RetrogeneDB ID:

retro_ptro_954

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:14:19653147..19654961(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:XPO6
Ensembl ID:ENSPTRG00000007919
Aliases:XPO6, exportin-6
Description:None


Retrocopy-Parental alignment summary:






>retro_ptro_954
ATGGCATCTGAAGAAGCCTCTCTCAGGGCATTGGAAAGGCTGAAGACAGAACTTTTTCACGATGGTACGACCAATGAAAG
AAAACGTGAGATAGAGGAGCTTCTTAATAACTTTGCCCAGCAAATAGGAGCCTGGAGATTCTTCCTGTACTTTCTCTCCA
GCACTAGGAATGGCTATGTAATGATGTACAGTTTAACAGTTTTTGAGAATCTGATCAATAAAATGTGGCTTGGGGTCCCA
TCTCAGGATGAGATGGAAATCCACAGCTGACTGCCCAAACTCCTTTTGGCTCACCATAAAACCTTACCTTACTTTATCCA
GAGCAAGCTCTGCAAAGTTATTGTTGATATTGGACGTCAGGATTGGCCCATGTTCTACCATGACTGTTTTACTAACATTT
TGCAGTTGAACCAATCCCCTGTGACAACCCCCCTTGGGCCGATCATGTTGAAGACAACTTCAGAGGAGCTGGCTTGTCCC
CATGAGGACCTCAGTGTGACTTGGAAGGAGGAGTTGCAGAAGCTGCTACTGGACCAGGTGCAGACAGTGCTTGGGCTGCT
GACCGGTATCTTGGAGACTGTCTGGGACAAAGACAGTGTTACTGCTGCCACTCCACTACCCTCCCCGACCTCAGGAGAAA
GTGGTGACTTAACTGAGTAACCTGTTGCAGAGTCCTAGTTCAGCCAAACTGTTGAATCAGCCAATTCCCATCCTTGATGT
GGTGAGTGAGTATATCTGTTCCCTGGCCTTGGAGTGCCTGGCCCATCTCTTCAGTTGGATTCCTCTGTCTGCCGGCATCA
CCCCATCCCTCCTTACCACCACCTTCCACTTTGCGTGATTTGGCTGTGACATCCGTGCCAGAAAGATGGCGTCAGTTAAC
GGCAGCAGCCAGAACTGTGTCTCGGTTCAGGAGCGGAGCCGGCTGGGGGTCCCGGCCATGCCCTGCATCAATGAACTCAC
TTCCAAGAGCTGTGTGCCGATGGAATTCGAGGAGTATTTGCTGCTTATGTTCCAGCAGACTTTCTACCTCCTGCAGAAAA
TCACCAAGGATAACAATGCCCACACAGTGAAGAGCAGGCTAGAAGAGCTCGATGAGAGCTTTATTGAGAAGTTTACTGAC
TTTCTTTGGCTCTTTGTGAGTGTTCACCTAAGAAGAATCGAGTCTTACTCCCAGTTCCCTGTGGTGGAGTTTTTGACACT
TTTGTTCAAGTACACATTTCATCAGCCTACTCATGAAGGTTAATTCTCTTGTTTGGATACTGGACACTCTTTTTGGACTA
TCTGACAAATAAAATTAAAAGTCATCTTGAAGACAAGGAAGCAGTTCTCAACAGGTACGAAGATGCCCTGGTGCTCCTCC
CCACAGAGGTGTTGAATCAAATCCAGTTCAGATACAACCAGGCCAGCTGGAGGAGTTGGATGACGAGACTGTGGATGACG
ACCAGCAGATGGAGTGACAGCGGTACTTACGGCAGAGCTTGGAGGTGGCGGTCAAAGCGATGGAGCTCCTGCCCACGCAC
ACGTTGTCCACACTGTTCCCAGTTCTTCAGGGCAATTTAGAAGTTTATTTGGGATTACAGCAATTTATAGTTACTTCAGT
GTCAGGACACAGGTTGAACATCATGGCAGAGAACGACTGCTGGTGGCTGCACTGCTCCCTGAGAGACTTGAGCTCCCTGC
TGCAGGCCATGGGCCACCTGGCTGGGTACTTTATTGAGGATGTGTTTGCTGCATGGTTCAATGATGCCCTCACAGTTGTG
GAGAGGTTGGTCAAAGTCACTCTGTATGGATCTCAGATAAAGTTGTACAACATT

