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    RANBP3L RAN binding protein 3 like [ Homo sapiens (human) ]

    Gene ID: 202151, updated on 27-Aug-2024

    Summary

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    Official Symbol
    RANBP3Lprovided by HGNC
    Official Full Name
    RAN binding protein 3 likeprovided by HGNC
    Primary source
    HGNC:HGNC:26353
    See related
    Ensembl:ENSG00000164188 MIM:616391; AllianceGenome:HGNC:26353
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables SMAD binding activity. Predicted to be involved in several processes, including mesenchymal cell differentiation involved in bone development; negative regulation of osteoblast differentiation; and positive regulation of myoblast differentiation. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in brain (RPKM 8.6), kidney (RPKM 8.4) and 11 other tissues See more
    Orthologs
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    Genomic context

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    See RANBP3L in Genome Data Viewer
    Location:
    5p13.2
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (36246913..36301902, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (36495219..36550209, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (36247015..36302004, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1305, pseudogene Neighboring gene S-phase kinase associated protein 2 Neighboring gene NAD kinase 2, mitochondrial Neighboring gene NADK2 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15972 Neighboring gene uncharacterized LOC124900962 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 22478 Neighboring gene NANOG hESC enhancer GRCh37_chr5:36359316-36360151 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:36417632-36418831 Neighboring gene Sharpr-MPRA regulatory region 12809 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:36422736-36423935 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:36442158-36443357 Neighboring gene uncharacterized LOC124900963 Neighboring gene Sharpr-MPRA regulatory region 9147 Neighboring gene RNA, 5S ribosomal pseudogene 181

    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 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. Loss of RANBP3L leads to transformation of renal epithelial cells towards a renal clear cell carcinoma like phenotype. Chernyakov D, et al. J Exp Clin Cancer Res, 2021 Jul 7. PMID 34233711, Free PMC Article
    2. Genetic variants in 5p13.2 and 7q21.1 are associated with treatment for benign prostatic hyperplasia with the α-adrenergic receptor antagonist. Qian X, et al. Aging Male, 2017 Dec. PMID 28787260
    3. Impact of four loci on serum tamsulosin hydrochloride concentration. Takata R, et al. J Hum Genet, 2013 Jan. PMID 23151678
    4. Nuclear Export of Smads by RanBP3L Regulates Bone Morphogenetic Protein Signaling and Mesenchymal Stem Cell Differentiation. Chen F, et al. Mol Cell Biol, 2015 May. PMID 25755279, Free PMC Article
    5. Two-marker association tests yield new disease associations for coronary artery disease and hypertension. Slavin TP, et al. Hum Genet, 2011 Dec. PMID 21626137, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Changes in expression of VGF, SPECC1L, HLA-DRA and RANBP3L act with APOE E4 to alter risk for late onset Alzheimer's disease.
      Title: Changes in expression of VGF, SPECC1L, HLA-DRA and RANBP3L act with APOE E4 to alter risk for late onset Alzheimer's disease.
    2. Loss of RANBP3L leads to transformation of renal epithelial cells towards a renal clear cell carcinoma like phenotype.
      Title: Loss of RANBP3L leads to transformation of renal epithelial cells towards a renal clear cell carcinoma like phenotype.
    3. The single nucleotide polymorphism, rs16902947 in RANBP3L at 5p13.2 (p = .01), is significantly associated with Benign Prostate Hyperplasia. Rs16902947 in RANBP3L at 5p13.2 (p = .0388) is associated withalpha-adrenergic receptor antagonist drug effect in Benign Prostate Hyperplasia.
      Title: Genetic variants in 5p13.2 and 7q21.1 are associated with treatment for benign prostatic hyperplasia with the α-adrenergic receptor antagonist.
    4. Results demonstrate that RanBP3L, as a nuclear exporter for BMP-specific Smads, plays a critical role in terminating BMP signaling and regulating mesenchymal stem cell differentiation.
      Title: Nuclear Export of Smads by RanBP3L Regulates Bone Morphogenetic Protein Signaling and Mesenchymal Stem Cell Differentiation.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Impact of four loci on serum tamsulosin hydrochloride concentration.
    EBI GWAS Catalog
    Two-marker association tests yield new disease associations for coronary artery disease and hypertension.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ25422

