RetrogeneDB ID:

retro_pabe_467

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:1:176727201..176728088(-)
Located in intron of:ENSPPYG00000001340
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TUBB
Ensembl ID:ENSPPYG00000016419
Aliases:TUBB2A, TUBB, TUBB5
Description:Tubulin beta chain [Source:UniProtKB/Swiss-Prot;Acc:Q5R943]


Retrocopy-Parental alignment summary:






>retro_pabe_467
ATGAGGGAAATTGTGCATATCCAGGCCTGTCAGTGTGGCAACCAGACGGGTGCCAAGTGCTGGGATGTGATCAGTGATGA
ACGTGAAATCGACCCCACCAGCACCTAACATGGGGACAGCGACCTGCAGCTGGACTGTGTCTCCATGTACTACAGTGAAG
CCACAGATGGCAAATATGTTCCTTGTGCTATCCTGGTGGATCTAGAACCTGGGACCATGGACTCTGCTAGCTCAGGCCCT
TTTGGCCAGGTGTTTAAACCAGACAACTTTGTTTTTGGTCAATCTGGGGCATGCAACAACTGGGCCAAAGGCCACTACAT
AGAGGGGGCCAAGCTGGTTGATTCAGTTGTAGATGTGGTACAGGAGGAGTAAGAGAGCTGTGACTGCCTGCAGGGTTTCC
AGCTGACCCACTCAATGGGCTTTGGAATGGGTACTCTCTTTATCAGCAAGATCCAAGAAGAGTGCCCTGATTGCATCATG
AACACCTTCAGTGTGGTGCCTCCACCCAAAGTGTCTGACACTGTGGTCGGGCCCTATAACATCACCCTTTCCGTCCATCA
GTCGTTAGAGAACACGGATGAGACCTACTGCATTGACAATGAGGCCCTCTATGACATCTGCTTCCGCACTTTGAAGCTGA
CCACACCAAACTATGGGGACTTGAACCACCTTGTCTCAGCCACCATAAGCAGTGTTACCATCTGTCTCCGCTTCCCTGGC
CAGCTCAATGCTGACCTCCACAAGTTGGCAGTCAAACTGGTGCCCTTACCACGTCTCCACTACTTCATGGCTGGCTTTGC
CCTCTCACCAGCTGTGGAAGCCAGCAGCATCGAGCTTTCACGGTGCCCGAACTCATCTGGCAGGATTTCAATGCCATGAA
CATAATG

ORF - retro_pabe_467 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.07 %
Parental protein coverage: 67.57 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYVPRAILVDLEP
MREIVHIQA.QCGNQ.GAK.W.VISDE..IDPT.T.HGDSDLQLD..S.YY.EAT.GKYVP.AILVDLEP
RetrocopyMREIVHIQACQCGNQTGAKCWDVISDEREIDPTST*HGDSDLQLDCVSMYYSEATDGKYVPCAILVDLEP
ParentalGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKEAESCDCLQGFQLTHSLG
GTMDS..SGPFGQ.F.PDNFVFGQSGA.NNWAKGHY.EGA.LVDSV.DVV..E.ESCDCLQGFQLTHS.G
RetrocopyGTMDSASSGPFGQVFKPDNFVFGQSGACNNWAKGHYIEGAKLVDSVVDVVQEE*ESCDCLQGFQLTHSMG
ParentalGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSVHQLVENTDETYCIDNEALYDI
.G....MGTL.ISKI.EE.PD.IMNTFSVVP.PKVSDTVV.PYN.TLSVHQ..ENTDETYCIDNEALYDI
RetrocopyFG----MGTLFISKIQEECPDCIMNTFSVVPPPKVSDTVVGPYNITLSVHQSLENTDETYCIDNEALYDI
ParentalCFRTLKLTTPTYGDLNHLVSATMSGVTTCLRFPGQLNADLRKLAVNMVPFPRLHFFMPGFA-PLTSRGSQ
CFRTLKLTTP.YGDLNHLVSAT.S.VT.CLRFPGQLNADL.KLAV..VP.PRLH.FM.GFA.PLTS.GSQ
RetrocopyCFRTLKLTTPNYGDLNHLVSATISSVTICLRFPGQLNADLHKLAVKLVPLPRLHYFMAGFA<PLTSCGSQ
ParentalQYRALTVPELTQQVFDAKNMM
Q.RA.TVPEL..Q.F.A.N.M
RetrocopyQHRAFTVPELIWQDFNAMNIM

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 .06 RPM 297 .35 RPM
SRP007412_cerebellum 0 .49 RPM 155 .53 RPM
SRP007412_heart 0 .12 RPM 108 .46 RPM
SRP007412_kidney 0 .23 RPM 127 .75 RPM
SRP007412_liver 2 .02 RPM 135 .81 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_467 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_467 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_467 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_155
Pan troglodytes retro_ptro_151
Gorilla gorilla retro_ggor_244
Macaca mulatta retro_mmul_375

Parental genes homology:
Parental genes homology involve 8 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000069692 retrocopies
Canis familiaris ENSCAFG000000004431 retrocopy
Macaca mulatta ENSMMUG000000236842 retrocopies
Nomascus leucogenys ENSNLEG000000053481 retrocopy
Otolemur garnettii ENSOGAG000000322131 retrocopy
Ochotona princeps ENSOPRG000000147704 retrocopies
Pongo abelii ENSPPYG000000111801 retrocopy
Pongo abelii ENSPPYG00000016419 4 retrocopies



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