RetrogeneDB ID:

retro_hsap_3337

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:5:75127088..75128578(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000251419
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KPNA7
Ensembl ID:ENSG00000185467
Aliases:None
Description:karyopherin alpha 7 (importin alpha 8) [Source:HGNC Symbol;Acc:21839]


Retrocopy-Parental alignment summary:






>retro_hsap_3337
TACTGAGGCAAAGATGCATCTCGGAGGCGACAGCAGAGGATAGCAGTCAGCCTGGAGCTCCGAAAGGCCAAGAAAGATGA
ACGGATCTTAAAGAAAAAGAATATCACCAGCTTCTGCCCTGATACAGCTTCCGAAAAACCAGCCAAAGAGGTGGCAGTCA
GCTTCACTCTGGTGAAATAATCAAAGGTGTGAATAGCTCAGATTCAGTCCCACGTTTCCAGGCCACCCAGACAGCCAGGA
AAATGCTATCCCAGGAAAAGAACCCCCTTCTGAAATTGATCATTGAAGCGGGCCTCATTCCCAGGATGGTAGAGTTCCTG
AAGTCATCACTTTACCCCTGCTTGCAGTTTGAGGCTGCCTGGGCCCTGACCAACATTGCTTCAGGGACTTCCGAGCAGAT
TTGAGCCGTGGTAGAAGGGGGACCCATCCAGCCCTTGATCAAGCTCCTGTCTTCCCCCAACGTGGCTGTGTGTGAACAGG
CAATGTGGGCTCTTGGTAATATACCCAGTGACGGCCTGGAGTTCAGAGATAATGTCATCTCAAGCAATGCCATCCCACAT
CTGCGGGCCTTGATTTCACCCACCCTACCAATCACATTTATGCGGAACATCACGTGGACCTGGTCGAACCTATGCCGAAA
AAAGACCCCGTACCCTTGCGAAACTGCAGTGAAGCAGATGCTGCGTGCCCTCTCACTCCTGCAGCGCCACCACAGCGAGG
TTCTCTCAGAAGCCTGCTGGTCACTGTCCTACCTCACCTACGGCTGCAAAGAGCTCATCGGCCAAGTGGATGACACAGGG
GTCCTGCTCAGGCTAGTAGCCCTCATGACCATCTCAGAACTCAATGTCTGGACCCCTTCTCTCCCGTACCATGGGGAACA
TTATCACAGGCACAAATGAACAGAAGCAGATGGCCATTGACGCGGGCATGCTGAACGTGCTGCCCCAGTTCCTGCAGCAC
AACAAGTCCTCCATCCAGGAGGCGGCCTGGGCCCTGAGCAACGTGGCGGCAGGGCCCTCTCACCACACCCAGCAGCTGCT
TGCCTACAACGTCTTGCCTCCCGTGGTGGCTCTGCTAAAAAAAATGGAGAATTTAAAGTCCAGAAAGAGGCTGTCTGGAC
GGTGGCTAACTTTGCAATGTGGGTCACCGTGGATAAGTTGATCCTCCACTCTGGGGTCCTGGAGCCACTGGCAAATCTGC
TCATTGCCCCAGATGTTAAAATTGTTCTCATCATCCTCGATGTAATCTCTTGCATCCTCCAGGCGGCAGAGAAACGGTCT
GAGAAGGAAATCCTATGTTTTCTGATAGAACAACTCGGTGGGATCGATAGAATTGAGGCTTTACAACTGCATGAGAACTG
TCAGATTGGCCAGTCTGCTTTGAACATCATTGAGAAGCACTTTGGTGAGGAAGAAGATGAGAGTCTAACTTTACTGAGCC
AAGTCCTAGACCAAGATTGTGAATTTATAGATTGTGAATGCTTAGCAAAA

