Human Gene RANBP3 (ENST00000439268.6) Description and Page Index
  Description: Homo sapiens RAN binding protein 3 (RANBP3), transcript variant RANBP3-a, mRNA. (from RefSeq NM_003624)
RefSeq Summary (NM_003624): This gene encodes a protein with a RanBD1 domain that is found in both the nucleus and cytoplasm. This protein plays a role in nuclear export as part of a heteromeric complex. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000439268.6
Gencode Gene: ENSG00000031823.14
Transcript (Including UTRs)
   Position: hg38 chr19:5,916,139-5,978,108 Size: 61,970 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg38 chr19:5,917,610-5,978,082 Size: 60,473 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr19:5,916,139-5,978,108)mRNA (may differ from genome)Protein (562 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
LynxMGIneXtProtOMIMPubMedStanford SOURCE

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Ran-binding protein 3; Short=RanBP3;
FUNCTION: Acts as a cofactor for XPO1/CRM1-mediated nuclear export, perhaps as export complex scaffolding protein. Bound to XPO1/CRM1, stabilizes the XPO1/CRM1-cargo interaction. In the absence of Ran-bound GTP prevents binding of XPO1/CRM1 to the nuclear pore complex. Binds to CHC1/RCC1 and increases the guanine nucleotide exchange activity of CHC1/RCC1. Recruits XPO1/CRM1 to CHC1/RCC1 in a Ran-dependent manner. Negative regulator of TGF- beta signaling through interaction with the R-SMAD proteins, SMAD2 and SMAD3, and mediating their nuclear export.
SUBUNIT: Interacts with CHC1 in a Ran-stimulated manner. Interacts with XPO1. Interacts (via its C-terminal R domain) with SMAD2 (dephosphorylated form via its MH1 and MH2 domains); the interaction results in the nuclear export of SMAD2 and termination of the TGF-beta signaling. Interacts (via its C-terminal R domain) with SMAD3 (dephosphorylated form via its MH1 domain); the interaction results in the nuclear export of SMAD3 and termination of the TGF-beta signaling.
INTERACTION: P18754:RCC1; NbExp=2; IntAct=EBI-992681, EBI-992720;
TISSUE SPECIFICITY: Widely expressed with high levels in testis and heart.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Contains 1 RanBD1 domain.
SEQUENCE CAUTION: Sequence=AAH04349.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing; Sequence=CAB43293.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.09 RPKM in Testis
Total median expression: 823.05 RPKM

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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -1.2026-0.046 Picture PostScript Text
3' UTR -560.701471-0.381 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
IPR011993 - PH_like_dom
IPR000156 - Ran_bind_dom

Pfam Domains:
PF00638 - RanBP1 domain

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


- X-ray MuPIT

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q9H6Z4
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 BrowserNo orthologGenome BrowserNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
Protein SequenceProtein Sequence Protein Sequence Protein Sequence
AlignmentAlignment Alignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008536 Ran GTPase binding
GO:0070412 R-SMAD binding
GO:0005096 GTPase activator activity

Biological Process:
GO:0000082 G1/S transition of mitotic cell cycle
GO:0006405 RNA export from nucleus
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006606 protein import into nucleus
GO:0007051 spindle organization
GO:0015031 protein transport
GO:0043547 positive regulation of GTPase activity
GO:0046604 positive regulation of mitotic centrosome separation
GO:0046907 intracellular transport

