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

Gene ID: 202151, updated on 27-Nov-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 protein export from nucleus. Predicted to be located in nucleus. Predicted to be part of nuclear pore. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
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)
RS_2024_09 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
  • 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. Changes in expression of VGF, SPECC1L, HLA-DRA and RANBP3L act with APOE E4 to alter risk for late onset Alzheimer's disease. Branciamore S, et al. Sci Rep, 2024 Jun 28. PMID 38942763, Free PMC Article
  5. 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

See all (14) 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)

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
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
  

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

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