RetrogeneDB ID:

retro_ptro_1244

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:18:1998016..1998610(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CXADR
Ensembl ID:ENSPTRG00000013795
Aliases:None
Description:coxsackie virus and adenovirus receptor [Source:HGNC Symbol;Acc:2559]


Retrocopy-Parental alignment summary:






>retro_ptro_1244
ATGGCGCTCTTGCTGCGCTTCGTGCTCCTGTGCAGAGTCGCGGATTTCATCAGAGGTTGGAGTATCACTACTCCTGAGCA
GATGATTGAAAAAGCCAAAGGGGAAACTACCTATCTGCCATGCAAATTTACGCTTAGTCCTGAAGACCAGGGACCACTGG
ACATCGAGTGGCTGATATCACCAGCTGATAATCAGAAGGTGGATCAAGTGGTTATTTTATATTCTGGAAACAAAATTTAT
GATGATTACTATCCAGAATTGAAAGGCCGAGTACATTTTAAGAGTAATGATCTCAAATCTGGTGATGCATCAATAAATGT
ACTGAATTTACAGCTGTCAGATATTGGCACAGATCAGTGCAAAGTGAAAAAAGCTCCTGGTGTTGCAAATAAGAAGATTC
AGCTGGTAGTTCTTGGTAAGCCTTCAGGTACAAGATGTTATGTTGATGGTTCAGAAGAAATTGGAAGTGACTTTAAACTA
AAATGTGAACCAAAAGAAGGTTCACTTCCATTACAGTATGAGTGGCAAAAATTGTCTGACTCACAGAAAATGCCCACTTC
ATGGTTAGCAGAAATGACTTCATCTGTTATATCT

ORF - retro_ptro_1244 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.91 %
Parental protein coverage: 54.25 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALLLCFVLLCGVVDFARSLSITTPEEMIEKAKGETAYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
MALLL.FVLLC.V.DF.R..SITTPE.MIEKAKGET.YLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
RetrocopyMALLLRFVLLCRVADFIRGWSITTPEQMIEKAKGETTYLPCKFTLSPEDQGPLDIEWLISPADNQKVDQV
ParentalIILYSGDKIYDDYYPDLKGRVHFTSNDLKSGDASINVTNLQLSDIGTYQCKVKKAPGVANKKIHLVVLVK
.ILYSG.KIYDDYYP.LKGRVHF.SNDLKSGDASINV.NLQLSDIGT.QCKVKKAPGVANKKI.LVVL.K
RetrocopyVILYSGNKIYDDYYPELKGRVHFKSNDLKSGDASINVLNLQLSDIGTDQCKVKKAPGVANKKIQLVVLGK
ParentalPSGARCYVDGSEEIGSDFKIKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVIS
PSG.RCYVDGSEEIGSDFK.KCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVIS
RetrocopyPSGTRCYVDGSEEIGSDFKLKCEPKEGSLPLQYEWQKLSDSQKMPTSWLAEMTSSVIS

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 9 .54 RPM
SRP007412_cerebellum 0 .00 RPM 7 .17 RPM
SRP007412_heart 0 .00 RPM 14 .72 RPM
SRP007412_kidney 0 .00 RPM 13 .44 RPM
SRP007412_liver 0 .00 RPM 19 .35 RPM
SRP007412_testis 0 .53 RPM 11 .28 RPM
Pan troglodytes was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_ptro_1244 retrocopy.
Pan troglodytes was not studied using FANTOM5 data.
retro_ptro_1244 was not experimentally validated.


Parental genes homology:
Parental genes homology involve 6 parental genes, and 16 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000129751 retrocopy
Homo sapiens ENSG000001546396 retrocopies
Nomascus leucogenys ENSNLEG000000020632 retrocopies
Pongo abelii ENSPPYG000000112952 retrocopies
Pan troglodytes ENSPTRG00000013795 4 retrocopies
Sarcophilus harrisii ENSSHAG000000053091 retrocopy



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