RetrogeneDB ID:

retro_pabe_2222

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:68769894..68770249(+)
Located in intron of:ENSPPYG00000013706
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CRB3
Ensembl ID:ENSPPYG00000009457
Aliases:None
Description:crumbs homolog 3 (Drosophila) [Source:HGNC Symbol;Acc:20237]


Retrocopy-Parental alignment summary:






>retro_pabe_2222
GGCCTGGGGCTGCTCCTGGCGCTGGGCCTGCCGCTGCTGTCGTCCCCGGGAACGACCCTGGGCGCAAATATCAACCCCTT
CTGCAAATGAGAGTAGCATTGTTTTGCCTACACCCACCAGCTCCGGCTCCAATGGAGCCCTGTTTCGGGGGGCCGTCACT
GCTATCATCTTGGTCCTCTGATTCCTGGCCGTCTTGTTCCTGGCAGTGGGGCTGGCACTATTGGTGCGGAAGCTTTGGGA
GATGCGGCAGACGGAGGGCACCTACTGGCCCAGCAGCAAGGAGCAGTTCTCCTATGTGGCTGAGGCCTGGGCCCCTCAGT
ACTCCAATGAGACCTTGTGGGGCTGCCTGCACATC

ORF - retro_pabe_2222 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.67 %
Parental protein coverage: 96.75 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGLGLLLALGLPFLLARWG-RAWGQIRTASTNENSTVLPSSTSSSSDSNLPQGAITAIIVVFSILAALLLA
GLGLLLALGLP.LL...G.R.W.QI.T.S.NE.S.VLP..TSS.S...L..GA.TAII.V...LA.L.LA
RetrocopyGLGLLLALGLP-LLSSPG>RPWAQISTPSANESSIVLPTPTSSGSNGALFRGAVTAIILVL*FLAVLFLA
ParentalVGLALLVWKLREKRQTEGTYRPSSEEQFSHAAEARAPQDSKETVRGCLPI
VGLALLV.KL.E.RQTEGTY.PSS.EQFS..AEA.APQ.S.ET..GCL.I
RetrocopyVGLALLVRKLWEMRQTEGTYWPSSKEQFSYVAEAWAPQYSNETLWGCLHI

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 .11 RPM
SRP007412_cerebellum 0 .49 RPM 0 .12 RPM
SRP007412_heart 0 .00 RPM 0 .00 RPM
SRP007412_kidney 0 .00 RPM 2 .15 RPM
SRP007412_liver 0 .00 RPM 2 .14 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2222 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2222 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2222 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2747
Gorilla gorilla retro_ggor_1910
Macaca mulatta retro_mmul_1434

Parental genes homology:
Parental genes homology involve 9 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000165671 retrocopy
Homo sapiens ENSG000001305452 retrocopies
Gorilla gorilla ENSGGOG000000070702 retrocopies
Macaca mulatta ENSMMUG000000055991 retrocopy
Nomascus leucogenys ENSNLEG000000159361 retrocopy
Pongo abelii ENSPPYG00000009457 2 retrocopies
retro_pabe_2222 , retro_pabe_2873,
Pan troglodytes ENSPTRG000000103671 retrocopy
Rattus norvegicus ENSRNOG000000473221 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000023961 retrocopy



Copyright © RetrogeneDB 2014-2017