RetrogeneDB ID:

retro_pabe_376

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1:38567747..38568220(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ARPC3
Ensembl ID:ENSPPYG00000004947
Aliases:None
Description:actin related protein 2/3 complex, subunit 3, 21kDa [Source:HGNC Symbol;Acc:706]


Retrocopy-Parental alignment summary:






>retro_pabe_376
CCGGCTTACCACTCTTCTCTCATGGATCCTGACAACAAACTCATTGGAAAACATGGCACTCTTACCCTATCAGAAGTCAA
TTCAAAGGACCTGCCCCCAGAGAGACAAAAAGATACAGATATTGTGGTTGAAGCCCTCTATTACTTTCAAGGTCAATGTC
TTCTTCAAAAACTATGAAATTAAGAATGAAGCTGATAGGACCTTGATATATATACCTCTCTACATTTCTGAGTGTCTGAA
GAAACTCCAAAAGTGGTAATTCCAGAAGCCAAGGTGAGAAAGAAATGTATACACAGGGAATCACTAATTTTCCCATTCCT
GGAGAGCCTGGTTTTCCACTTAATGCAATTTATGCCAAACCTGCAAACAAACAGGAAGATGAAGTGATGAGAGCCTGTTT
ACAACAGCTAAGGCAAGAGACTGGTCTGAGACTTTGTGAGCAAGTTTTCAACCCGCGGAATGATAAACCCAGC

ORF - retro_pabe_376 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.44 %
Parental protein coverage: 92.86 %
Number of stop codons detected: 0
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalPAYHSSLMDPDTKLIG-NMALLP-IRSQFKGPAPRETK-DTDIVDEAIYYF-KANVFFKNYEIKNEADRT
PAYHSSLMDPD.KLIG.NMALLP.IRSQFKGPAPRETK.DTDIV.EA.YYF.K.NVFFKNYEIKNEADRT
RetrocopyPAYHSSLMDPDNKLIG>NMALLP>IRSQFKGPAPRETK>DTDIVVEALYYF>KVNVFFKNYEIKNEADRT
ParentalLIYITLYISECLKKLQKC-NSKSQGEKEMYTLGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRAYLQQL
LIYI.LYISECLKKLQK..NS.SQGEKEMYT.GITNFPIPGEPGFPLNAIYAKPANKQEDEVMRA.LQQL
RetrocopyLIYIPLYISECLKKLQKW>NSRSQGEKEMYTQGITNFPIPGEPGFPLNAIYAKPANKQEDEVMRACLQQL
ParentalRQETGLRLCEKVFDPQNDKPS
RQETGLRLCE.VF.P.NDKPS
RetrocopyRQETGLRLCEQVFNPRNDKPS

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 14 .76 RPM
SRP007412_cerebellum 0 .00 RPM 12 .40 RPM
SRP007412_heart 0 .00 RPM 6 .35 RPM
SRP007412_kidney 0 .00 RPM 16 .81 RPM
SRP007412_liver 0 .00 RPM 17 .44 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_376 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_376 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_376 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_303
Macaca mulatta retro_mmul_543

Parental genes homology:
Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000084561 retrocopy
Callithrix jacchus ENSCJAG000000093601 retrocopy
Dasypus novemcinctus ENSDNOG000000049872 retrocopies
Dipodomys ordii ENSDORG000000082121 retrocopy
Erinaceus europaeus ENSEEUG000000115312 retrocopies
Felis catus ENSFCAG000000041322 retrocopies
Loxodonta africana ENSLAFG000000061663 retrocopies
Macaca mulatta ENSMMUG000000064923 retrocopies
Monodelphis domestica ENSMODG000000116281 retrocopy
Nomascus leucogenys ENSNLEG000000028024 retrocopies
Oryctolagus cuniculus ENSOCUG000000119081 retrocopy
Otolemur garnettii ENSOGAG000000134241 retrocopy
Oreochromis niloticus ENSONIG000000037851 retrocopy
Procavia capensis ENSPCAG000000118582 retrocopies
Pongo abelii ENSPPYG00000004947 6 retrocopies
Sarcophilus harrisii ENSSHAG000000148053 retrocopies
Tupaia belangeri ENSTBEG000000112191 retrocopy
Tarsius syrichta ENSTSYG000000029534 retrocopies
Tursiops truncatus ENSTTRG000000150832 retrocopies
Vicugna pacos ENSVPAG000000084041 retrocopy



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