RetrogeneDB ID:

retro_pabe_3537

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:Un:8394238..8394862(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAB6A
Ensembl ID:ENSPPYG00000003663
Aliases:None
Description:Ras-related protein Rab-6A [Source:UniProtKB/Swiss-Prot;Acc:Q5RAV6]


Retrocopy-Parental alignment summary:






>retro_pabe_3537
ATGTCCGCGGGCGGAGACTTCGGGAATCCGCTGACGAAATTCAAGCTGGTGTTCCTGGGGGAGCAAAGCGTTGCAAAGAC
ATCTTTGATCACCAGATTCATGTATGACAGTTTTGACAACACCTATCAGGCAACGATTGGCATTGACTTTTTATCAAAAA
CTATGTACTTGGAGGATGGAACAATCAGGCTTCCGCTGTGGGATACTGCGGGTCAGGAACGTCTCCGTAGCCTCATTCCC
AGTTACATCCGTGATTCTGCTGCAGCTGTAGTAGTTTACGGTATCACAAATGTTAACTCATTCCAGCAAACTACAAAGTG
GATTGATGATGTCAGAACAGAAAGAGGAAGTGATGTTATCATCACGCTAGTAGGAAATAAAACAGATCTTGCTGACAAGA
GGCAAGTGTCAATTGAGGAGGGAGAGAGGAAAGCCAAACAGCTGAATGTTATGTTTATTGAAACTAGTGCAAAAGCTGGA
TACAATGTAAAGCAGCTCTTTCGACGTGTAGCAGCAGTTTTGCCGGGAATGGAAAGCACACAGGACGGAAGCAGAGAAGA
CATGAGTGACATAAAACTGGAAAAGCCTCAGGAGCAACCAGTCAGCGAAAGAGGCTGTTCCTGC

ORF - retro_pabe_3537 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.31 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSTGGDFGNPLRKFKLVFLGEQSVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTA
MS.GGDFGNPL.KFKLVFLGEQSV.KTSLITRFMYDSFDNTYQATIGIDFLSKTMYLED.T.RL.LWDTA
RetrocopyMSAGGDFGNPLTKFKLVFLGEQSVAKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDGTIRLPLWDTA
ParentalGQERFRSLIPSYIRDSTVAVVVYDITNVNSFQQTTKWIDDVRTERGSDVIIMLVGNKTDLADKRQVSIEE
GQER.RSLIPSYIRDS..AVVVY.ITNVNSFQQTTKWIDDVRTERGSDVII.LVGNKTDLADKRQVSIEE
RetrocopyGQERLRSLIPSYIRDSAAAVVVYGITNVNSFQQTTKWIDDVRTERGSDVIITLVGNKTDLADKRQVSIEE
ParentalGERKAKELNVMFIETSAKAGYNVKQLFRRVAAALPGMESTQDRSREDMIDIKLEKPQEQPVSEGGCSC
GERKAK.LNVMFIETSAKAGYNVKQLFRRVAA.LPGMESTQD.SREDM.DIKLEKPQEQPVSE.GCSC
RetrocopyGERKAKQLNVMFIETSAKAGYNVKQLFRRVAAVLPGMESTQDGSREDMSDIKLEKPQEQPVSERGCSC

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 .44 RPM 213 .03 RPM
SRP007412_cerebellum 0 .00 RPM 129 .63 RPM
SRP007412_heart 0 .09 RPM 37 .87 RPM
SRP007412_kidney 0 .00 RPM 52 .80 RPM
SRP007412_liver 0 .00 RPM 32 .38 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3537 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3537 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3537 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000009921 retrocopy
Echinops telfairi ENSETEG000000094121 retrocopy
Homo sapiens ENSG000001755821 retrocopy
Loxodonta africana ENSLAFG000000099051 retrocopy
Mus musculus ENSMUSG000000307041 retrocopy
Nomascus leucogenys ENSNLEG000000170981 retrocopy
Ornithorhynchus anatinus ENSOANG000000316231 retrocopy
Ochotona princeps ENSOPRG000000011645 retrocopies
Ochotona princeps ENSOPRG000000103556 retrocopies
Pongo abelii ENSPPYG00000003663 3 retrocopies
retro_pabe_2097, retro_pabe_2191, retro_pabe_3537 ,
Ictidomys tridecemlineatus ENSSTOG000000234973 retrocopies



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