RetrogeneDB ID:

retro_hsap_1390

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:14:21189477..21191287(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000259144
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:XPO6
Ensembl ID:ENSG00000169180
Aliases:XPO6, EXP6, RANBP20
Description:exportin 6 [Source:HGNC Symbol;Acc:19733]


Retrocopy-Parental alignment summary:






>retro_hsap_1390
ATGGCATCTGAAGAAGCCCCTCTCAGAGCATTGGAAAGGCTGATGACAGAACTTTTTCACGATGGTACGACCAATGAAAG
AAAACGTGAGATAGAGGAGCTTCTTAATAACATTGCCCAGCAAATAGGAGCCTGGAGATTCTTCCTGTACTTTCTCTCCA
GCACTAGGAATGGCTATGTAATGATGTACAGTTTAACAGTTTTTGAGAATCTGATCAATAAAATGTGGCTTGGGGTCCCA
TCTCAGGATGAGATGGAAATCCACAGCTGACTGCCCAAACTCCTTTTGGCTCACCATAAAACCTTACCTTACTTTATCCA
GAGCAAGTTCTGCAAAGTTATTGTTGATATTGGACGTCAGGATCGGCCCATGTTCTACCATGACTTTTTTACTAACATTT
TGCAGTTGAACCAATCCCCTGTGACAACCCCCCTTGGGCCGATCATGTTGAAGACAACTTCAGAGGAGCTGGCTTGTCCC
CACGAGGACCTCAGTGTGGCTTGGAAGGAGGAGTTGCAGAAGCTGCCACTGGACCAGGTGCAGACAGTGCTTGGGCTGCT
GACCGCTATCTTGGGGACTGTCTGGGACAAACACAGTGTTACTGCTGCCACTCCACCACCCTCCCCGACAGGAGAAAGTG
GTGACTTACTGAGTAACCTGTGGCAGAGTCCTAGTTCAGCCAAACTGTTGAATCAGCCAATTCCCATCCTTGATGTGGTG
AGTGAGTATATCTGTTCCCTTGCCTTGGAGTGCCTAGCCCATCTCTTCAGTTGTATTCCTCTGTCTGCCGGCATCACCCC
ATCCCTCCTTACCACCACCTTCCACTTTGCGTGATTTGGCTGTGACATCCGTGCCAGAAAGATGGCGTCAGTTAACGGCA
GCAGCCAGAACTGTGTCTCGGTTCAGGAGCGGAGCCGGCCGGGGGTCCTGGCCATGCCCTGCATCAGTGAACTCATTTCC
AAGAGCTGTGTGCCGATGGAGTTCGAGGAGTATTTACTGCTTATGTTCCAGCAGACTTTCTACCTCCTGCAGAAGATCAC
CAAGGATAACAATGCCCACACAGTGAAGAGCAGGCTAGAAGAGCTCGATGAGAGCTTTATTGAGAAGTTTACTGACTTTC
TTTGGCTCTTTGTGAGTGTTCACCTAAGAAGAATCGAGTCTTACTCCCAGTTCTCTGTGGTGGAGTTTTTGACACTTTTG
TTCAAGTACACATTTCATCAGCCTACTCATGAAGGTTAATTCTCTTGTTTGGATACTGGACACTCTTTTTGGACTATCTG
ACAAATAAAATTAAAAGTCATCTTGAAGACAAGGAAGCAGTTCTCAACAGGTACGAAGATGCCCTGGTGCTCCTCCCCAC
AGAGGTGTTGAATCAAATCCAGTTCAGATACAACCAGGCCAGCTGGAGGAGTTGGATGACGAGACTCTGGATGACGATCA
GCAGATGGAGTGACAGCGGTACTTACGGCAGAGCTTGGAGGTGGCGGTCAAAGTGATGGAGCTCCTGCCCACGCACACGT
TGTCCACACTGTTCCCAGTTCTTCAGGGCAATTTAGAAGTTTATTTGGGATTACAGCAAGTTATAGTTACATCAGGGTCA
GGACACAGGTTGAACATCATGGCAGAGAACGACTGCTGGTGGCTGCACTGCTCCCTGAGAGACTTGAGCTCCCTGCTGCA
GGCCATGGGCCACCTGGCCGGGTACTTTATTGGGGATGTGTTTGCTGCATGGTTCAATGATGCCCTCACAGTTGTGGAGA
GTTTGGTCAAAGTCACTCTGTATGGATCTCAGATAAAGTTGTACAACATT

