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RANBP3 RAN binding protein 3 [ Homo sapiens (human) ]

Gene ID: 8498, updated on 3-Apr-2024

Summary

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Official Symbol
RANBP3provided by HGNC
Official Full Name
RAN binding protein 3provided by HGNC
Primary source
HGNC:HGNC:9850
See related
Ensembl:ENSG00000031823 MIM:603327; AllianceGenome:HGNC:9850
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
Summary
This gene encodes a protein with a RanBD1 domain that is found in both the nucleus and cytoplasm. This protein plays a role in nuclear export as part of a heteromeric complex. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 18.0), lung (RPKM 13.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
19p13.3
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (5916139..5978140, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (5903579..5965589, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (5916150..5978151, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5892267-5893073 Neighboring gene MPRA-validated peak3300 silencer Neighboring gene Sharpr-MPRA regulatory region 9916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13817 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9938 Neighboring gene NADH:ubiquinone oxidoreductase subunit A11 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13818 Neighboring gene vimentin type intermediate filament associated coiled-coil protein Neighboring gene calcyphosine Neighboring gene ReSE screen-validated silencer GRCh37_chr19:5939785-5939965 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5944489-5945129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5952179-5952738 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:5953075-5954274 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5957025-5957534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5958162-5958810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5959460-5960108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:5960757-5961406 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13819 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9939 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5962704-5963351 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5963485-5964036 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:5964037-5964587 Neighboring gene Sharpr-MPRA regulatory region 310 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9941 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9942 Neighboring gene RANBP3 divergent transcript Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6015021-6015520 Neighboring gene regulatory factor X2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:6018397-6018898 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9943 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:6065893-6066394 Neighboring gene ribosomal protein L32 pseudogene 37

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Ran-binding protein 3 is associated with human spermatogenesis and male infertility. Tang W, et al. Andrologia, 2020 Mar. PMID 31833110
  2. Crystal structure of importin-α3 bound to the nuclear localization signal of Ran-binding protein 3. Koyama M, et al. Biochem Biophys Res Commun, 2017 Sep 23. PMID 28760339
  3. RanBP3 Regulates Melanoma Cell Proliferation via Selective Control of Nuclear Export. Pathria G, et al. J Invest Dermatol, 2016 Jan. PMID 26763446
  4. The role of Ran-binding protein 3 during influenza A virus replication. Predicala R, et al. J Gen Virol, 2013 May. PMID 23303829
  5. Ran-binding protein 3 phosphorylation links the Ras and PI3-kinase pathways to nucleocytoplasmic transport. Yoon SO, et al. Mol Cell, 2008 Feb 15. PMID 18280241, Free PMC Article

See all (61) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Ran-binding protein 3 is associated with human spermatogenesis and male infertility.
    Title: Ran-binding protein 3 is associated with human spermatogenesis and male infertility.
  2. Computational docking simulation indicates that phosphorylation of RanBP3 at Ser58 could potentially stabilize the association of RanBP3 with importin-alpha through interactions between the phosphate moiety of phospho-Ser58 of RanBP3 and a cluster of basic residues (Arg96 and Lys97 in importin-alpha3) on armadillo repeat 1 of importin-alpha.
    Title: Crystal structure of importin-α3 bound to the nuclear localization signal of Ran-binding protein 3.
  3. RANBP3 regulates melanoma cell proliferation and probably a potential target for molecular targeted therapy.
    Title: RanBP3 Regulates Melanoma Cell Proliferation via Selective Control of Nuclear Export.
  4. RanBP3 is involved in vRNP nuclear export. The function of RanBP3 during vRNP nuclear export is regulated by phosphorylation at Ser58. RanBP3 phosphorylation is modulated by both PI3K/Akt and Ras/ERK/RSK pathways in the late phase of viral infection.
    Title: The role of Ran-binding protein 3 during influenza A virus replication.
  5. Crystal structure of the Ran-binding domain (RBD) from RanBP3 and compare it to RBD structures from RanBP1 and RanBP2 in complex with Ran and CRM1.
    Title: Insights into the function of the CRM1 cofactor RanBP3 from the structure of its Ran-binding domain.
  6. RanBP3 directly recognizes dephosphorylated Smad2/3, which results from the activity of nuclear Smad phosphatases, and mediates nuclear export of Smad2/3 in a Ran-dependent manner.
    Title: Nuclear export of Smad2 and Smad3 by RanBP3 facilitates termination of TGF-beta signaling.
  7. RANBP3 phosphorylation links the Ras and PI3-kinase pathways to nucleocytoplasmic transport.
    Title: Ran-binding protein 3 phosphorylation links the Ras and PI3-kinase pathways to nucleocytoplasmic transport.
  8. A multifunctional domain in CRM1 (exportin 1) mediates RanBP3 binding and multimerization of human T-cell leukemia virus type 1 Rex protein.
    Title: A multifunctional domain in human CRM1 (exportin 1) mediates RanBP3 binding and multimerization of human T-cell leukemia virus type 1 Rex protein.
  9. RanBP3 stimulates export by enhancing the affinity of Crm1 for Ran-GTP and cargo.
    Title: Ran-binding protein 3 links Crm1 to the Ran guanine nucleotide exchange factor.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • DKFZp586I1520

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to GTPase activator activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables R-SMAD binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein export from nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of nuclear pore IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
ran-binding protein 3
Names
epididymis secretory sperm binding protein

