RetrogeneDB ID:

retro_pabe_2422

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:4:3372700..3373027(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:XAGE3
Ensembl ID:ENSPPYG00000020369
Aliases:None
Description:X antigen family, member 3 [Source:HGNC Symbol;Acc:14618]


Retrocopy-Parental alignment summary:






>retro_pabe_2422
ATGAGTTGGCAAGGAAGATCAGCATGTAGGCTTAGACCAAGACGGTATCTGCAGCCCCTGAGCTAACTGGGTCTGTGCTT
GAGCCCAGTGATGAGAAGCCTCAACTAGAGGAACCACCACCTGAAAGTCGGGGTCCTACACCTGGCCAGGAGAGAGAGGA
TGATCACGGTGCCGCTGAGATTCTTGTGCTTGACCAGGAAGCTGATCTCTGGGAGCTGTCTCAAAAGACTGGGATGAATG
TGGAGATGGTCCTGATGTCCGGGGAAGATTCTGCCGAAATCAGAGCAATTTAAATTGCCAGAAGGAGGTGAAGGGCAACC
ACAGGTT

ORF - retro_pabe_2422 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.05 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMIWRGRSTYRPRPRRSVPP-PELIGPMLEPSDEEPQQEEPPTESQDPAPGQEREEDQGAAEIQVPDLEAD
M.W.GRS..R.RPRR...P.PEL.G..LEPSDE.PQ.EEPP.ES..P.PGQERE.D.GAAEI.V.D.EAD
RetrocopyMSWQGRSACRLRPRRYLQP<PELTGSVLEPSDEKPQLEEPPPESRGPTPGQEREDDHGAAEILVLDQEAD
ParentalLQELSQSKTG-DECGNGPDDQ-GKILPKSEQFKMPEGGDRQPQV
L.ELSQ.KTG.DECG.GPD...GKILPKSEQFK.PEGG..QPQV
RetrocopyLWELSQ-KTG<DECGDGPDVR<GKILPKSEQFKLPEGGEGQPQV

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 0 .00 RPM
SRP007412_cerebellum 0 .24 RPM 0 .00 RPM
SRP007412_heart 0 .03 RPM 0 .09 RPM
SRP007412_kidney 0 .00 RPM 0 .00 RPM
SRP007412_liver 0 .00 RPM 0 .03 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2422 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2422 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2422 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Callithrix jacchus retro_cjac_2302

Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Gorilla gorilla ENSGGOG000000274041 retrocopy
Pongo abelii ENSPPYG000000203451 retrocopy
Pongo abelii ENSPPYG00000020369 1 retrocopy
retro_pabe_2422 ,
Pan troglodytes ENSPTRG000000219221 retrocopy



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