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IGF2BP3 insulin like growth factor 2 mRNA binding protein 3 [ Homo sapiens (human) ]

Gene ID: 10643, updated on 11-Apr-2024

Summary

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Official Symbol
IGF2BP3provided by HGNC
Official Full Name
insulin like growth factor 2 mRNA binding protein 3provided by HGNC
Primary source
HGNC:HGNC:28868
See related
Ensembl:ENSG00000136231 MIM:608259; AllianceGenome:HGNC:28868
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
KOC; CT98; IMP3; KOC1; IMP-3; VICKZ3
Summary
The protein encoded by this gene is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. The encoded protein contains several KH domains, which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. A pseudogene exists on chromosome 7, and there are putative pseudogenes on other chromosomes. [provided by RefSeq, Jul 2008]
Annotation information
Note: IMP3 (Gene ID: 55272) and IGF2BP3 (Gene ID: 10643) share the IMP3 symbol/alias in common. IMP3 is a widely used alternative name for insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), which can be confused with the official symbol for IMP3, U3 small nucleolar ribonucleoprotein (IMP3). [17 May 2018]
Expression
Biased expression in placenta (RPKM 12.9), testis (RPKM 2.5) and 2 other tissues See more
Orthologs
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Genomic context

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See IGF2BP3 in Genome Data Viewer
Location:
7p15.3
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (23310209..23470491, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (23446649..23606903, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (23349828..23510110, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25722 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25723 Neighboring gene MPRA-validated peak6433 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr7:23311287-23311491 Neighboring gene glycoprotein nmb Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18007 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18008 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25724 Neighboring gene MPRA-validated peak6435 silencer Neighboring gene mitochondrial assembly of ribosomal large subunit 1 Neighboring gene Sharpr-MPRA regulatory region 6228 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:23394340-23394499 Neighboring gene Sharpr-MPRA regulatory region 10260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25725 Neighboring gene small nucleolar RNA, C/D box 65C Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:23474935-23475436 Neighboring gene RNA, U7 small nuclear 143 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25726 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:23508953-23509537 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18011 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25727 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25729 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25730 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25731 Neighboring gene chromosome 5 open reading frame 13 pseudogene Neighboring gene ribosomal protein S2 pseudogene 32

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. Targeting IGF2BP3 in Cancer. Liu X, et al. Int J Mol Sci, 2023 May 29. PMID 37298373, Free PMC Article
  2. Expression pattern analysis of m6A regulators reveals IGF2BP3 as a key modulator in osteoarthritis synovial macrophages. Lu Y, et al. J Transl Med, 2023 May 22. PMID 37217897, Free PMC Article
  3. IGF2BP3 aggravates lung adenocarcinoma progression by modulation of PI3K/AKT signaling pathway. Chen X, et al. Immunopharmacol Immunotoxicol, 2023 Jun. PMID 36972188
  4. IGF2BP3 overexpression predicts poor prognosis and correlates with immune infiltration in bladder cancer. Huang W, et al. BMC Cancer, 2023 Feb 3. PMID 36732736, Free PMC Article
  5. Insulin-like growth factor-2 mRNA-binding protein 3 promotes cell migration, invasion, and epithelial-mesenchymal transition of esophageal squamous cell carcinoma cells by targeting zinc finger E-box-binding homeobox 1 mRNA. Feng Y, et al. Mol Carcinog, 2023 Apr. PMID 36688673

See all (417) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. m[6]A-dependent upregulation of DDX21 by super-enhancer-driven IGF2BP2 and IGF2BP3 facilitates progression of acute myeloid leukaemia.
    Title: m(6)A-dependent upregulation of DDX21 by super-enhancer-driven IGF2BP2 and IGF2BP3 facilitates progression of acute myeloid leukaemia.
  2. Knockdown of RNA-binding protein IMP3 suppresses oral squamous cell carcinoma proliferation by destabilizing E2F5 transcript.
    Title: Knockdown of RNA-binding protein IMP3 suppresses oral squamous cell carcinoma proliferation by destabilizing E2F5 transcript.
  3. NONO promotes gallbladder cancer cell proliferation by enhancing oncogenic RNA splicing of DLG1 through interaction with IGF2BP3/RBM14.
    Title: NONO promotes gallbladder cancer cell proliferation by enhancing oncogenic RNA splicing of DLG1 through interaction with IGF2BP3/RBM14.
  4. Depletion of the N[6]-Methyladenosine (m6A) reader protein IGF2BP3 induces ferroptosis in glioma by modulating the expression of GPX4.
    Title: Depletion of the N(6)-Methyladenosine (m6A) reader protein IGF2BP3 induces ferroptosis in glioma by modulating the expression of GPX4.
  5. The RNA m[6]A reader IGF2BP3 regulates NFAT1/IRF1 axis-mediated anti-tumor activity in gastric cancer.
    Title: The RNA m(6)A reader IGF2BP3 regulates NFAT1/IRF1 axis-mediated anti-tumor activity in gastric cancer.
  6. Insulin-like growth factor 2 mRNA-binding protein 3 enhanced melanoma migration through regulation of AKT1 and RELA expression.
    Title: Insulin-like growth factor 2 mRNA-binding protein 3 enhanced melanoma migration through regulation of AKT1 and RELA expression.
  7. IGF2BP3 enhances lipid metabolism in cervical cancer by upregulating the expression of SCD.
    Title: IGF2BP3 enhances lipid metabolism in cervical cancer by upregulating the expression of SCD.
  8. Regulation of ULK1 by WTAP/IGF2BP3 axis enhances mitophagy and progression in epithelial ovarian cancer.
    Title: Regulation of ULK1 by WTAP/IGF2BP3 axis enhances mitophagy and progression in epithelial ovarian cancer.
  9. Hypoxia increases the biogenesis of IGF2BP3-bound circular RNAs.
    Title: Hypoxia increases the biogenesis of IGF2BP3-bound circular RNAs.
  10. Association of the m[6] A reader IGF2BP3 with tumor progression and brain-specific metastasis in breast cancer.
    Title: Association of the m(6) A reader IGF2BP3 with tumor progression and brain-specific metastasis in breast cancer.
Submit: New GeneRIF Correction See all GeneRIFs (248)

