RetrogeneDB ID:

retro_pabe_1143

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:14:97637935..97638172(+)
Located in intron of:ENSPPYG00000006122
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPPYG00000000768
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_1143
ATGTCACACAAACAAATTTACTATTCGGACAAATACGACGACGAGGAGTTTGAGTATCGACAGGTCATGCTGCCCAAGGA
CATAGCCAAGCTGGTCCTTAAAGCACATTTGATGTCTGAATCTGAGTGGAGGAATCTTGGCATTCAGCAGAGCCAGGGAT
GGGTCCATTATATGATCCACGAATCAGAATCTCACATCTCGCTGTTCCGGCACCCACTACCCAAGAAGCCAAAGAAA

ORF - retro_pabe_1143 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.87 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSHKQIYYSDKYDDEEFEYRHVMLPKDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILLFR
MSHKQIYYSDKYDDEEFEYR.VMLPKDIAKLV.K.HLMSESEWRNLG.QQSQGWVHYMIHE.E.HI.LFR
RetrocopyMSHKQIYYSDKYDDEEFEYRQVMLPKDIAKLVLKAHLMSESEWRNLGIQQSQGWVHYMIHESESHISLFR
ParentalRPLPKKPKK
.PLPKKPKK
RetrocopyHPLPKKPKK

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 5 .81 RPM
SRP007412_cerebellum 0 .00 RPM 1 .58 RPM
SRP007412_heart 0 .15 RPM 5 .54 RPM
SRP007412_kidney 0 .17 RPM 8 .49 RPM
SRP007412_liver 0 .00 RPM 8 .29 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1143 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1143 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1143 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_944
Gorilla gorilla retro_ggor_1070

Parental genes homology:
Parental genes homology involve 17 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Dipodomys ordii ENSDORG000000037646 retrocopies
Equus caballus ENSECAG000000034601 retrocopy
Echinops telfairi ENSETEG000000033374 retrocopies
Felis catus ENSFCAG000000013471 retrocopy
Homo sapiens ENSG000001732071 retrocopy
Loxodonta africana ENSLAFG000000322131 retrocopy
Mus musculus ENSMUSG000000280441 retrocopy
Nomascus leucogenys ENSNLEG000000115323 retrocopies
Oryctolagus cuniculus ENSOCUG000000162042 retrocopies
Otolemur garnettii ENSOGAG0000000638410 retrocopies
Pongo abelii ENSPPYG00000000768 3 retrocopies
retro_pabe_1143 , retro_pabe_3625, retro_pabe_717,
Pongo abelii ENSPPYG000000258431 retrocopy
Pan troglodytes ENSPTRG000000013984 retrocopies
Rattus norvegicus ENSRNOG000000425611 retrocopy
Sorex araneus ENSSARG000000123832 retrocopies
Sus scrofa ENSSSCG000000297371 retrocopy
Vicugna pacos ENSVPAG000000121821 retrocopy



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