RetrogeneDB ID:

retro_pabe_452

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1:148779642..148780022(-)
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:ENSPPYG00000005546
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_452
GGCCATGGAGATCCTGTGAAAGCTGAGAGGCAAAATGTCATCATATGTATTTTTTGTGCAAAATTGTCAGGAGGAGCACA
GGAAATGGTATCCAGATACTTCTGTCACCTTCTCACAGTTTTCTAAGAAGTGCTTAGAGAGGTGGAAGACCATGTGTGTT
GAAGAGAAGGGAAAATCTGAAGACACAGCAAAATCAGGCAAGCCTTGTTATGATAGAGAAATGAAAACCTATATCCGTCC
TAAAGGGGAAACAAAATGAAGTTCAAGGATCCCAATCCACCCCAGAGGCCTCCTTCTGACTTTTTTGGTTCTATTCTGAG
TAGTGTTCAAAAATCAAAGGAGAACATTCCGGCCTATCCATTGATGATGTTTCAAAGAAA

ORF - retro_pabe_452 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70. %
Parental protein coverage: 59.07 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalGKGDPKKP-RGKMSSYAFFVQTCREEHKKKHPDASVNFSEFSKKCSERWKTMSAKEKGKFEDMAKADKAR
G.GDP.K..RGKMSSY.FFVQ.C.EEH.K..PD.SV.FS.FSKKC.ERWKTM...EKGK.ED.AK..K..
RetrocopyGHGDPVKA>RGKMSSYVFFVQNCQEEHRKWYPDTSVTFSQFSKKCLERWKTMCVEEKGKSEDTAKSGKPC
ParentalYEREMKTYIPPKGET-KKKFKDPNAPKRPPSAF-FLFCSEYRPKIKGEHPGLSIGDVAKK
Y.REMKTYI.PKGET.K.KFKDPN.P.RPPS.F.F.F.SE...KIKGEH.GLSI.DV.KK
RetrocopyYDREMKTYIRPKGET<KMKFKDPNPPQRPPSDF<FWFYSE*CSKIKGEHSGLSIDDVSKK

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 108 .09 RPM
SRP007412_cerebellum 0 .00 RPM 110 .54 RPM
SRP007412_heart 0 .00 RPM 71 .83 RPM
SRP007412_kidney 0 .00 RPM 98 .31 RPM
SRP007412_liver 0 .00 RPM 70 .75 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_452 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_452 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_452 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_176
Gorilla gorilla retro_ggor_259
Macaca mulatta retro_mmul_385
Callithrix jacchus retro_cjac_2934

Parental genes homology:
Parental genes homology involve 17 parental genes, and 205 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG0000000659713 retrocopies
Choloepus hoffmanni ENSCHOG0000000242316 retrocopies
Homo sapiens ENSG0000018940337 retrocopies
Gorilla gorilla ENSGGOG0000002676423 retrocopies
Loxodonta africana ENSLAFG000000002694 retrocopies
Macropus eugenii ENSMEUG000000013802 retrocopies
Macaca mulatta ENSMMUG000000233993 retrocopies
Monodelphis domestica ENSMODG0000000923814 retrocopies
Ochotona princeps ENSOPRG000000035078 retrocopies
Procavia capensis ENSPCAG000000022012 retrocopies
Pongo abelii ENSPPYG00000005546 35 retrocopies
Pongo abelii ENSPPYG000000152043 retrocopies
Pongo abelii ENSPPYG0000002081822 retrocopies
Pteropus vampyrus ENSPVAG000000014316 retrocopies
Rattus norvegicus ENSRNOG000000298131 retrocopy
Sorex araneus ENSSARG0000000447014 retrocopies
Sarcophilus harrisii ENSSHAG000000140342 retrocopies



Copyright © RetrogeneDB 2014-2017