RetrogeneDB ID:

retro_pabe_814

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:12:7896913..7898659(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:TBCCD1
Ensembl ID:ENSPPYG00000014379
Aliases:None
Description:TBCC domain containing 1 [Source:HGNC Symbol;Acc:25546]


Retrocopy-Parental alignment summary:






>retro_pabe_814
GAAGTGTGGCGGTGCGGCGCCTGCATTAGCAGGTATGCAAAGAAGCCTTTTCACCCAGATGTCCTTAGAGATAATATGGA
TCAGTCCAGAGTTCTCCTCTGGGTGAAAGCAGAACCCTTTATAGTGGGTGCCTTGCAGGTCCCCCCTCCATCCAAGTTTA
GTCTTCACTATCTCAGGAAGATATCCACCTATGTGCAAATCCGGGCCACAGAAGGAGCTTACCTGCACCTCTACTGGTCT
ACATGGAGGCACATCACTTGTGGGAAGCTGCAGTTGGCCAAGGACCTGGCGTGGCTTTACTTCGAAATATTTGATAGTCT
TTCAGTGGAGACACCTGAGGAGCACCTGGAATGGTCTGAGGTTCTGTCCAACTGCATGTCTGAGGAGGAAGTTGAAAAGC
AGAGAAATCAGCTTTCAGTGGACACGCTACAGTTTCTGCTCTTCTTATACATTCAAGAGTTGAACAAGGTCTCCCTAAGG
ACATCTTTGATTGGCGAAGAGTGGCCCAGTCCCAGAAACAGATCTCGGTCTCCTGACCTGACTGTAAAATCTAATTGTCA
TAATAAGAACTGGAATGATTACAGTCACCAAGCTTTTGTCTATGATCATCTGTCTGATCTCCTCGAGCTGCTTTTAGATC
CAGAACAACTCACTGCATCATTTCATTCAACCCATAGTAGTCTAGTGTCCCGAGAAGCTGTTGTGGTGCTCAGCTTCCTT
ACTGAAGGTACAATAAGTAGAGCCAGGAAGATCTATCCACTTCATGAACTTGCACTGTGGCAGCCACTGCATGCAGATAG
TGGCTTCTCGAAGATCTCTAAGACTTTCTCTTTCTACAAACCGGAAACCTGGTTGAGGTCCTGTTTGACTGGGAATCCAT
TTGGTACATCAGCTTGCCTCAAGTCTGGAAAGAAATTGGCTTGGGCTCATCAAGTTGAAGGGACCACCAAAAGAGCTAAG
ATTGCTTGTAATACTCATGTGGCCCCTAGGATGCACCAACTGGTAGTGATGAGCCAGGTTTACAAGCAGACACTGGCTAA
GAGCTCAGATACTCTGGTGGGAGCACATGTAAAGATTCATCATTGCAACGAATCTTTTATATATCTGCTCTCTCCCTTAT
GATCTGTAACAATTGAGAAGTGAAGGAATAGCATCTTTGTCTTGGGCCCTGTAGGGACTACACTTCACCTCCACAGTTGT
GACAATGTTAAAGTCATTGCTGTTTGCCATCGTTTGTCCATCTTTTCTACAGCAGGTTGCATCTGTCACATTCTGATGCC
TATGCGCCCACTTATTCTCTCTGGGAACCAAACAGTAACTTTTGCCCCTTTTCATACCCATTACCCAATGCTAGAGGACC
ATACGGCCAGGACTGGCCTTGCTACAGTGCCTAACTATTGGGATAATCCAATGGTTGTGTGCAGAGAGAACAGTGACACC
AGTGTCTTCCGGCTTTTACCACCTTGTGAATTCTATGTATTTATTATTCCCTTTGAAATGGAAGGGGACACAACAGAGAT
ACCCGGAGGTCTTCCATCTGTATATCAGAAAGCACTGGGTCAAAGAGAACAGAAGATACAGATCTGGCAGAAAACTGTAA
AGGAGGCTCATTTGACAAAGGATCAAAGGAAGCAGTTCCAGGTACTGGTAGAGAACAAGTTTTATGAATGGTTGATTAAT
ACAGGACATCACCAACAGCTGGACAGCCTTGTACCCCCTGCAGCAGGCTCCAAACAAGCAGCTGGA

