RetrogeneDB ID:

retro_pabe_2696

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:146831080..146831625(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ASS1
Ensembl ID:ENSPPYG00000019692
Aliases:None
Description:argininosuccinate synthase [Source:RefSeq peptide;Acc:NP_001126812]


Retrocopy-Parental alignment summary:






>retro_pabe_2696
GCTCCCTGGAGGATGCCCGAGTTCTACAACTGGTTCAAGGGCTGCAGTAACCTGATGGAATATGCAAAGCAACACGGGAT
TCCCATCCTGGTCACCCCCAAGAACCTGTAGAGCATGGACAAGAACCTCATGCACATCAGCTACGAGGCTGGAATACCGG
AGAACCCCAAGAACAAAGTGCCTCCAGGTCTCTACACGAAGACCCAGGACCCAGCCAAAGCCCCCAACACCCCTGGCATT
CTCAAGATCCAATTCAAAAAAGGGGTCCCCGTGAAGGTGACCAACGTCAAGGATGGCAACACCCACCAGACCTCCTTGGA
GCTCTTCGTGTACTTGAACGAAGTTGCAGGCAAGCACGACGGTGTGGGCTGTATTGCCATCGTGGAGAATAACTTCACTG
GACAAAGGCCTGAGGTATCTACCAGACTCCGGTAGGCACCATCCTTTACCATGTTCATTTAGACATCAAGGTCTTCACCA
CAGACTGGGAAGTGCACAAAACCAAACAAGGCCTGGGCTTGAAATTTGCTGAGCTGATATACACC

ORF - retro_pabe_2696 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.87 %
Parental protein coverage: 50.42 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalAPWRMPEFYNRFKGRNDLMEYAKQHGIPIPVTPKNPWSMDENLMHISYEAGILENPKNQAPPGLYTKTQD
APWRMPEFYN.FKG...LMEYAKQHGIPI.VTPKN..SMD.NLMHISYEAGI.ENPKN..PPGLYTKTQD
RetrocopyAPWRMPEFYNWFKGCSNLMEYAKQHGIPILVTPKNL*SMDKNLMHISYEAGIPENPKNKVPPGLYTKTQD
ParentalPAKAPNTPDILEIEFKKGVPVKVTNVKDGTTHQTSLELFMYLNEVAGKH-GVGRIDIVENRFIGM-KSRG
PAKAPNTP.IL.I.FKKGVPVKVTNVKDG.THQTSLELF.YLNEVAGKH.GVG.I.IVEN.F.G..K..G
RetrocopyPAKAPNTPGILKIQFKKGVPVKVTNVKDGNTHQTSLELFVYLNEVAGKHDGVGCIAIVENNFTGQ<KA*G
ParentalIYETPAGTILYHAHLDIEAFTMDREVRKIKQGLGLKFAELVYT
IY.TP.GTILYH.HLDI..FT.D.EV.K.KQGLGLKFAEL.YT
RetrocopyIYQTPVGTILYHVHLDIKVFTTDWEVHKTKQGLGLKFAELIYT

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 .11 RPM 45 .84 RPM
SRP007412_cerebellum 0 .00 RPM 1 .09 RPM
SRP007412_heart 0 .00 RPM 5 .81 RPM
SRP007412_kidney 0 .03 RPM 673 .87 RPM
SRP007412_liver 0 .00 RPM 332 .55 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2696 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2696 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2696 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3252
Pan troglodytes retro_ptro_2199

Parental genes homology:
Parental genes homology involve 8 parental genes, and 68 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000205543 retrocopies
Homo sapiens ENSG0000013070714 retrocopies
Gorilla gorilla ENSGGOG000000102288 retrocopies
Myotis lucifugus ENSMLUG000000060662 retrocopies
Mus musculus ENSMUSG000000764411 retrocopy
Nomascus leucogenys ENSNLEG0000001250013 retrocopies
Pongo abelii ENSPPYG00000019692 13 retrocopies
Pan troglodytes ENSPTRG0000002147314 retrocopies



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