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

EBI GWAS Catalog

Description
A novel common variant in DCST2 is associated with length in early life and height in adulthood.
EBI GWAS Catalog
Genome-wide association study of the five-factor model of personality in young Korean women.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
EBI GWAS Catalog
Hundreds of variants clustered in genomic loci and biological pathways affect human height.
EBI GWAS Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify insulin-like growth factor 2 mRNA binding protein 3 (IGF2BP3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

Go to the HIV-1, Human Interaction Database

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

  • DKFZp686F1078

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables N6-methyladenosine-containing RNA reader activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding HDA PubMed 
enables mRNA 3'-UTR binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mRNA 3'-UTR binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables mRNA 5'-UTR binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables translation regulator activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
Process Evidence Code Pubs
involved_in CRD-mediated mRNA stabilization IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in CRD-mediated mRNA stabilization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in anatomical structure morphogenesis TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA transport IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of translation ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
involved_in nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of cytokine production IC
Inferred by Curator
more info
 PubMed 
involved_in translation TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in P-body IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasmic stress granule IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
insulin-like growth factor 2 mRNA-binding protein 3
Names
IGF-II mRNA-binding protein 3
IGF2 mRNA-binding protein 3
KH domain containing protein overexpressed in cancer
VICKZ family member 3
cancer/testis antigen 98

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_006547.3 → NP_006538.2  insulin-like growth factor 2 mRNA-binding protein 3

    See identical proteins and their annotated locations for NP_006538.2

    Status: REVIEWED

    Source sequence(s)
    AC005082, AC021876, AC079780
    Consensus CDS
    CCDS5382.1
    UniProtKB/Swiss-Prot
    A0A4Z5, O00425, Q63HM0, Q6MZZ2, Q86VB1
    Related
    ENSP00000258729.3, ENST00000258729.8
    Conserved Domains (5) summary
    cd00105
    Location:279 → 344
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    cd02396
    Location:407 → 470
    PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
    cd12627
    Location:1 → 77
    RRM1_IGF2BP3; RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)
    cd12630
    Location:81 → 156
    RRM2_IGF2BP3; RNA recognition motif 2 in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)
    pfam00013
    Location:492 → 555
    KH_1; KH 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_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    23310209..23470491 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011515089.3 → XP_011513391.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X2

    Conserved Domains (5) summary
    COG0724
    Location:2 → 87
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd00105
    Location:284 → 349
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    cd02396
    Location:412 → 475
    PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
    cd12627
    Location:1 → 77
    RRM1_IGF2BP3; RNA recognition motif 1 in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)
    cd12630
    Location:81 → 161
    RRM2_IGF2BP3; RNA recognition motif 2 in vertebrate insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3)

  2. XM_047419782.1 → XP_047275738.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X1

  3. XM_011515092.3 → XP_011513394.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X5

    See identical proteins and their annotated locations for XP_011513394.1

    Conserved Domains (3) summary
    cd00105
    Location:186 → 251
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    cd02396
    Location:314 → 377
    PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
    cl17169
    Location:3 → 63
    RRM_SF; RNA recognition motif (RRM) superfamily

  4. XM_011515090.4 → XP_011513392.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X4

    Conserved Domains (3) summary
    cd00105
    Location:171 → 236
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    cd02396
    Location:299 → 362
    PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
    cl17169
    Location:26 → 48
    RRM_SF; RNA recognition motif (RRM) superfamily

  5. XM_011515093.3 → XP_011513395.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X5

    See identical proteins and their annotated locations for XP_011513395.1

    Conserved Domains (3) summary
    cd00105
    Location:186 → 251
    KH-I; K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that ...
    cd02396
    Location:314 → 377
    PCBP_like_KH; K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are ...
    cl17169
    Location:3 → 63
    RRM_SF; RNA recognition motif (RRM) superfamily

  6. XM_047419784.1 → XP_047275740.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    23446649..23606903 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054357097.1 → XP_054213072.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X2

  2. XM_054357096.1 → XP_054213071.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X1

  3. XM_054357100.1 → XP_054213075.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X6

  4. XM_054357101.1 → XP_054213076.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X5

  5. XM_054357099.1 → XP_054213074.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X4

  6. XM_054357102.1 → XP_054213077.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X5

  7. XM_054357098.1 → XP_054213073.1  insulin-like growth factor 2 mRNA-binding protein 3 isoform X3

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O00425.2 GenPept UniProtKB/Swiss-Prot:O00425

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