ORF - retro_hsap_1390 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.29 %
Parental protein coverage: 53.78 %
Number of stop codons detected: 4
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMASEEASLRALESLMTEFFHDCTTNERKREIEELLNNFAQQIGAWRFCLYFLSSTRNDYVMMYSLTVFEN
MASEEA.LRALE.LMTE.FHD.TTNERKREIEELLNN.AQQIGAWRF.LYFLSSTRN.YVMMYSLTVFEN
RetrocopyMASEEAPLRALERLMTELFHDGTTNERKREIEELLNNIAQQIGAWRFFLYFLSSTRNGYVMMYSLTVFEN
ParentalLINKMWLGVPSQDKMEIRSCLPKLLLAHHKTLPYFIRNKLCKVIVDIGRQDWPMFYHDFFTNILQLIQSP
LINKMWLGVPSQD.MEI.S.LPKLLLAHHKTLPYFI..K.CKVIVDIGRQD.PMFYHDFFTNILQL.QSP
RetrocopyLINKMWLGVPSQDEMEIHS*LPKLLLAHHKTLPYFIQSKFCKVIVDIGRQDRPMFYHDFFTNILQLNQSP
ParentalVTTPLGLIMLKTTSEELACPREDLSVARKEELRKLLLDQVQTVLGLLTGILETVWDKHSVTAATPPPSPT
VTTPLG.IMLKTTSEELACP.EDLSVA.KEEL.KL.LDQVQTVLGLLT.IL.TVWDKHSVTAATPPPSPT
RetrocopyVTTPLGPIMLKTTSEELACPHEDLSVAWKEELQKLPLDQVQTVLGLLTAILGTVWDKHSVTAATPPPSPT
ParentalSGESGDLLSNLLQSPSSAKLLNQPIPILDVESEYICSLALECLAHLFSWIPLSASITPSLLTTIFHFARF
.GESGDLLSNL.QSPSSAKLLNQPIPILDV.SEYICSLALECLAHLFS.IPLSA.ITPSLLTT.FHFA.F
Retrocopy-GESGDLLSNLWQSPSSAKLLNQPIPILDVVSEYICSLALECLAHLFSCIPLSAGITPSLLTTTFHFA*F
ParentalGCDIRARKMASVNGSSQNCVSGQERGRLGVLAMSCINELMSKNCVPMEFEEYLLRMFQQTFYLLQKITKD
GCDIRARKMASVNGSSQNCVS.QER.R.GVLAM.CI.EL.SK.CVPMEFEEYLL.MFQQTFYLLQKITKD
RetrocopyGCDIRARKMASVNGSSQNCVSVQERSRPGVLAMPCISELISKSCVPMEFEEYLLLMFQQTFYLLQKITKD
ParentalNNAHTVKSRLEELDESYIEKFTDFLRLFVSVHLRRIESYSQFPVVEFLTLLFKYTFHQPTHEGYFSCLD-
NNAHTVKSRLEELDES.IEKFTDFL.LFVSVHLRRIESYSQF.VVEFLTLLFKYTFHQPTHEG.FSCLD.
RetrocopyNNAHTVKSRLEELDESFIEKFTDFLWLFVSVHLRRIESYSQFSVVEFLTLLFKYTFHQPTHEG*FSCLD<
ParentalIWTLFLDYLTSKIKSRLGDKEAVLNRYEDALVLLLTEVLNRIQFRYNQA-QLEELDDETLDDDQQTEWQR
.WTLFLDYLT.KIKS.L.DKEAVLNRYEDALVLL.TEVLN.IQFRYNQA.QLEELDDETLDDDQQ.E.QR
RetrocopyYWTLFLDYLTNKIKSHLEDKEAVLNRYEDALVLLPTEVLNQIQFRYNQA<QLEELDDETLDDDQQME*QR
ParentalYLRQSLEVVAKVMELLPTHAFSTLFPVLQDNLEVYLGLQQFIVTSGSGHRLNITAENDCRRLHCSLRDLS
YLRQSLEV..KVMELLPTH..STLFPVLQ.NLEVYLGLQQ.IVTSGSGHRLNI.AENDC..LHCSLRDLS
RetrocopyYLRQSLEVAVKVMELLPTHTLSTLFPVLQGNLEVYLGLQQVIVTSGSGHRLNIMAENDCWWLHCSLRDLS
ParentalSLLQAVGRLAEYFIGDVFAARFNDALTVVERLVKVTLYGSQIKLYNI
SLLQA.G.LA.YFIGDVFAA.FNDALTVVE.LVKVTLYGSQIKLYNI
RetrocopySLLQAMGHLAGYFIGDVFAAWFNDALTVVESLVKVTLYGSQIKLYNI

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
bodymap2_adipose 0 .00 RPM 51 .92 RPM
bodymap2_adrenal 0 .04 RPM 79 .28 RPM
bodymap2_brain 0 .00 RPM 48 .01 RPM
bodymap2_breast 0 .00 RPM 45 .10 RPM
bodymap2_colon 0 .00 RPM 35 .71 RPM
bodymap2_heart 0 .00 RPM 15 .34 RPM
bodymap2_kidney 0 .00 RPM 44 .88 RPM
bodymap2_liver 0 .00 RPM 26 .26 RPM
bodymap2_lung 0 .00 RPM 60 .25 RPM
bodymap2_lymph_node 0 .00 RPM 81 .32 RPM
bodymap2_ovary 0 .12 RPM 69 .86 RPM
bodymap2_prostate 0 .14 RPM 47 .70 RPM
bodymap2_skeletal_muscle 0 .00 RPM 17 .61 RPM
bodymap2_testis 0 .79 RPM 96 .17 RPM
bodymap2_thyroid 0 .08 RPM 49 .49 RPM
bodymap2_white_blood_cells 0 .00 RPM 258 .28 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1390 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1390 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1390 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1390 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1390 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_954
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 ENSG00000169180 1 retrocopy
retro_hsap_1390 ,
Gorilla gorilla ENSGGOG000000056091 retrocopy
retro_ggor_1078,
Pan troglodytes ENSPTRG000000079191 retrocopy
retro_ptro_954,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 RPM
TSI_NA20513 0 .05 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .00 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .03 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .02 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





Copyright © RetrogeneDB 2014-2017