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    KPNA1 karyopherin subunit alpha 1 [ Homo sapiens (human) ]

    Gene ID: 3836, updated on 3-Nov-2024

    Summary

    Official Symbol
    KPNA1provided by HGNC
    Official Full Name
    karyopherin subunit alpha 1provided by HGNC
    Primary source
    HGNC:HGNC:6394
    See related
    Ensembl:ENSG00000114030 MIM:600686; AllianceGenome:HGNC:6394
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RCH2; SRP1; IPOA5; NPI-1
    Summary
    The transport of molecules between the nucleus and the cytoplasm in eukaryotic cells is mediated by the nuclear pore complex (NPC), which consists of 60-100 proteins. Small molecules (up to 70 kD) can pass through the nuclear pore by nonselective diffusion while larger molecules are transported by an active process. The protein encoded by this gene belongs to the importin alpha family, and is involved in nuclear protein import. This protein interacts with the recombination activating gene 1 (RAG1) protein and is a putative substrate of the RAG1 ubiquitin ligase. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]
    Expression
    Ubiquitous expression in brain (RPKM 10.0), testis (RPKM 7.9) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See KPNA1 in Genome Data Viewer
    Location:
    3q21.1
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (122421902..122514939, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (125141131..125234261, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (122140749..122233786, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene HNF4 motif-containing MPRA enhancer 1/2 Neighboring gene mitochondrial matrix import factor 23 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:122102840-122103340 Neighboring gene family with sequence similarity 162 member A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20368 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20369 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:122134889-122135706 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:122135707-122136522 Neighboring gene WDR5B divergent transcript Neighboring gene WD repeat domain 5B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20373 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20374 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:122215008-122216207 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20376 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14641 Neighboring gene uncharacterized LOC107984000 Neighboring gene uncharacterized LOC105374071 Neighboring gene Sharpr-MPRA regulatory region 13157 Neighboring gene poly(ADP-ribose) polymerase family member 9

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 NL4-3 replication requires KPNA1 as replication is inhibited when KPNA1 is deleted through CRISPR/Cas9 genome editing PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, karyopherin alpha 1 (KPNA1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed
    Vpr vpr HIV-1 Vpr interacts with both karyopherin alpha 1 and alpha 2 to facilitate nuclear import of the HIV-1 preintegration complex, however conflicting reports indicate it may also be imported by other mechanisms independently of karyopherin alpha 1 and 2 PubMed
    vpr CAS regulates the NPI-1-mediated nuclear entry of full-length Vpr PubMed
    vpr Full-length HIV-1 Vpr is preferentially imported into nuclei by NPI-1 through its binding to the CAS-binding domain (residues 413-457) of NPI-1 PubMed
    vpr A small molecule hematoxylin, which suppresses Vpr-Importin alpha interaction, blocks Vpr nuclear entry in a dose-dependent manner PubMed
    vpr The nuclear import of Vpr is promoted by the addition of cytoplasmic extracts from macrophages but not of that from monocytes, and the nuclear import activity is lost with immunodepletion of importin alpha from the cytoplasmic extract PubMed
    vpr HIV-1 Vpr interacts with importin-alpha through alphaH1 (residues 17-34) and alphaH2 (residues 46-74); the interaction via alphaH1 is indispensable for the nuclear entry of Vpr, and residues 393-462 of importin-alpha promote entry of Vpr into the nucleus PubMed
    integrase gag-pol HIV-1 IN interacts with importin alpha by the BiFC assay and amino acids 161-173 in IN are required for the interaction with importin alpha PubMed
    gag-pol HIV-1 Rev disrupts both IN-TNPO3 and IN-importin alpha complexes PubMed
    gag-pol Some reports indicate a possible role for the interactions between karyopherin alpha and beta with HIV-1 integrase in the nuclear import of HIV-1 preintegration complexes (PIC), while other reports indicate integrase is not involved in PIC nuclear import PubMed
    gag-pol Karyopherin alpha binds to a bipartite nuclear localization signal in HIV-1 integrase (amino acids 186-189 and 211-219) PubMed
    gag-pol Karyopherin alpha and beta are reported to interact with HIV-1 integrase (IN) to facilitate nuclear import of IN, however a conflicting report indicates nuclear accumulation of IN does not involve karyopherin alpha, beta 1, or beta 2 mediated pathways PubMed
    matrix gag Nuclear import of HIV-1 preintegration complexes by karyopherin alpha is governed by phosphorylation of HIV-1 Matrix on tyrosine and serine, however the exact role of phosphorylation of the C-terminal tyrosine of Matrix has been debated PubMed
    gag HIV-1 Matrix increases intracellular ATP content, an effect hypothesized to support the ATP-dependent nuclear import of HIV-1 preintegration complexes by karyopherin alpha PubMed
    gag HIV-1 Vpr increases the affinity of karyopherin alpha to the HIV-1 Matrix nuclear localization signal, thereby mediating the nuclear import of HIV-1 preintegration complexes PubMed
    gag Hsp70 stimulates the binding of HIV-1 matrix to karyopherin alpha PubMed
    gag The role of HIV-1 Matrix during nuclear import of the HIV-1 preintegration complex has been controversial, however recent understanding indicates HIV-1 Matrix and Vpr proteins act in concert to facilitate nuclear import by binding to karyopherin alpha PubMed
    gag HIV-1 Matrix contains two nuclear localization signals (NLS) spanning amino acids 24-33 and 110-114 that are recognized by karyopherin alpha and mediate the nuclear import of HIV-1 preintegration complexes PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables nuclear import signal receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables nuclear import signal receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables nuclear localization sequence binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of NLS-dependent protein nuclear import complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    located_in cytoplasm TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in dendrite ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    part_of nuclear pore TAS
    Traceable Author Statement
    more info
    PubMed 
    is_active_in nucleoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    importin subunit alpha-5
    Names
    RAG cohort protein 2
    SRP1-beta
    importin alpha 5
    importin subunit alpha-1
    importin-alpha-S1
    karyopherin alpha 1 (importin alpha 5)
    nucleoprotein interactor 1
    recombination activating gene cohort 2