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    contributes_to GTPase activator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 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 mesenchymal cell differentiation involved in bone development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in negative regulation of osteoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of myoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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
    		  

    General protein information

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    Preferred Names
    ran-binding protein 3-like

    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_001161429.3 → NP_001154901.1  ran-binding protein 3-like isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC008807, AC114277, AK302947
      Consensus CDS
      CCDS54843.1
      UniProtKB/Swiss-Prot
      Q86VV4
      Related
      ENSP00000421853.1, ENST00000502994.5
      Conserved Domains (1) summary
      cd13180
      Location:316 → 431
      RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

    2. NM_001323273.2 → NP_001310202.1  ran-binding protein 3-like isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC008807, BC047660
      UniProtKB/Swiss-Prot
      Q86VV4
      Conserved Domains (1) summary
      cd13180
      Location:291 → 406
      RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

    3. NM_001323274.2 → NP_001310203.1  ran-binding protein 3-like isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC008807, AK302947, BC047660, BQ774461
      UniProtKB/Swiss-Prot
      Q86VV4

    4. NM_001323275.2 → NP_001310204.1  ran-binding protein 3-like isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC008807, AK302947, BC047660
      UniProtKB/Swiss-Prot
      Q86VV4

    5. NM_001323276.2 → NP_001310205.1  ran-binding protein 3-like isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC008807, AK302947, BC047660, BQ774461
      UniProtKB/Swiss-Prot
      Q86VV4

    6. NM_001323277.2 → NP_001310206.1  ran-binding protein 3-like isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC008807, BC047660, BQ774461
      UniProtKB/Swiss-Prot
      Q86VV4

    7. NM_001323278.2 → NP_001310207.1  ran-binding protein 3-like isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC008807, BC047660
      UniProtKB/Swiss-Prot
      Q86VV4

    8. NM_001323279.2 → NP_001310208.1  ran-binding protein 3-like isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC008807, BC047660
      UniProtKB/Swiss-Prot
      Q86VV4

    9. NM_001323280.2 → NP_001310209.1  ran-binding protein 3-like isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC008807, BC047660, BQ774461
      UniProtKB/Swiss-Prot
      Q86VV4

    10. NM_145000.5 → NP_659437.3  ran-binding protein 3-like isoform 2

      See identical proteins and their annotated locations for NP_659437.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
      Source sequence(s)
      AC008807, BC047660
      Consensus CDS
      CCDS3918.1
      UniProtKB/Swiss-Prot
      B7Z866, E9PGP9, Q86VV4, Q96LK2
      Related
      ENSP00000296604.3, ENST00000296604.8
      Conserved Domains (1) summary
      cd13180
      Location:291 → 406
      RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      36246913..36301902 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006714455.5 → XP_006714518.1  ran-binding protein 3-like isoform X3

      Conserved Domains (1) summary
      cd13180
      Location:271 → 386
      RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

    2. XM_006714453.5 → XP_006714516.1  ran-binding protein 3-like isoform X2

      Conserved Domains (1) summary
      cd13180
      Location:296 → 411
      RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

    3. XM_006714452.5 → XP_006714515.1  ran-binding protein 3-like isoform X1

      Conserved Domains (1) summary
      cd13180
      Location:316 → 431
      RanBD_RanBP3; Ran-binding protein 3 Ran-binding domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      36495219..36550209 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054351977.1 → XP_054207952.1  ran-binding protein 3-like isoform X3

    2. XM_054351976.1 → XP_054207951.1  ran-binding protein 3-like isoform X2

    3. XM_054351975.1 → XP_054207950.1  ran-binding protein 3-like isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86VV4.2 GenPept UniProtKB/Swiss-Prot:Q86VV4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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