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

Gene ID: 3836, updated on 29-Mar-2020

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
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

Genomic context

See KPNA1 in Genome Data Viewer
Location:
3q21.1
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (122421902..122514939, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (122140748..122233786, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene HNF4 motif-containing MPRA enhancer 1/2 Neighboring gene coiled-coil domain containing 58 Neighboring gene family with sequence similarity 162 member A Neighboring gene uncharacterized LOC102723582 Neighboring gene WD repeat domain 5B Neighboring gene uncharacterized LOC107984000 Neighboring gene uncharacterized LOC105374071 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

NHGRI GWAS Catalog

Description
Common variants in the calcium-sensing receptor gene are associated with total serum calcium levels.
NHGRI GWA 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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
nuclear import signal receptor activity IEA
Inferred from Electronic Annotation
more info
 
nuclear localization sequence binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
NLS-bearing protein import into nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
apoptotic DNA fragmentation TAS
Traceable Author Statement
more info
 
intracellular transport of virus TAS
Traceable Author Statement
more info
 
modulation by virus of host process TAS
Traceable Author Statement
more info
 
postsynapse to nucleus signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of DNA recombination TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
dendrite ISS
Inferred from Sequence or Structural Similarity
more info
 
glutamatergic synapse IEA
Inferred from Electronic Annotation
more info
 
host cell nucleus IEA
Inferred from Electronic Annotation
more info
 
nuclear pore IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
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)

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
    P52294
    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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_005247437.4XP_005247494.1  importin subunit alpha-5 isoform X1

    See identical proteins and their annotated locations for XP_005247494.1

    UniProtKB/Swiss-Prot
    P52294
    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_017006363.1XP_016861852.1  importin subunit alpha-5 isoform X3

    UniProtKB/TrEMBL
    B3KXZ2
    Conserved Domains (4) summary
    cd00020
    Location:52166
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam00514
    Location:240
    Arm; Armadillo/beta-catenin-like repeat
    pfam16186
    Location:265309
    Arm_3; Atypical Arm repeat
    sd00043
    Location:172208
    ARM; armadillo repeat [structural motif]
  3. XM_017006364.1XP_016861853.1  importin subunit alpha-5 isoform X3

    UniProtKB/TrEMBL
    B3KXZ2
    Conserved Domains (4) summary
    cd00020
    Location:52166
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam00514
    Location:240
    Arm; Armadillo/beta-catenin-like repeat
    pfam16186
    Location:265309
    Arm_3; Atypical Arm repeat
    sd00043
    Location:172208
    ARM; armadillo repeat [structural motif]
  4. XM_011512795.3XP_011511097.1  importin subunit alpha-5 isoform X2

    Conserved Domains (5) summary
    cd00020
    Location:59180
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam01749
    Location:143
    IBB; Importin beta binding domain
    pfam13646
    Location:67176
    HEAT_2; HEAT repeats
    pfam16186
    Location:405449
    Arm_3; Atypical Arm repeat
    sd00043
    Location:6793
    ARM; armadillo repeat [structural motif]
  5. XM_011512797.3XP_011511099.1  importin subunit alpha-5 isoform X3

    See identical proteins and their annotated locations for XP_011511099.1

    UniProtKB/TrEMBL
    B3KXZ2
    Conserved Domains (4) summary
    cd00020
    Location:52166
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam00514
    Location:240
    Arm; Armadillo/beta-catenin-like repeat
    pfam16186
    Location:265309
    Arm_3; Atypical Arm repeat
    sd00043
    Location:172208
    ARM; armadillo repeat [structural motif]
  6. XM_024453514.1XP_024309282.1  importin subunit alpha-5 isoform X1

    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
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