RetrogeneDB ID:

retro_hsap_2950

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:4:81000685..81002273(+)
Located in intron of:ENSG00000163297
Retrocopy
information
Ensembl ID:ENSG00000236530
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:KPNA2
Ensembl ID:ENSG00000182481
Aliases:KPNA2, IPOA1, QIP2, RCH1, SRP1alpha
Description:karyopherin alpha 2 (RAG cohort 1, importin alpha 1) [Source:HGNC Symbol;Acc:6395]


Retrocopy-Parental alignment summary:






>retro_hsap_2950
ATGTCTACCAACGAGAATGCTAATATACCAGTTGCCCGACTTAACAGATTCAAGAACAAGTGAAAAGACAGTACAGAAAT
GAGGTGTCGCAGAATAGAAGTCAATGTGAAGCTGAGGAAAGCTAAGAGGAATGACCAGATGCTGAAGAGGAGAAATGCAA
GCTCATTTCCTGATGTTGCTGCTTCTCCGCTGGAGAAAAACCGCAAAAACCAGGGCACTGTAAATTGGTCTGTTGATGAC
ATTGTCAAAGGCACAAATAGCAACAATATGGAAAGTCAGCTCCAAGCTACTCAAGCTGCCATGAAACTACTTTCTAGAGA
AAAACAGCCCCCCATAGGCAACATAATCTGGGCTGGTTTGATTCCAAAATTTGTGTCCTTCTTGGGCAGAACTGATTGTA
GTCCCATTCAGTTTGAATCTGCTTGGGCACTCGCTAACATTGCTTCTGGGACATCAGAATAAACCAAGGCTGTGGTAGAT
GGAGGTGCCATCCCAGCATTCATTTCTCTGTTAGCATCTCCCCATGCTCACATCAGTGAACAAGCTGTATGGGCTCTAGG
AAACATTGCAGGTGATGGTTTAGTTTTCCGAGACTTGGTTATTAAGTATGGTGCAGTTGACCCACTCTTGGCTCTTCTTG
CAGTTCCCGATATGTCATCTTTAGTATGTGGTTACTTATGTCATCTTACCTGGACACTTTCAATCCTCTGCTGCTACAAG
AATCCTGCACCCCAGTTAGATGCTGTTGAGCAAATTCTTTCTACCTTAGTTTGGCTCCTGCATCATGATGATCCAGAAGT
ATTAGCAGATAGCTGTTGGGCTATTTCCTACCTTACTGATGGTCCAAATAAACGAACTGACATGTTCTTGAAAATAGGAG
TTTTGCCCCAACTTGTGAAGCTTCTAGGAGCTTCTGAATTGCCAACTGTGACTCCTGCACTAAGACCCATAGGGAATATT
GTCACTGGTACAGATGAAGAGACTCAGGTTGTGATCGATGCAGGAGCTCTTGCTGTCTTTCCCAACCTGCTCATCAACTC
CAAAACTAACTTTCAGAAGGAAGGTACATGGACAATGTCAAACATCACAGCTGACCCTCAGGATGAGATACAGCAAGTTG
TGAATCATGGATTAGTCCCGTTCCTCACAATGTTCTCTCTAAGGCAGATTTTAAAGACACAAAAGGAAGCTGTATGGGGC
CATGACCAACTATACCAGTGGTGGAACAGTTGAACAGGCTGTATACCTCATTCATTGTGGCCTAATAAAACCATTGATGA
ATCTCTTAACTTCAAAAGATACCAAGGTTATTCTGGTTATCCTGGATGCCATTTCGAACATCTTTCAGGCTGCTGAGAAA
CTAGGTGAAACTGAGAAACTTAGTATAATGATTGAAGAATGTGGAGGCTTAGACAAAATTGAGGCTCTACAAAACCATGA
AAATGAGTCTGTGTATAAGGCTTTGTTAAGCTTAATTGAGAAGAATTTCTTGGTAGAGGAAGAGGAAGATCAAAATGCTG
TGCCAGAAACTAACTCTGAAGGCTGTACCTTCCAAGTTCAGAATGGGACTCCTGGAACGTTTAACTTT