ORF - retro_hsap_3337 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.35 %
Parental protein coverage: 96.9 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalYRGKDVSLRRQQRMAVSLELRKAKKDEQTLKRRNITSFCPDTPSEKTAKGVAVSLTL-GEIIKGVNSSDP
Y.GKD.S.RRQQR.AVSLELRKAKKDE..LK..NITSFCPDT.SEK.AK.VAVS.TL.GEIIKGVNSSD.
RetrocopyY*GKDASRRRQQRIAVSLELRKAKKDERILKKKNITSFCPDTASEKPAKEVAVSFTL<GEIIKGVNSSDS
ParentalVLCFQATQTARKMLSQEKNPPLKLVIEAGLIPRMVEFLKSSLYPCLQFEAAWALTNIASGTSEQTRAVVE
V..FQATQTARKMLSQEKNP.LKL.IEAGLIPRMVEFLKSSLYPCLQFEAAWALTNIASGTSEQ..AVVE
RetrocopyVPRFQATQTARKMLSQEKNPLLKLIIEAGLIPRMVEFLKSSLYPCLQFEAAWALTNIASGTSEQI*AVVE
ParentalGGAIQPLIELLSSSNVAVCEQAVWALGNIAGDGPEFRDNVITSNAIPHLLALISPTLPITFLRNITWTLS
GG.IQPLI.LLSS.NVAVCEQA.WALGNI..DG.EFRDNVI.SNAIPHL.ALISPTLPITF.RNITWT.S
RetrocopyGGPIQPLIKLLSSPNVAVCEQAMWALGNIPSDGLEFRDNVISSNAIPHLRALISPTLPITFMRNITWTWS
ParentalNLCRNKNPYPCDTAVKQILPALLHLLQHQDSEVLSDACWALSYLTDGSNKRIGQVVNTGVLPRLVVLMTS
NLCR.K.PYPC.TAVKQ.L.A.L.LLQ...SEVLS.ACW.LSYLT.G....IGQV..TGVL.RLV.LMT.
RetrocopyNLCRKKTPYPCETAVKQMLRA-LSLLQRHHSEVLSEACWSLSYLTYGCKELIGQVDDTGVLLRLVALMTI
ParentalSELNVLTPSL-RTVGNIVTGTDEQTQMAIDAGMLNVLPQLLQHNKPSIQKEAAWALSNVAAGPCHHIQQL
SELNV.TPSL.RT.GNI.TGT.EQ.QMAIDAGMLNVLPQ.LQHNK.SIQ.EAAWALSNVAAGP.HH.QQL
RetrocopySELNVWTPSL>RTMGNIITGTNEQKQMAIDAGMLNVLPQFLQHNKSSIQ-EAAWALSNVAAGPSHHTQQL
ParentalLAYDVLPPLVALLKNGE-FKVQK-EAVWMVANFATGATMDQLIQLVHSGVLEPLVNLLTAPDVKIVLIIL
LAY.VLPP.VAL....E..K..K.EAVW.VANFA...T.D.LI...HSGVLEPL.NLL.APDVKIVLIIL
RetrocopyLAYNVLPPVVALXXXXENLKSRK<EAVWTVANFAMWVTVDKLI--LHSGVLEPLANLLIAPDVKIVLIIL
ParentalDVISCILQAAEKRSEKENLCLLIEELGGIDRIEALQLHENRQIGQSALNIIEKHFGEEEDESQTLLSQVI
DVISCILQAAEKRSEKE.LC.LIE.LGGIDRIEALQLHEN.QIGQSALNIIEKHFGEEEDES.TLLSQV.
RetrocopyDVISCILQAAEKRSEKEILCFLIEQLGGIDRIEALQLHENCQIGQSALNIIEKHFGEEEDESLTLLSQVL
ParentalDQDYEFIDYECLAK
DQD.EFID.ECLAK
RetrocopyDQDCEFIDCECLAK

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 0 .00 RPM
bodymap2_adrenal 0 .00 RPM 0 .16 RPM
bodymap2_brain 0 .00 RPM 0 .28 RPM
bodymap2_breast 0 .00 RPM 0 .06 RPM
bodymap2_colon 0 .00 RPM 0 .04 RPM
bodymap2_heart 0 .00 RPM 0 .04 RPM
bodymap2_kidney 0 .00 RPM 0 .00 RPM
bodymap2_liver 0 .00 RPM 0 .13 RPM
bodymap2_lung 0 .00 RPM 0 .47 RPM
bodymap2_lymph_node 0 .00 RPM 0 .00 RPM
bodymap2_ovary 0 .12 RPM 0 .37 RPM
bodymap2_prostate 0 .00 RPM 0 .33 RPM
bodymap2_skeletal_muscle 0 .00 RPM 0 .00 RPM
bodymap2_testis 0 .00 RPM 0 .09 RPM
bodymap2_thyroid 0 .00 RPM 0 .00 RPM
bodymap2_white_blood_cells 0 .00 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3337 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3337 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3337 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3337 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3337 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2142
Pongo abelii retro_pabe_2750
Parental genes homology:
Parental genes homology involve 15 parental genes, and 24 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000151252 retrocopies
retro_cfam_459, retro_cfam_861,
Choloepus hoffmanni ENSCHOG000000042431 retrocopy
retro_chof_805,
Callithrix jacchus ENSCJAG000000159431 retrocopy
retro_cjac_2964,
Equus caballus ENSECAG000000005541 retrocopy
retro_ecab_981,
Echinops telfairi ENSETEG000000000961 retrocopy
retro_etel_1548,
Homo sapiens ENSG000001824811 retrocopy
retro_hsap_2950,
Homo sapiens ENSG00000185467 1 retrocopy
retro_hsap_3337 ,
Mus musculus ENSMUSG000000387702 retrocopies
retro_mmus_2844, retro_mmus_3301,
Nomascus leucogenys ENSNLEG000000108271 retrocopy
retro_nleu_1680,
Otolemur garnettii ENSOGAG000000311063 retrocopies
retro_ogar_1289, retro_ogar_3237, retro_ogar_353,
Ochotona princeps ENSOPRG000000154342 retrocopies
retro_opri_1101, retro_opri_118,
Pongo abelii ENSPPYG000000173691 retrocopy
retro_pabe_2750,
Pan troglodytes ENSPTRG000000194462 retrocopies
retro_ptro_102, retro_ptro_2142,
Tupaia belangeri ENSTBEG000000090073 retrocopies
retro_tbel_1475, retro_tbel_3862, retro_tbel_3962,
Tursiops truncatus ENSTTRG000000029982 retrocopies
retro_ttru_1426, retro_ttru_430,

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 ) 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 .00 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 .00 RPM
TSI_NA20513 0 .00 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 .00 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 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

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





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