Human Gene IGF2BP3 (ENST00000258729.8) from GENCODE V44
  Description: Homo sapiens insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3), mRNA. (from RefSeq NM_006547)
RefSeq Summary (NM_006547): 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].
Gencode Transcript: ENST00000258729.8
Gencode Gene: ENSG00000136231.14
Transcript (Including UTRs)
   Position: hg38 chr7:23,310,209-23,470,491 Size: 160,283 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg38 chr7:23,312,362-23,470,110 Size: 157,749 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:23,310,209-23,470,491)mRNA (may differ from genome)Protein (579 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Insulin-like growth factor 2 mRNA-binding protein 3; Short=IGF2 mRNA-binding protein 3; Short=IMP-3; AltName: Full=IGF-II mRNA-binding protein 3; AltName: Full=KH domain-containing protein overexpressed in cancer; Short=hKOC; AltName: Full=VICKZ family member 3;
FUNCTION: RNA-binding protein that act as a regulator of mRNA translation and stability. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binds to sequences in the 3'-UTR of CD44 mRNA.
SUBUNIT: Homodimer and multimer (By similarity). Interacts with IGF2BP1.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Found in lamellipodia of the leading edge, in the perinuclear region, and beneath the plasma membrane. The subcytoplasmic localization is cell specific and regulated by cell contact and growth. Localized at the connecting piece and the tail of the spermatozoa. Colocalized with CD44 mRNA in RNP granules.
TISSUE SPECIFICITY: Expressed in fetal liver, fetal lung, fetal kidney, fetal thymus, fetal placenta, fetal follicles of ovary and gonocytes of testis, growing oocytes, spermatogonia and semen (at protein level). Expressed in cervix adenocarcinoma, in testicular, pancreatic and renal-cell carcinomas (at protein level). Expressed ubiquitously during fetal development at 8 and 14 weeks of gestation. Expressed in ovary, testis, brain, placenta, pancreatic cancer tissues and pancreatic cancer cell lines.
DOMAIN: The third and fourth KH domains are important for binding to the untranslated region (UTR) of target mRNA.
MISCELLANEOUS: Autoantibodies against IGF2BP3 are detected in sera from some patients with a variety of carcinomas.
SIMILARITY: Belongs to the RRM IMP/VICKZ family.
SIMILARITY: Contains 4 KH domains.
SIMILARITY: Contains 2 RRM (RNA recognition motif) domains.

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: IGF2BP3
Diseases sorted by gene-association score: pancreatic cancer (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 5.85 RPKM in Cells - Cultured fibroblasts
Total median expression: 14.91 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -103.10381-0.271 Picture PostScript Text
3' UTR -497.572153-0.231 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004087 - KH_dom
IPR004088 - KH_dom_type_1
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00013 - KH domain
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2E44 - NMR MuPIT

ModBase Predicted Comparative 3D Structure on O00425
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003730 mRNA 3'-UTR binding
GO:0005515 protein binding
GO:0045182 translation regulator activity
GO:0048027 mRNA 5'-UTR binding

Biological Process:
GO:0006412 translation
GO:0006417 regulation of translation
GO:0009653 anatomical structure morphogenesis
GO:0017148 negative regulation of translation
GO:0042035 regulation of cytokine biosynthetic process
GO:0043488 regulation of mRNA stability
GO:0051028 mRNA transport