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_002264.4NP_002255.3  importin subunit alpha-5

      See identical proteins and their annotated locations for NP_002255.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) lacks an alternate exon compared to variant 2 and represents the protein-coding transcript.
      Source sequence(s)
      AC083798, BC003009, DA308391, U20620
      Consensus CDS
      CCDS3013.1
      UniProtKB/Swiss-Prot
      D3DN93, P52294, Q6IBQ9, Q9BQ56
      UniProtKB/TrEMBL
      Q5BKZ2
      Related
      ENSP00000343701.6, ENST00000344337.11
      Conserved Domains (3) summary
      sd00044
      Location:88116
      HEAT; HEAT repeat [structural motif]
      sd00043
      Location:128154
      ARM; armadillo repeat [structural motif]
      cl25709
      Location:33516
      Arm_3; Atypical Arm repeat

    RNA

    1. NR_026698.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is the longer transcript and is likely not protein-coding.
      Source sequence(s)
      AC083798, BC003009, DA308391, DN991078, U20620

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      122421902..122514939 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005247437.5XP_005247494.1  importin subunit alpha-5 isoform X1

      See identical proteins and their annotated locations for XP_005247494.1

      UniProtKB/Swiss-Prot
      D3DN93, P52294, Q6IBQ9, Q9BQ56
      UniProtKB/TrEMBL
      Q5BKZ2
      Conserved Domains (3) summary
      sd00044
      Location:88116
      HEAT; HEAT repeat [structural motif]
      sd00043
      Location:128154
      ARM; armadillo repeat [structural motif]
      cl25709
      Location:33516
      Arm_3; Atypical Arm repeat
    2. XM_024453514.2XP_024309282.1  importin subunit alpha-5 isoform X1

      UniProtKB/Swiss-Prot
      D3DN93, P52294, Q6IBQ9, Q9BQ56
      UniProtKB/TrEMBL
      Q5BKZ2
      Conserved Domains (3) summary
      sd00044
      Location:88116
      HEAT; HEAT repeat [structural motif]
      sd00043
      Location:128154
      ARM; armadillo repeat [structural motif]
      cl25709
      Location:33516
      Arm_3; Atypical Arm repeat

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      125141131..125234261 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054346465.1XP_054202440.1  importin subunit alpha-5 isoform X1

    2. XM_054346466.1XP_054202441.1  importin subunit alpha-5 isoform X1