RetrogeneDB ID:

retro_pabe_2460

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:4:107423537..107424502(+)
Located in intron of:ENSPPYG00000014969
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ACTR3B
Ensembl ID:ENSPPYG00000018206
Aliases:None
Description:ARP3 actin-related protein 3 homolog B (yeast) [Source:HGNC Symbol;Acc:17256]


Retrocopy-Parental alignment summary:






>retro_pabe_2460
TATTCTGAGCTTGGCCATGCAGGCAACACTGAGCCATAGTTTACTATTCTTTCATGCATTTCTATCAGAGAGTCAGCAAA
GGTAGTTGACAAAGCCCAAAGGAGAATGTTGAGGGGAGTTGATGACCTTGACTTTTTCATACAGGATGAAGCCATTGAGA
AATCTATGTATGCTTCAAAGTGGTCAATATGACATGGAATCACTGAAGACTGGGATATTATGGAAAGGTTCATGGAGCAA
GTGGTTTTTAAATATCTTTGAGCAGAATCTGAGGACCATTATTTTTTAATGACAGAACTTCCACTGAATACACTAGAAAA
TACAGAGCATTTTTGCAGAAATTATGTTTGAATTATTTAATGTACCAGGATTCTACATTGCAATTCAGGAGGTACTGGCC
TTGGCAGTATCTTGGACATCTCAACAAGTGAGTGAATGTATGTTAATGAGTATAGTCATTGACAAAGGAGATGGAGTCAC
CCATGTTCTCCCAGTTGTAGGTTATGTAATTGGGAGCTGCATCAATCACATCCTGATTGTAGGTGATACTGTGTATTTCA
TTCAACAGCTGCTAAGGGAGAGGGAGGTAGGAATCCCTCTTGAGCAGTCACTGGAGACCACAAAAGCCATTAAGGAGAAA
TACTGTTACATTTGCCCGGATATAGTCAAGGAATTTGCTAAGTACGATGTGAATTCCTGGAAGTGGATCAAACAATACAC
AGGTATCAATGTGATCAACCAGGAGAAGTTCATAATAGATGTTGGTTACAAAAGGTTCCCGCAACTTGAAATATTTTTTT
ACCCAGAGTTTGCCAACCCAGACTTTATGGAATCCATCTTGAATGTTGTTGATGAATACAAAACTGTCCCATTGATGTGC
ATCGTCCACTGTATAAGACTGTTGTTCTTTCAAGGGGTTTGACCATATTCGGGGATTTGAACCTCAACTACAGAGAGATT
TGAAG

ORF - retro_pabe_2460 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.91 %
Parental protein coverage: 77.75 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalYTKLGYAGNTEPQFIIPSCIAIRESAKVVDQAQRRVLRGVDDLDFFIGDEAIDKPTYATKWPIRHGIIED
Y..LG.AGNTEP.F.I.SCI.IRESAKVVD.AQRR.LRGVDDLDFFI.DEAI.K..YA.KW.I.HGI.ED
RetrocopyYSELGHAGNTEP*FTILSCISIRESAKVVDKAQRRMLRGVDDLDFFIQDEAIEKSMYASKWSI*HGITED
ParentalWDLMERFMEQVVFKYLRAEPEDHYFLMTEPPLNTPENREYL-AEIMFESFNVPGLYIAVQAVLALAASWT
WD.MERFMEQVVFKYL.AE.EDHYFLMTE.PLNT.EN.E...AEIMFE.FNVPG.YIA.Q.VLALA.SWT
RetrocopyWDIMERFMEQVVFKYL*AESEDHYFLMTELPLNTLENTEHF>AEIMFELFNVPGFYIAIQEVLALAVSWT
ParentalSRQVGERTLTGIVIDSGDGVTHVIPVAEGYVIGSCIKHIPIAGRDITYFIQQLLREREVGIPPEQSLETA
S.QV.E..L..IVID.GDGVTHV.PV..GYVIGSCI.HI.I.G.D..YFIQQLLREREVGIP.EQSLET.
RetrocopySQQVSECMLMSIVIDKGDGVTHVLPVV-GYVIGSCINHILIVG-DTVYFIQQLLREREVGIPLEQSLETT
ParentalKAIKEKYCYICPDIVKEFAKYDVDPRKWIKQYTGINAINQKKFVIDVGYERFLGPEIFFHPEFANPDFME
KAIKEKYCYICPDIVKEFAKYDV...KWIKQYTGIN.INQ.KF.IDVGY.RF...EIFF.PEFANPDFME
RetrocopyKAIKEKYCYICPDIVKEFAKYDVNSWKWIKQYTGINVINQEKFIIDVGYKRFPQLEIFFYPEFANPDFME
ParentalSISDVVDEVIQNCPI-DVRRPLYKNVVLSGGSTMF-RDFGRRLQRDLK
SI..VVDE.....P..DV.RPLYK.VVLS.G.T.F.R.F...LQRDLK
RetrocopySILNVVDE-YKTVPL<DVHRPLYKTVVLSRGLTIF<RGFEPQLQRDLK

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 78 .02 RPM
SRP007412_cerebellum 0 .00 RPM 28 .58 RPM
SRP007412_heart 0 .00 RPM 9 .90 RPM
SRP007412_kidney 0 .03 RPM 11 .30 RPM
SRP007412_liver 0 .00 RPM 8 .75 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_2460 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_2460 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2460 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2966
Pan troglodytes retro_ptro_2007

Parental genes homology:
Parental genes homology involve 8 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000077305 retrocopies
Dasypus novemcinctus ENSDNOG000000192882 retrocopies
Homo sapiens ENSG000001336277 retrocopies
Macropus eugenii ENSMEUG000000048855 retrocopies
Nomascus leucogenys ENSNLEG000000156881 retrocopy
Pongo abelii ENSPPYG000000127981 retrocopy
Pongo abelii ENSPPYG00000018206 1 retrocopy
retro_pabe_2460 ,
Pan troglodytes ENSPTRG000000198978 retrocopies



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