RetrogeneDB ID:

retro_pabe_1265

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:15:86608149..86608876(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:C6orf106
Ensembl ID:ENSPPYG00000016519
Aliases:None
Description:chromosome 6 open reading frame 106 [Source:HGNC Symbol;Acc:21215]


Retrocopy-Parental alignment summary:






>retro_pabe_1265
GTGGGCCTGGACCCAGGGCTGGTGCAGAAGTTTGGCTGCCTGGGCACCACCGACAAGGACGTGCTCATCTCTGAGTTCCA
GTGTCTGCTTGGCTTCCAGCTCAACCCTGATGACAGCACCTTCTTCCTGGACACGACCAACTGGAACCTAACAGCAATTG
GTGCCTGTTGTGACTCTGATAGCCCAAACATCAGTGTGCCCTCTATGTCCTTTGTTGAAGATGTCACCAAAGGAGAAGCA
GAGTCAATACCTCCTGATACTTAGTTTGTAAAATCATGGTAGATCCAGAATTCTGGGACAGAGGCCTGGCTTCCAGGGGT
TCGTCTTAAGTATGTTGGGGGAGACCAATTTGGACGTGTGAATGTGGTGATAGTGAGAGGGCTAGAAGCCCCTCAAAATT
GCAGATGTCAGCGTCCAGATGTGCAGCTCCAGCAGAGCAGGAATGTATCAGAGACAGTGGTGAATGTGCACCGCTACAGG
GCTCTGCTATGGAGCTGTTACCAGGAAGATTCTCAGTGTAAAGGTGGGTGGACTTTTAGGAGTAATGCAGCTGCCGTCAT
CTTTTGAAACGCAGCTCAATGCACCGCTGCATCCCAAGGTAGAAGGAAACTTCAATCAGTTTGCCTCTTCCCAAAAGAAC
CAATAATCAGATGAAAACAACTTAAAAGACCCTGGGGCATCCGGGTTCCACCCAATCAGCGAAAACACAAGGGCTCCTGC
TCCTGAC

ORF - retro_pabe_1265 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.41 %
Parental protein coverage: 81.54 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalVDLDPELMQKFSCLGTTDKDVLISEFQRLLGFQLNPAGCAFFLDMTNWNLQAAIGAYYDFESPNISVPSM
V.LDP.L.QKF.CLGTTDKDVLISEFQ.LLGFQLNP....FFLD.TNWNL..AIGA..D..SPNISVPSM
RetrocopyVGLDPGLVQKFGCLGTTDKDVLISEFQCLLGFQLNPDDSTFFLDTTNWNL-TAIGACCDSDSPNISVPSM
ParentalSFVEDVTIGEGESIPPDTQFVKTWRIQNSGAEAWPPGVCLKYVGGDQFGHVNMVMVRSLE-PQEIADVSV
SFVEDVT.GE.ESIPPDT.FVK.W.IQNSG.EAW.PGV.LKYVGGDQFG.VN.V.VR.LE.P..IADVSV
RetrocopySFVEDVTKGEAESIPPDT*FVKSW*IQNSGTEAWLPGVRLKYVGGDQFGRVNVVIVRGLE>PLKIADVSV
ParentalQMCSPSRAGMYQGQWRMCTATGLYYGDVIWVILSVEVGGLLGVTQQLSSFETEFNTQPHRKVEGNFNPFA
QMCS.SRAGMYQ.QW.MCTATGL.YG.V...ILSV.VGGLLGV.Q..SSFET..N...H.KVEGNFN.FA
RetrocopyQMCSSSRAGMYQRQW*MCTATGLCYGAVTRKILSVKVGGLLGVMQLPSSFETQLNAPLHPKVEGNFNQFA
ParentalSPQKNRQSDENNLKDRGGSEFDSISKNTWAPAPD
S.QKN..SDENNLKD.G.S.F..IS.NT.APAPD
RetrocopySSQKNQ*SDENNLKDPGASGFHPISENTRAPAPD

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 220 .17 RPM
SRP007412_cerebellum 0 .00 RPM 220 .83 RPM
SRP007412_heart 0 .00 RPM 60 .33 RPM
SRP007412_kidney 0 .00 RPM 111 .84 RPM
SRP007412_liver 0 .00 RPM 75 .04 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_1265 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_1265 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_1265 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000344931 retrocopy
Callithrix jacchus ENSCJAG000000153041 retrocopy
Homo sapiens ENSG000001968211 retrocopy
Gorilla gorilla ENSGGOG000000003881 retrocopy
Microcebus murinus ENSMICG000000134421 retrocopy
Macaca mulatta ENSMMUG000000228241 retrocopy
Nomascus leucogenys ENSNLEG000000083872 retrocopies
Otolemur garnettii ENSOGAG000000112641 retrocopy
Ochotona princeps ENSOPRG000000093501 retrocopy
Pongo abelii ENSPPYG00000016519 2 retrocopies
retro_pabe_1265 , retro_pabe_1928,
Pan troglodytes ENSPTRG000000180681 retrocopy



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