ORF - retro_hsap_2950 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.28 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMSTNENANTPAARLHRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
MSTNENAN.P.ARL.RFKNK.KDSTEMR.RRIEVNV.LRKAK..DQMLKRRN.SSFPD.A.SPL..NR.N
RetrocopyMSTNENANIPVARLNRFKNK*KDSTEMRCRRIEVNVKLRKAKRNDQMLKRRNASSFPDVAASPLEKNRKN
ParentalQGTVNWSVDDIVKGINSSNVENQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGRTDCSPIQFES
QGTVNWSVDDIVKG.NS.N.E.QLQATQAA.KLLSREKQPPI.NII.AGLIPKFVSFLGRTDCSPIQFES
RetrocopyQGTVNWSVDDIVKGTNSNNMESQLQATQAAMKLLSREKQPPIGNIIWAGLIPKFVSFLGRTDCSPIQFES
ParentalAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKYGAVDPLL
AWAL.NIASGTSE.TKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDG.VFRDLVIKYGAVDPLL
RetrocopyAWALANIASGTSE*TKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGLVFRDLVIKYGAVDPLL
ParentalALLAVPDMSSLACGYLRNLTWTLSNLCRNKNPAPPIDAVEQILPTLVRLLHHDDPEVLADTCWAISYLTD
ALLAVPDMSSL.CGYL..LTWTLS.LC..KNPAP..DAVEQIL.TLV.LLHHDDPEVLAD.CWAISYLTD
RetrocopyALLAVPDMSSLVCGYLCHLTWTLSILCCYKNPAPQLDAVEQILSTLVWLLHHDDPEVLADSCWAISYLTD
ParentalGPNERIGMVVKTGVVPQLVKLLGASELPIVTPALRAIGNIVTGTDEQTQVVIDAGALAVFPSLLTNPKTN
GPN.R..M..K.GV.PQLVKLLGASELP.VTPALR.IGNIVTGTDE.TQVVIDAGALAVFP.LL.N.KTN
RetrocopyGPNKRTDMFLKIGVLPQLVKLLGASELPTVTPALRPIGNIVTGTDEETQVVIDAGALAVFPNLLINSKTN
ParentalIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLV-SVLSKADF-KTQKEAVW-AVTNYTSGGTVEQIVYLV
.QKE.TWTMSNITA..QD.IQQVVNHGLVPFL...VLSKADF.KTQKEAVW.A.TNYTSGGTVEQ.VYL.
RetrocopyFQKEGTWTMSNITADPQDEIQQVVNHGLVPFLT<NVLSKADF>KTQKEAVW>AMTNYTSGGTVEQAVYLI
ParentalHCGIIEPLMNLLTAKDTKIILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKA
HCG.I.PLMNLLT.KDTK.ILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKA
RetrocopyHCGLIKPLMNLLTSKDTKVILVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQNHENESVYKA
ParentalSLSLIEKYFSVEEEEDQNVVPETTSEGYTFQVQDGAPGTFNF
.LSLIEK.F.VEEEEDQN.VPET.SEG.TFQVQ.G.PGTFNF
RetrocopyLLSLIEKNFLVEEEEDQNAVPETNSEGCTFQVQNGTPGTFNF

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 19 .72 RPM
bodymap2_adrenal 0 .00 RPM 30 .72 RPM
bodymap2_brain 0 .00 RPM 47 .33 RPM
bodymap2_breast 0 .00 RPM 25 .14 RPM
bodymap2_colon 0 .00 RPM 22 .66 RPM
bodymap2_heart 0 .00 RPM 22 .50 RPM
bodymap2_kidney 0 .00 RPM 37 .04 RPM
bodymap2_liver 0 .00 RPM 21 .29 RPM
bodymap2_lung 0 .00 RPM 33 .77 RPM
bodymap2_lymph_node 0 .00 RPM 37 .04 RPM
bodymap2_ovary 0 .00 RPM 27 .47 RPM
bodymap2_prostate 0 .00 RPM 11 .66 RPM
bodymap2_skeletal_muscle 0 .20 RPM 12 .55 RPM
bodymap2_testis 0 .00 RPM 347 .33 RPM
bodymap2_thyroid 0 .00 RPM 20 .62 RPM
bodymap2_white_blood_cells 0 .00 RPM 29 .85 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2950 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2950 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2950 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2950 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2950 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_2044
Parental genes homology:
Parental genes homology involve 20 parental genes, and 50 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG000000191516 retrocopies
retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Homo sapiens ENSG00000182481 1 retrocopy
retro_hsap_2950 ,
Homo sapiens ENSG000001854671 retrocopy
retro_hsap_3337,
Gorilla gorilla ENSGGOG000000275352 retrocopies
retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Nomascus leucogenys ENSNLEG000000017493 retrocopies
retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pteropus vampyrus ENSPVAG000000049762 retrocopies
retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus ENSRNOG000000153291 retrocopy
retro_rnor_42,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,
Vicugna pacos ENSVPAG000000018553 retrocopies
retro_vpac_124, retro_vpac_162, retro_vpac_163,

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 = 0.03 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 .03 RPM
FIN_HG00183 0 .03 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 .02 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 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 .02 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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