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol

-  Descriptions from all associated GenBank mRNAs
  AF117108 - Homo sapiens IGF-II mRNA-binding protein 3 (IMP-3) mRNA, complete cds.
LF384107 - JP 2014500723-A/191610: Polycomb-Associated Non-Coding RNAs.
MA619684 - JP 2018138019-A/191610: Polycomb-Associated Non-Coding RNAs.
U76705 - Human putative RNA binding protein Koc1 mRNA, complete cds.
U97188 - Homo sapiens putative RNA binding protein KOC (koc) mRNA, complete cds.
BX640800 - Homo sapiens mRNA; cDNA DKFZp686K2175 (from clone DKFZp686K2175).
BX648488 - Homo sapiens mRNA; cDNA DKFZp686F1078 (from clone DKFZp686F1078).
BC065269 - Homo sapiens insulin-like growth factor 2 mRNA binding protein 3, mRNA (cDNA clone MGC:75347 IMAGE:6154021), complete cds.
KJ898269 - Synthetic construct Homo sapiens clone ccsbBroadEn_07663 IGF2BP3 gene, encodes complete protein.
AB529064 - Synthetic construct DNA, clone: pF1KB3919, Homo sapiens IGF2BP3 gene for insulin-like growth factor 2 mRNA binding protein 3, without stop codon, in Flexi system.
CU688032 - Synthetic construct Homo sapiens gateway clone IMAGE:100021787 5' read IGF2BP3 mRNA.
BC019258 - Homo sapiens insulin-like growth factor 2 mRNA binding protein 3, mRNA (cDNA clone IMAGE:3542483), with apparent retained intron.
BC051296 - Homo sapiens insulin-like growth factor 2 mRNA binding protein 3, mRNA (cDNA clone IMAGE:3687722), with apparent retained intron.
KJ902140 - Synthetic construct Homo sapiens clone ccsbBroadEn_11534 IGF2BP3 gene, encodes complete protein.
JD112633 - Sequence 93657 from Patent EP1572962.
LF362262 - JP 2014500723-A/169765: Polycomb-Associated Non-Coding RNAs.
MA597839 - JP 2018138019-A/169765: Polycomb-Associated Non-Coding RNAs.
JD248918 - Sequence 229942 from Patent EP1572962.
LF362263 - JP 2014500723-A/169766: Polycomb-Associated Non-Coding RNAs.
MA597840 - JP 2018138019-A/169766: Polycomb-Associated Non-Coding RNAs.
JD235214 - Sequence 216238 from Patent EP1572962.
JD410178 - Sequence 391202 from Patent EP1572962.
JD234771 - Sequence 215795 from Patent EP1572962.
LF362264 - JP 2014500723-A/169767: Polycomb-Associated Non-Coding RNAs.
MA597841 - JP 2018138019-A/169767: Polycomb-Associated Non-Coding RNAs.
JD067925 - Sequence 48949 from Patent EP1572962.
JD284079 - Sequence 265103 from Patent EP1572962.
LF362265 - JP 2014500723-A/169768: Polycomb-Associated Non-Coding RNAs.
MA597842 - JP 2018138019-A/169768: Polycomb-Associated Non-Coding RNAs.
JD166642 - Sequence 147666 from Patent EP1572962.
JD043590 - Sequence 24614 from Patent EP1572962.
JD111144 - Sequence 92168 from Patent EP1572962.
JD304103 - Sequence 285127 from Patent EP1572962.
JD510074 - Sequence 491098 from Patent EP1572962.
LF362266 - JP 2014500723-A/169769: Polycomb-Associated Non-Coding RNAs.
MA597843 - JP 2018138019-A/169769: Polycomb-Associated Non-Coding RNAs.
LF362267 - JP 2014500723-A/169770: Polycomb-Associated Non-Coding RNAs.
MA597844 - JP 2018138019-A/169770: Polycomb-Associated Non-Coding RNAs.
JD058600 - Sequence 39624 from Patent EP1572962.
JD303168 - Sequence 284192 from Patent EP1572962.
JD486812 - Sequence 467836 from Patent EP1572962.
JD058282 - Sequence 39306 from Patent EP1572962.
JD307620 - Sequence 288644 from Patent EP1572962.
JD147962 - Sequence 128986 from Patent EP1572962.
LF362268 - JP 2014500723-A/169771: Polycomb-Associated Non-Coding RNAs.
MA597845 - JP 2018138019-A/169771: Polycomb-Associated Non-Coding RNAs.
JD544281 - Sequence 525305 from Patent EP1572962.
LF362269 - JP 2014500723-A/169772: Polycomb-Associated Non-Coding RNAs.
MA597846 - JP 2018138019-A/169772: Polycomb-Associated Non-Coding RNAs.
JD390348 - Sequence 371372 from Patent EP1572962.
JD369501 - Sequence 350525 from Patent EP1572962.
LF362270 - JP 2014500723-A/169773: Polycomb-Associated Non-Coding RNAs.
MA597847 - JP 2018138019-A/169773: Polycomb-Associated Non-Coding RNAs.
LF362271 - JP 2014500723-A/169774: Polycomb-Associated Non-Coding RNAs.
MA597848 - JP 2018138019-A/169774: Polycomb-Associated Non-Coding RNAs.
LF362279 - JP 2014500723-A/169782: Polycomb-Associated Non-Coding RNAs.
MA597856 - JP 2018138019-A/169782: Polycomb-Associated Non-Coding RNAs.
LF362282 - JP 2014500723-A/169785: Polycomb-Associated Non-Coding RNAs.
MA597859 - JP 2018138019-A/169785: Polycomb-Associated Non-Coding RNAs.
LF362283 - JP 2014500723-A/169786: Polycomb-Associated Non-Coding RNAs.
MA597860 - JP 2018138019-A/169786: Polycomb-Associated Non-Coding RNAs.
LF362295 - JP 2014500723-A/169798: Polycomb-Associated Non-Coding RNAs.
MA597872 - JP 2018138019-A/169798: Polycomb-Associated Non-Coding RNAs.
JD203151 - Sequence 184175 from Patent EP1572962.
JD043270 - Sequence 24294 from Patent EP1572962.
JD287485 - Sequence 268509 from Patent EP1572962.
JD359720 - Sequence 340744 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O00425 (Reactome details) participates in the following event(s):

R-HSA-428287 IGF2BP3 binds specific RNAs
R-HSA-428359 Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A0A4Z5, ENST00000258729.1, ENST00000258729.2, ENST00000258729.3, ENST00000258729.4, ENST00000258729.5, ENST00000258729.6, ENST00000258729.7, IF2B3_HUMAN, IMP3, KOC1, NM_006547, O00425, Q63HM0, Q6MZZ2, Q86VB1, uc003swg.1, uc003swg.2, uc003swg.3, uc003swg.4, uc003swg.5, VICKZ3
UCSC ID: ENST00000258729.8
RefSeq Accession: NM_006547
Protein: O00425 (aka IF2B3_HUMAN)
CCDS: CCDS5382.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.