RetrogeneDB ID:

retro_pabe_3835

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X_random:6892624..6892963(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HNRNPA1L2
Ensembl ID:ENSPPYG00000025850
Aliases:None
Description:heterogeneous nuclear ribonucleoprotein A1-like 2 [Source:HGNC Symbol;Acc:27067]


Retrocopy-Parental alignment summary:






>retro_pabe_3835
CCTGGTTACTCTGAGGAAGCAGAGGCTATGAAAGTGGTGGACAGAGTTTGGAAACCAGGACAGTGGCTATGGCGGGAGTG
GCAGCTATGACAGCTGTAACAAGGGAGGCAGAGGCGGCTTTGGCAGTGGTAGTGGAAGCAGTTTTGGAGGTGGTGGAAGC
TACAATGATTTGGGCAATTACAACAGTCAGTCTTCAAATTTGGGACCCGTGAAGGGAGGAAATTTTGGGGCAGAAGCTCT
GGCCCCTATGGTGGTGGAGGCCAATACTTTGCCAAACCACCAAACCACAGTGGCTGTGGTGGTTCCAGTAGCAGCAGTAG
CTATGGCAGTGGCAGAAGA

ORF - retro_pabe_3835 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.34 %
Parental protein coverage: 58.46 %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalPGYSG-GSRGYGSGGQG-YGNQGSGYGGSGSYDSYNNGGGGCFGGGSGSNFGGGGSYNDFGNYNNQSSNF
PGYS..GSRGY.SGGQ...GNQ.SGYGGSGSYDS.N.GG.G.FG.GSGS.FGGGGSYND.GNYN.QSSN.
RetrocopyPGYSE<GSRGYESGGQS<FGNQDSGYGGSGSYDSCNKGGRGGFGSGSGSSFGGGGSYNDLGNYNSQSSNL
ParentalGPMKGGNFG-GRSSGPYGGGGQYFAKPRNQGGYGSSSSSSSYGSGRR
GP.KGGNFG.GRSSGPYGGGGQYFAKP.N..G.G.SSSSSSYGSGRR
RetrocopyGPVKGGNFG<GRSSGPYGGGGQYFAKPPNHSGCGGSSSSSSYGSGRR

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 57 .06 RPM
SRP007412_cerebellum 0 .00 RPM 45 .97 RPM
SRP007412_heart 0 .00 RPM 44 .37 RPM
SRP007412_kidney 0 .00 RPM 78 .09 RPM
SRP007412_liver 0 .00 RPM 46 .97 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3835 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3835 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3835 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 10 parental genes, and 28 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000092287 retrocopies
Loxodonta africana ENSLAFG000000295875 retrocopies
Mustela putorius furoENSMPUG000000046201 retrocopy
Mustela putorius furoENSMPUG000000057352 retrocopies
Oryctolagus cuniculus ENSOCUG000000133501 retrocopy
Oreochromis niloticus ENSONIG000000122481 retrocopy
Procavia capensis ENSPCAG000000018675 retrocopies
Pongo abelii ENSPPYG000000129671 retrocopy
Pongo abelii ENSPPYG000000161071 retrocopy
Pongo abelii ENSPPYG00000025850 4 retrocopies



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