RetrogeneDB ID:

retro_pabe_3739

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:41909214..41909616(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SHISA5
Ensembl ID:ENSPPYG00000013902
Aliases:None
Description:protein shisa-5 [Source:RefSeq peptide;Acc:NP_001124981]


Retrocopy-Parental alignment summary:






>retro_pabe_3739
TTCAGAGCAACCGTGGCCGTCGGCCTGACCATCTTTGTGCTGTCTGTCGTCACTATCATCATCTGCTTCACCTGCTCCTG
CTGCTCCCTCTACAAGATGTGCCGTTGACCACGTCCAGTTGTGACCACCATCACGTCCACCACTGTGGTGCATGCCCCTT
ACCCTCAGCCTCCAAGTGTGCCACCTAGCTACCCTGGACTACCAGGGCTACCACCCCATGGCCCCCGCCCCCAGCCGGGA
ATGCCAGCAGCACCCTACCCAATGCAGTACCCATCACCTTACCCGGCCCAGCCCATGGGCCCGCCGGCCTACTTCGAGAC
CCTGGCTGGAGGAGCAGCCACGCCCTACCCCACCAGCCAGCCTCCTTCCAACCCAGACTACATGAATGCCCCGAAGGCGG
CC

ORF - retro_pabe_3739 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.58 %
Parental protein coverage: 64.11 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFGATLAVGLTIFVLSVVTIIICFTCSCCCLYKTCRRPRPVVTTTTSTTVVHAPYPQPPSVPPSYPGPSYQ
F.AT.AVGLTIFVLSVVTIIICFTCSCC.LYK.CR.PRPVVTT.TSTTVVHAPYPQPPSVPPSYPG....
RetrocopyFRATVAVGLTIFVLSVVTIIICFTCSCCSLYKMCR*PRPVVTTITSTTVVHAPYPQPPSVPPSYPGLPGL
ParentalGYHTMPPQPGMPAAPYPMQYPPPYPAQPMGPPAYHETLAGGAAAPYPASQPPYNPAYMDAPKAA
..H...PQPGMPAAPYPMQYP.PYPAQPMGPPAY.ETLAGGAA.PYP.SQPP.NP.YM.APKAA
RetrocopyPPHGPRPQPGMPAAPYPMQYPSPYPAQPMGPPAYFETLAGGAATPYPTSQPPSNPDYMNAPKAA

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 111 .47 RPM
SRP007412_cerebellum 0 .00 RPM 38 .91 RPM
SRP007412_heart 0 .00 RPM 23 .54 RPM
SRP007412_kidney 0 .00 RPM 88 .80 RPM
SRP007412_liver 0 .00 RPM 70 .51 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3739 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3739 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3739 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 7 parental genes, and 12 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000029152 retrocopies
Homo sapiens ENSG000001640542 retrocopies
Gorilla gorilla ENSGGOG000000282072 retrocopies
Macaca mulatta ENSMMUG000000100621 retrocopy
Nomascus leucogenys ENSNLEG000000064851 retrocopy
Pongo abelii ENSPPYG00000013902 3 retrocopies
retro_pabe_2120, retro_pabe_3653, retro_pabe_3739 ,
Pan troglodytes ENSPTRG000000148881 retrocopy



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