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

Summary

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: mouse all
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Genomic context

Location:: 7p15.3

Exon count:: 18

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (23310209..23470491, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (23446649..23606903, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (23349828..23510110, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Association of insulin-like growth factor II mrna-binding protein 3 (IMP3) expression with prognostic and morphological factors in endometrial cancer.
Title: Association of insulin-like growth factor II mrna-binding protein 3 (IMP3) expression with prognostic and morphological factors in endometrial cancer.
METTL5: A Potential Biomarker for Nonsmall Cell Lung Cancer That Promotes Cancer Cell Proliferation by Interacting with IGF2BP3.
Title: METTL5: A Potential Biomarker for Nonsmall Cell Lung Cancer That Promotes Cancer Cell Proliferation by Interacting with IGF2BP3.
Oncofetal IGF2BP3-mediated control of microRNA structural diversity in the malignancy of early-stage lung adenocarcinoma.
Title: Oncofetal IGF2BP3-mediated control of microRNA structural diversity in the malignancy of early-stage lung adenocarcinoma.
IGF2BP3 promotes mRNA degradation through internal m[7]G modification.
Title: IGF2BP3 promotes mRNA degradation through internal m(7)G modification.
IGF2BP3 participates in the pathogenesis of recurrent spontaneous abortion by regulating ferroptosis.
Title: IGF2BP3 participates in the pathogenesis of recurrent spontaneous abortion by regulating ferroptosis.
Epigenetically associated IGF2BP3 upregulation promotes cell proliferation by regulating E2F1 expression in hepatocellular carcinoma.
Title: Epigenetically associated IGF2BP3 upregulation promotes cell proliferation by regulating E2F1 expression in hepatocellular carcinoma.
circATAD2 mitigates CD8[+] T cells antitumor immune surveillance in breast cancer via IGF2BP3/m[6]A/PD-L1 manner.
Title: circATAD2 mitigates CD8(+) T cells antitumor immune surveillance in breast cancer via IGF2BP3/m(6)A/PD-L1 manner.
IGF2BP3 regulates the expression of RRM2 and promotes the progression of rheumatoid arthritis via RRM2/Akt/MMP-9 pathway.
Title: IGF2BP3 regulates the expression of RRM2 and promotes the progression of rheumatoid arthritis via RRM2/Akt/MMP-9 pathway.
Hsa_circ_0005320 affects cell proliferation and the cell cycle via the IGF2BP3/CDK2 axis in bladder cancer.
Title: Hsa_circ_0005320 affects cell proliferation and the cell cycle via the IGF2BP3/CDK2 axis in bladder cancer.
N6-methyladenosine-modified SENP1, identified by IGF2BP3, is a novel molecular marker in acute myeloid leukemia and aggravates progression by activating AKT signal via de-SUMOylating HDAC2.
Title: N6-methyladenosine-modified SENP1, identified by IGF2BP3, is a novel molecular marker in acute myeloid leukemia and aggravates progression by activating AKT signal via de-SUMOylating HDAC2.

Submit: New GeneRIF Correction See all GeneRIFs (261)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AFMa044zb5 (e-PCR)
- UniSTS:46619

D8S2279 (e-PCR)
- UniSTS:473907

A009H11 (e-PCR)
- UniSTS:39235

RH65486 (e-PCR)
- UniSTS:85324

D10S16 (e-PCR)
- UniSTS:155756

G32538 (e-PCR)
- UniSTS:117122

RH18504 (e-PCR)
- UniSTS:19341

GDB:4585511 (e-PCR)
- UniSTS:51343

SHGC-58242 (e-PCR)
- UniSTS:73884

G63591 (e-PCR)
- UniSTS:140702

SGC34281 (e-PCR)
- UniSTS:4773

STS-R78376 (e-PCR)
- UniSTS:36024

RH36584 (e-PCR)
- UniSTS:83651

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 more info	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)

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

23310209..23470491 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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)
XM_047419782.1 → XP_047275738.1 insulin-like growth factor 2 mRNA-binding protein 3 isoform X1
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
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
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
XM_047419784.1 → XP_047275740.1 insulin-like growth factor 2 mRNA-binding protein 3 isoform X3

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

23446649..23606903 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054357097.1 → XP_054213072.1 insulin-like growth factor 2 mRNA-binding protein 3 isoform X2
XM_054357096.1 → XP_054213071.1 insulin-like growth factor 2 mRNA-binding protein 3 isoform X1
XM_054357100.1 → XP_054213075.1 insulin-like growth factor 2 mRNA-binding protein 3 isoform X6
XM_054357101.1 → XP_054213076.1 insulin-like growth factor 2 mRNA-binding protein 3 isoform X5
XM_054357099.1 → XP_054213074.1 insulin-like growth factor 2 mRNA-binding protein 3 isoform X4
XM_054357102.1 → XP_054213077.1 insulin-like growth factor 2 mRNA-binding protein 3 isoform X5
XM_054357098.1 → XP_054213073.1 insulin-like growth factor 2 mRNA-binding protein 3 isoform X3