RetrogeneDB ID:

retro_ptro_1602

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:2A:60267047..60268704(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KLHL5
Ensembl ID:ENSPTRG00000015989
Aliases:None
Description:kelch-like family member 5 [Source:HGNC Symbol;Acc:6356]


Retrocopy-Parental alignment summary:






>retro_ptro_1602
AGCCCGACGCGGACTTCCAATAGTAGTCAGACATTATCATCCTGTCATACTATGGAGCCATGTACATCAGATGAATTTTT
CCAAGCCCTTAATCATGCCGAGCAAACATTTAAAAAAATGGAAAACTATTTGAGACATAAACAGTTGTGCGATGTAATTT
TAGTCGCTGGTGATCGCAGAATTCCAGCTCACAGATTGGTGCTCTCCTCTGTCTCAGACTATTTTGCTGCCATGTTTACT
AATGATGTCAGAGAGGCAAGACAAGAAGAAATAAAAATGGAAGGTGTAGAACCAAATTCATTGTGGTCCTTGATCCAGTA
TGCTTATACAGGCCGCCTTGAATTAAAAGAAGATAATATTGAGTGCCTGTTATCTACAGCTTGCCTTCTTCAGCTTTCAC
AGGTTGTAGAAGCATGCTGTAAGTTTTTAATGAAACAGCTTCATCCATCCAACTGTCTTGGAATTCGTTCTTTTGCTGAT
GCCCAAGGTTGTACAGATTTGCATAAAGTGGCTCACAATTATACTATGGATCATTTCATGGAAGTAATCAGAAACCAGGA
ATTTGTATTATTACCAGCCAGTGAAATTGCAAAGCTCTTGGCTAGTGATGACATGAACATTCCTAATGAGGAGACAATAT
TGAATGCACTTCTTACTTGGGTCCGTCATGATTTGGAACAGAGACGGAAAGATCTAAGTAAACTTTTGGCTTATATTAGG
CTACCTCTTCTTGCACCACAGTTCCTGGCAGACATGGAAAATAATGCACTTTTTCGGGATGATATAGAATGTCAGAAACT
CATTATGGAAGCAATGAAGTACCATTTATTACCAGAGAGACGACCCATGTTACAAAGTCCTCGGACAAAACCTAGGAAGT
CAACTGTTGGTACATTATTTGCAGTTGGGGGAATGGATTCAACAAAAGGAGCAACAAGCATTTGAAAGTATGACTTCCGT
ACAAATATGTGGACTCCAGTAACAAATATGAATGGGAGGAGGCTACAGTCCGGTGGTCCAGTGCTAGATGACAAACTGTA
TGTGGTTGGAGGAAGAGATGGACTGAAGACTTTGAATACTGTAGAGTGCTACAACCCCAAAACAAAAACTTGGAGTGTGA
TGCCACCTATGTCCACACATAGACATGGCCTTGGTGTGGCTGTACTGGAAGGTCCCATGTATGCCGTAGGAGGACATGAT
GGCTGGAGCTATCTGAACACAGTGGAAAGATGGGACCCTCAGGCTCGCCAGTGGAATTTTGTTGCCACTATGTCTACCCC
TAGGAGTACAGTAGGTGTGGCAGTACTAAGTGGAAAACTTTATGCAGTTGGTGGTCGTGATGGAAGTTCTTGTCTCAAAT
CAGTAGAATGTTTTGATCCTCATACTACTAAGTGGACACTGTGTGCACAGATGTCAAAAAGGAGAGGTGGCGTAGGAGTG
ACGACCTGGAATGGACTGCTGTATGCTATAGGGGGGCACGATGCTCCCGCATCCAACTTGACTTCCAGACTCTCAGACTG
TGTGTAAAGATATGATCCCAAAACAGACATGTGGACTGCAGTAGCATCCATGAGCATCAGCAGAGATGCAGTCGGGGTCT
GTTTACTTGGTGATAAAGTTAATATGCTTGTTGGGGGGTTATGATGGACAGGCATAC

