RetrogeneDB ID:

retro_pabe_2345

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:130205270..130205533(-)
Located in intron of:ENSPPYG00000014078
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSPPYG00000029910
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_pabe_2345
ATGGCCAAGAACAAACTGAAGAGGGAAGAAGTCCAGCAATGTATTTCACATATCCAGTTAAAAAAACTTTAGGGTTCAAA
ACAAAGCAAAACCAATTACCACTAATCTTGTAAACAATTTAAACACTGGAAAAGTTAGCAGAGTGAATAAAGTTTTTATA
CATATACAGAAAACAACTTGCTCACTTCTCAAAAGGCATTCCCCTTGAACCTCTGCAGAAACGGCTGATTCCTCAGCAGC
ATCATGACAACAAACCAGTTAAT

ORF - retro_pabe_2345 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 67.03 %
Parental protein coverage: 89. %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAKNKL-RGPKSRNVFHIASQKNFKAKNKAKPVTTNLKKINIMNEEKVNRVNKAFVNVQK-ELAHFSKST
MAKNKL.RG.KS.NVFHI.S.KNF...NKAKP.TTNL...N..N..KV.RVNK.F...QK..LAHFSK..
RetrocopyMAKNKL>RGKKSSNVFHISS*KNFRVQNKAKPITTNL--VNNLNTGKVSRVNKVFIHIQK>QLAHFSKGI
ParentalSLEPLQKELIPQQRHESKPVN
.LEPLQK.LIPQQ.H..KPVN
RetrocopyPLEPLQKRLIPQQHHDNKPVN

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 1 .33 RPM
SRP007412_cerebellum 0 .00 RPM 3 .77 RPM
SRP007412_heart 0 .00 RPM 5 .24 RPM
SRP007412_kidney 0 .00 RPM 7 .96 RPM
SRP007412_liver 0 .03 RPM 7 .80 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2345 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2345 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2345 has 5 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2609
Pan troglodytes retro_ptro_1759
Gorilla gorilla retro_ggor_1828
Macaca mulatta retro_mmul_1475
Callithrix jacchus retro_cjac_1556

Parental genes homology:
Parental genes homology involve 15 parental genes, and 46 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000024092 retrocopies
Bos taurus ENSBTAG000000322272 retrocopies
Callithrix jacchus ENSCJAG000000003795 retrocopies
Cavia porcellus ENSCPOG000000219655 retrocopies
Felis catus ENSFCAG000000263661 retrocopy
Homo sapiens ENSG000001767314 retrocopies
Gorilla gorilla ENSGGOG000000274644 retrocopies
Loxodonta africana ENSLAFG000000326124 retrocopies
Myotis lucifugus ENSMLUG000000061551 retrocopy
Macaca mulatta ENSMMUG000000063813 retrocopies
Mus musculus ENSMUSG000000787843 retrocopies
Pongo abelii ENSPPYG00000029910 3 retrocopies
retro_pabe_2345 , retro_pabe_2630, retro_pabe_3633,
Pan troglodytes ENSPTRG000000203855 retrocopies
Rattus norvegicus ENSRNOG000000389022 retrocopies
Sus scrofa ENSSSCG000000061442 retrocopies



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