ORF - retro_pabe_814 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.19 %
Parental protein coverage: 98.15 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalEVRRSGPCISRYAKKPFHPDVLRDNMDQSRVLLWVKAEPFIVGALQVPPPSKFSLHYLRKISTYVKIRAT
EV.R.G.CISRYAKKPFHPDVLRDNMDQSRVLLWVKAEPFIVGALQVPPPSKFSLHYLRKISTYV.IRAT
RetrocopyEVWRCGACISRYAKKPFHPDVLRDNMDQSRVLLWVKAEPFIVGALQVPPPSKFSLHYLRKISTYVQIRAT
ParentalEGAYPRLYWSTWRHIACGKLQLAKDLAWLYFEIFDSLSVKTPEERLEWSEVLSNCMSEEEVEKQRNQLSV
EGAY..LYWSTWRHI.CGKLQLAKDLAWLYFEIFDSLSV.TPEE.LEWSEVLSNCMSEEEVEKQRNQLSV
RetrocopyEGAYLHLYWSTWRHITCGKLQLAKDLAWLYFEIFDSLSVETPEEHLEWSEVLSNCMSEEEVEKQRNQLSV
ParentalDTLQFLLFLYIQQLNKVSLRTSLIGEEWPSPRNRSQSPDLTEKSNCHNKNWNDYSHQAFVCDHLSDLLEL
DTLQFLLFLYIQ.LNKVSLRTSLIGEEWPSPRNRS.SPDLT.KSNCHNKNWNDYSHQAFV.DHLSDLLEL
RetrocopyDTLQFLLFLYIQELNKVSLRTSLIGEEWPSPRNRSRSPDLTVKSNCHNKNWNDYSHQAFVYDHLSDLLEL
ParentalLLDPEQLTASFHSTHSSLVSREAVVALSFLIEGTISRARKIYPLHELALWQPLHADSGFSKISKTFSFYK
LLDPEQLTASFHSTHSSLVSREAVV.LSFL.EGTISRARKIYPLHELALWQPLHADSGFSKISKTFSFYK
RetrocopyLLDPEQLTASFHSTHSSLVSREAVVVLSFLTEGTISRARKIYPLHELALWQPLHADSGFSKISKTFSFYK
ParentalLETWLRSCLTGNPFGTSACLKSGKKLAWAHQVEGTTKRAKIACNTHVAPRMHRLVVMSQVYKQTLAKSSD
.ETWLRSCLTGNPFGTSACLKSGKKLAWAHQVEGTTKRAKIACNTHVAPRMH.LVVMSQVYKQTLAKSSD
RetrocopyPETWLRSCLTGNPFGTSACLKSGKKLAWAHQVEGTTKRAKIACNTHVAPRMHQLVVMSQVYKQTLAKSSD
ParentalTLVGAHVKIHRCNESFIYLLSPLRSVTIEKCRNSIFVLGPVGTTLHLHSCDNVKVIAVCHRLSISSTTAC
TLVGAHVKIH.CNESFIYLLSPL.SVTIEK.RNSIFVLGPVGTTLHLHSCDNVKVIAVCHRLSI.ST..C
RetrocopyTLVGAHVKIHHCNESFIYLLSPL*SVTIEK*RNSIFVLGPVGTTLHLHSCDNVKVIAVCHRLSIFSTAGC
ParentalIFHILTPTRPLILSGNQTVTFAPFHTHYPMLEDHMARTGLATVPNYWDNPMVVCRENSDTSVFRLLPPCE
I.HIL.P.RPLILSGNQTVTFAPFHTHYPMLEDH.ARTGLATVPNYWDNPMVVCRENSDTSVFRLLPPCE
RetrocopyICHILMPMRPLILSGNQTVTFAPFHTHYPMLEDHTARTGLATVPNYWDNPMVVCRENSDTSVFRLLPPCE
ParentalFYVFIIPFEMEGDTTEIPGGLPSVYQKALGQREQKIQIWQKTVKEAHLTKDQRKQFQVLVENKFYEWLIN
FYVFIIPFEMEGDTTEIPGGLPSVYQKALGQREQKIQIWQKTVKEAHLTKDQRKQFQVLVENKFYEWLIN
RetrocopyFYVFIIPFEMEGDTTEIPGGLPSVYQKALGQREQKIQIWQKTVKEAHLTKDQRKQFQVLVENKFYEWLIN
ParentalTGHRQQLDSLVPPAAGSKQAAG
TGH.QQLDSLVPPAAGSKQAAG
RetrocopyTGHHQQLDSLVPPAAGSKQAAG

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 .11 RPM 5 .86 RPM
SRP007412_cerebellum 0 .12 RPM 14 .23 RPM
SRP007412_heart 0 .09 RPM 3 .49 RPM
SRP007412_kidney 0 .03 RPM 6 .20 RPM
SRP007412_liver 0 .21 RPM 6 .43 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_814 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_814 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_814 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_954
Pan troglodytes retro_ptro_661
Macaca mulatta retro_mmul_784
Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Pongo abelii ENSPPYG00000014379 1 retrocopy
retro_pabe_814 ,


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