ORF - retro_ptro_1602 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.11 %
Parental protein coverage: 72.98 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalSSCRTSNSSQTLSSCHTMEPCTSDEFFQALNHAEQTFKKMENYLRHKQLCDVILVAGDRRIPAHRLVLSS
S..RTSNSSQTLSSCHTMEPCTSDEFFQALNHAEQTFKKMENYLRHKQLCDVILVAGDRRIPAHRLVLSS
RetrocopySPTRTSNSSQTLSSCHTMEPCTSDEFFQALNHAEQTFKKMENYLRHKQLCDVILVAGDRRIPAHRLVLSS
ParentalVSDYFAAMFTNDVREARQEEIKMEGVEPNSLWSLIQYAYTGRLELKEDNIECLLSTACLLQLSQVVEACC
VSDYFAAMFTNDVREARQEEIKMEGVEPNSLWSLIQYAYTGRLELKEDNIECLLSTACLLQLSQVVEACC
RetrocopyVSDYFAAMFTNDVREARQEEIKMEGVEPNSLWSLIQYAYTGRLELKEDNIECLLSTACLLQLSQVVEACC
ParentalKFLMKQLHPSNCLGIRSFADAQGCTDLHKVAHNYTMEHFMEVIRNQEFVLLPASEIAKLLASDDMNIPNE
KFLMKQLHPSNCLGIRSFADAQGCTDLHKVAHNYTM.HFMEVIRNQEFVLLPASEIAKLLASDDMNIPNE
RetrocopyKFLMKQLHPSNCLGIRSFADAQGCTDLHKVAHNYTMDHFMEVIRNQEFVLLPASEIAKLLASDDMNIPNE
ParentalETILNALLTWVRHDLEQRRKDLSKLLAYIRLPLLAPQFLADMENNALFRDDIECQKLIMEAMKYHLLPER
ETILNALLTWVRHDLEQRRKDLSKLLAYIRLPLLAPQFLADMENNALFRDDIECQKLIMEAMKYHLLPER
RetrocopyETILNALLTWVRHDLEQRRKDLSKLLAYIRLPLLAPQFLADMENNALFRDDIECQKLIMEAMKYHLLPER
ParentalRPMLQSPRTKPRKSTVGTLFAVGGMDSTKGATSIEKYDLRTNMWTPVANMNGRRLQFGVAVLDDKLYVVG
RPMLQSPRTKPRKSTVGTLFAVGGMDSTKGATSI.KYD.RTNMWTPV.NMNGRRLQ.G..VLDDKLYVVG
RetrocopyRPMLQSPRTKPRKSTVGTLFAVGGMDSTKGATSI*KYDFRTNMWTPVTNMNGRRLQSGGPVLDDKLYVVG
ParentalGRDGLKTLNTVECYNPKTKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVERWDPQARQWNF
GRDGLKTLNTVECYNPKTKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVERWDPQARQWNF
RetrocopyGRDGLKTLNTVECYNPKTKTWSVMPPMSTHRHGLGVAVLEGPMYAVGGHDGWSYLNTVERWDPQARQWNF
ParentalVATMSTPRSTVGVAVLSGKLYAVGGRDGSSCLKSVECFDPHTNKWTLCAQMSKRRGGVGVTTWNGLLYAI
VATMSTPRSTVGVAVLSGKLYAVGGRDGSSCLKSVECFDPHT.KWTLCAQMSKRRGGVGVTTWNGLLYAI
RetrocopyVATMSTPRSTVGVAVLSGKLYAVGGRDGSSCLKSVECFDPHTTKWTLCAQMSKRRGGVGVTTWNGLLYAI
ParentalGGHDAPASNLTSRLSDCVERYDPKTDMWTAVASMSISRDAVGVCLLGDKL-YAVG-GYDGQAY
GGHDAPASNLTSRLSDCV.RYDPKTDMWTAVASMSISRDAVGVCLLGDK....VG.GYDGQAY
RetrocopyGGHDAPASNLTSRLSDCV*RYDPKTDMWTAVASMSISRDAVGVCLLGDKVNMLVG>GYDGQAY

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 1 .07 RPM 23 .15 RPM
SRP007412_cerebellum 0 .14 RPM 37 .50 RPM
SRP007412_heart 0 .09 RPM 21 .66 RPM
SRP007412_kidney 0 .10 RPM 29 .42 RPM
SRP007412_liver 0 .26 RPM 64 .39 RPM
SRP007412_testis 0 .21 RPM 41 .94 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_1602 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1602 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1602 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Pan troglodytes ENSPTRG000000018611 retrocopy
retro_ptro_1483,
Pan troglodytes ENSPTRG00000015989 1 retrocopy
retro_ptro_1602 ,


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