies
Rattus norvegicus ENSRNOG000000035202 retrocopies
Sorex araneus ENSSARG000000001461 retrocopy
Sarcophilus harrisii ENSSHAG000000155961 retrocopy
Sus scrofa ENSSSCG000000137362 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000258621 retrocopy



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