ORF - retro_ptro_954 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.97 %
Parental protein coverage: 53.78 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMASEEASLRALESLMTEFFHDCTTNERKREIEELLNNFAQQIGAWRFCLYFLSSTRNDYVMMYSLTVFEN
MASEEASLRALE.L.TE.FHD.TTNERKREIEELLNNFAQQIGAWRF.LYFLSSTRN.YVMMYSLTVFEN
RetrocopyMASEEASLRALERLKTELFHDGTTNERKREIEELLNNFAQQIGAWRFFLYFLSSTRNGYVMMYSLTVFEN
ParentalLINKMWLGVPSQDKMEIRSCLPKLLLAHHKTLPYFIRNKLCKVIVDIGRQDWPMFYHDFFTNILQLIQSP
LINKMWLGVPSQD.MEI.S.LPKLLLAHHKTLPYFI..KLCKVIVDIGRQDWPMFYHD.FTNILQL.QSP
RetrocopyLINKMWLGVPSQDEMEIHS*LPKLLLAHHKTLPYFIQSKLCKVIVDIGRQDWPMFYHDCFTNILQLNQSP
ParentalVTTPLGLIMLKTTSEELACPREDLSVARKEELRKLLLDQVQTVLGLLTGILETVWDKHSVTAATPPPSPT
VTTPLG.IMLKTTSEELACP.EDLSV..KEEL.KLLLDQVQTVLGLLTGILETVWDK.SVTAATP.PSPT
RetrocopyVTTPLGPIMLKTTSEELACPHEDLSVTWKEELQKLLLDQVQTVLGLLTGILETVWDKDSVTAATPLPSPT
ParentalSGESGDL-LSNLLQSPSSAKLLNQPIPILDVESEYICSLALECLAHLFSWIPLSASITPSLLTTIFHFAR
SGESGDL.LSNLLQSPSSAKLLNQPIPILDV.SEYICSLALECLAHLFSWIPLSA.ITPSLLTT.FHFA.
RetrocopySGESGDL>LSNLLQSPSSAKLLNQPIPILDVVSEYICSLALECLAHLFSWIPLSAGITPSLLTTTFHFA*
ParentalFGCDIRARKMASVNGSSQNCVSGQERGRLGVLAMSCINELMSKNCVPMEFEEYLLRMFQQTFYLLQKITK
FGCDIRARKMASVNGSSQNCVS.QER.RLGV.AM.CINEL.SK.CVPMEFEEYLL.MFQQTFYLLQKITK
RetrocopyFGCDIRARKMASVNGSSQNCVSVQERSRLGVPAMPCINELTSKSCVPMEFEEYLLLMFQQTFYLLQKITK
ParentalDNNAHTVKSRLEELDESYIEKFTDFLRLFVSVHLRRIESYSQFPVVEFLTLLFKYTFHQPTHEGYFSCLD
DNNAHTVKSRLEELDES.IEKFTDFL.LFVSVHLRRIESYSQFPVVEFLTLLFKYTFHQPTHEG.FSCLD
RetrocopyDNNAHTVKSRLEELDESFIEKFTDFLWLFVSVHLRRIESYSQFPVVEFLTLLFKYTFHQPTHEG*FSCLD
Parental-IWTLFLDYLTSKIKSRLGDKEAVLNRYEDALVLLLTEVLNRIQFRYNQA-QLEELDDETLDDDQQTEWQ
..WTLFLDYLT.KIKS.L.DKEAVLNRYEDALVLL.TEVLN.IQFRYNQA.QLEELDDET.DDDQQ.E.Q
Retrocopy<YWTLFLDYLTNKIKSHLEDKEAVLNRYEDALVLLPTEVLNQIQFRYNQA<QLEELDDETVDDDQQME*Q
ParentalRYLRQSLEVVAKVMELLPTHAFSTLFPVLQDNLEVYLGLQQFIVTSGSGHRLNITAENDCRRLHCSLRDL
RYLRQSLEV..K.MELLPTH..STLFPVLQ.NLEVYLGLQQFIVTS.SGHRLNI.AENDC..LHCSLRDL
RetrocopyRYLRQSLEVAVKAMELLPTHTLSTLFPVLQGNLEVYLGLQQFIVTSVSGHRLNIMAENDCWWLHCSLRDL
ParentalSSLLQAVGRLAEYFIGDVFAARFNDALTVVERLVKVTLYGSQIKLYNI
SSLLQA.G.LA.YFI.DVFAA.FNDALTVVERLVKVTLYGSQIKLYNI
RetrocopySSLLQAMGHLAGYFIEDVFAAWFNDALTVVERLVKVTLYGSQIKLYNI

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 103 .10 RPM
SRP007412_cerebellum 0 .22 RPM 70 .05 RPM
SRP007412_heart 0 .03 RPM 18 .16 RPM
SRP007412_kidney 0 .29 RPM 76 .44 RPM
SRP007412_liver 0 .10 RPM 61 .44 RPM
SRP007412_testis 1 .05 RPM 222 .46 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_954 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_954 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_954 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_1390
Gorilla gorilla retro_ggor_1078
Parental genes homology:
Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001691801 retrocopy
retro_hsap_1390,
Gorilla gorilla ENSGGOG000000056091 retrocopy
retro_ggor_1078,
Pan troglodytes ENSPTRG00000007919 1 retrocopy
retro_ptro_954 ,


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