NCBI Reference Sequences (RefSeq)

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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_001300865.2 → NP_001287794.1  ran-binding protein 3 isoform 4

    See identical proteins and their annotated locations for NP_001287794.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks an alternate in-frame exon and uses an alternate in-frame splice site in another exons, in the 5' coding region, compared to variant RANBP3-d. It encodes isoform 4, which is shorter than isoform RANBP3-d.
    Source sequence(s)
    AK025300, AK301942, AK314343, BM786367
    Consensus CDS
    CCDS74268.1
    UniProtKB/TrEMBL
    B7Z7F3, Q308M8
    Related
    ENSP00000465085.1, ENST00000591092.5
    Conserved Domains (1) summary
    cd13180
    Location:320 → 435
    RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

  2. NM_003624.3 → NP_003615.2  ran-binding protein 3 isoform RANBP3-a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (RANBP3-a) uses an alternate in-frame splice site in the 5' coding region, compared to variant RANBP3-d, resulting in a shorter protein (isoform RANBP3-a).
    Source sequence(s)
    AK025300, AK222990, BM786367, CB306615
    Consensus CDS
    CCDS45935.1
    UniProtKB/TrEMBL
    Q53GE1
    Related
    ENSP00000404837.1, ENST00000439268.6
    Conserved Domains (1) summary
    cd13180
    Location:388 → 503
    RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

  3. NM_007320.3 → NP_015559.2  ran-binding protein 3 isoform RANBP3-b

    See identical proteins and their annotated locations for NP_015559.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (RANBP3-b) lacks an alternate in-frame exon, compared to variant RANBP3-d, resulting in a shorter protein (isoform RANBP3-b), compared to isoform RANBP3-d.
    Source sequence(s)
    AK025300, AK314343
    Consensus CDS
    CCDS42477.1
    UniProtKB/TrEMBL
    Q308M8
    Related
    ENSP00000034275.7, ENST00000034275.12
    Conserved Domains (1) summary
    cd13180
    Location:325 → 440
    RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

  4. NM_007322.3 → NP_015561.1  ran-binding protein 3 isoform RANBP3-d

    See identical proteins and their annotated locations for NP_015561.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (RANBP3-d) represents the longest transcript and encodes the longest isoform (RANBP3-d).
    Source sequence(s)
    AK025300, BM786367
    Consensus CDS
    CCDS42478.1
    UniProtKB/Swiss-Prot
    B2RAT8, O60405, O75759, O75760, Q9BT47, Q9H6Z4, Q9UG74
    UniProtKB/TrEMBL
    Q53GE1
    Related
    ENSP00000341483.5, ENST00000340578.10
    Conserved Domains (1) summary
    cd13180
    Location:393 → 508
    RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    5916139..5978140 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047439570.1 → XP_047295526.1  ran-binding protein 3 isoform X2

  2. XM_047439569.1 → XP_047295525.1  ran-binding protein 3 isoform X1

  3. XM_011528394.2 → XP_011526696.1  ran-binding protein 3 isoform X3

    See identical proteins and their annotated locations for XP_011526696.1

    Conserved Domains (1) summary
    cd13180
    Location:112 → 227
    RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

  4. XM_011528393.2 → XP_011526695.1  ran-binding protein 3 isoform X3

    See identical proteins and their annotated locations for XP_011526695.1

    Conserved Domains (1) summary
    cd13180
    Location:112 → 227
    RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

  5. XM_047439575.1 → XP_047295531.1  ran-binding protein 3 isoform X3

  6. XM_047439577.1 → XP_047295533.1  ran-binding protein 3 isoform X3

  7. XM_047439571.1 → XP_047295527.1  ran-binding protein 3 isoform X3

  8. XM_047439576.1 → XP_047295532.1  ran-binding protein 3 isoform X3

  9. XM_047439574.1 → XP_047295530.1  ran-binding protein 3 isoform X3

  10. XM_047439572.1 → XP_047295528.1  ran-binding protein 3 isoform X3

  11. XM_047439573.1 → XP_047295529.1  ran-binding protein 3 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    5903579..5965589 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054322444.1 → XP_054178419.1  ran-binding protein 3 isoform X2

  2. XM_054322443.1 → XP_054178418.1  ran-binding protein 3 isoform X1

  3. XM_054322454.1 → XP_054178429.1  ran-binding protein 3 isoform X3

  4. XM_054322452.1 → XP_054178427.1  ran-binding protein 3 isoform X3

  5. XM_054322449.1 → XP_054178424.1  ran-binding protein 3 isoform X3

  6. XM_054322453.1 → XP_054178428.1  ran-binding protein 3 isoform X3

  7. XM_054322445.1 → XP_054178420.1  ran-binding protein 3 isoform X3

  8. XM_054322451.1 → XP_054178426.1  ran-binding protein 3 isoform X3

  9. XM_054322448.1 → XP_054178423.1  ran-binding protein 3 isoform X3

  10. XM_054322446.1 → XP_054178421.1  ran-binding protein 3 isoform X3

  11. XM_054322447.1 → XP_054178422.1  ran-binding protein 3 isoform X3

  12. XM_054322450.1 → XP_054178425.1  ran-binding protein 3 isoform X3

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_007321.1: Suppressed sequence

    Description
    NM_007321.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H6Z4.1 GenPept UniProtKB/Swiss-Prot:Q9H6Z4

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