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005813 centrosome

-  Descriptions from all associated GenBank mRNAs
  AK222813 - Homo sapiens mRNA, Splice isoform 4 of Q9H6Z4 variant, clone: HEP04963.
Y08698 - H.sapiens mRNA for RanBP3 (59 kDa).
AK025300 - Homo sapiens cDNA: FLJ21647 fis, clone COL08457.
JD190484 - Sequence 171508 from Patent EP1572962.
JD228806 - Sequence 209830 from Patent EP1572962.
JD168802 - Sequence 149826 from Patent EP1572962.
JD381989 - Sequence 363013 from Patent EP1572962.
JD379876 - Sequence 360900 from Patent EP1572962.
JD343768 - Sequence 324792 from Patent EP1572962.
JD108639 - Sequence 89663 from Patent EP1572962.
JD467585 - Sequence 448609 from Patent EP1572962.
JD253626 - Sequence 234650 from Patent EP1572962.
JD537464 - Sequence 518488 from Patent EP1572962.
JD076099 - Sequence 57123 from Patent EP1572962.
JD181503 - Sequence 162527 from Patent EP1572962.
BC004349 - Homo sapiens RAN binding protein 3, mRNA (cDNA clone MGC:1177 IMAGE:3350317), complete cds.
GQ901049 - Homo sapiens clone HEL-T-161 epididymis secretory sperm binding protein mRNA, complete cds.
AL050149 - Homo sapiens mRNA; cDNA DKFZp586I1520 (from clone DKFZp586I1520).
JD252223 - Sequence 233247 from Patent EP1572962.
JD146935 - Sequence 127959 from Patent EP1572962.
JD224563 - Sequence 205587 from Patent EP1572962.
KJ904601 - Synthetic construct Homo sapiens clone ccsbBroadEn_13995 RANBP3 gene, encodes complete protein.
JD104724 - Sequence 85748 from Patent EP1572962.
JD055777 - Sequence 36801 from Patent EP1572962.
JD137472 - Sequence 118496 from Patent EP1572962.
JD137474 - Sequence 118498 from Patent EP1572962.
Y08697 - H.sapiens mRNA for RanBP3 small splice variant (53 kDa).
JD057779 - Sequence 38803 from Patent EP1572962.
AK308205 - Homo sapiens cDNA, FLJ98153.
AK299260 - Homo sapiens cDNA FLJ55542 complete cds, highly similar to Ran-binding protein 3.
AK125183 - Homo sapiens cDNA FLJ43193 fis, clone FCBBF3028582, highly similar to Homo sapiens RAN binding protein 3 (RANBP3).
AK301942 - Homo sapiens cDNA FLJ58549 complete cds, highly similar to Ran-binding protein 3.
JD049493 - Sequence 30517 from Patent EP1572962.
AK222990 - Homo sapiens mRNA for RAN binding protein 3 isoform RANBP3-a variant, clone: HSI06902.
JD468282 - Sequence 449306 from Patent EP1572962.
JD386719 - Sequence 367743 from Patent EP1572962.
JD476285 - Sequence 457309 from Patent EP1572962.
DQ234346 - Homo sapiens RAN binding protein 3 transcript variant a mRNA, complete cds, alternatively spliced.
AK314343 - Homo sapiens cDNA, FLJ95105, highly similar to Homo sapiens RAN binding protein 3 (RANBP3), transcript variant RANBP3-b, mRNA.
Y08699 - H.sapiens mRNA for RanBP3, splice variant.
JD141950 - Sequence 122974 from Patent EP1572962.
CU678680 - Synthetic construct Homo sapiens gateway clone IMAGE:100018214 5' read RANBP3 mRNA.
JD180687 - Sequence 161711 from Patent EP1572962.
AK299856 - Homo sapiens cDNA FLJ59171 complete cds, highly similar to Ran-binding protein 3.
JD399423 - Sequence 380447 from Patent EP1572962.
JD373261 - Sequence 354285 from Patent EP1572962.
JD373262 - Sequence 354286 from Patent EP1572962.
JD388210 - Sequence 369234 from Patent EP1572962.
JD180495 - Sequence 161519 from Patent EP1572962.
JD446471 - Sequence 427495 from Patent EP1572962.
JD049014 - Sequence 30038 from Patent EP1572962.
JD187909 - Sequence 168933 from Patent EP1572962.
JD496973 - Sequence 477997 from Patent EP1572962.
JD456486 - Sequence 437510 from Patent EP1572962.
JD121014 - Sequence 102038 from Patent EP1572962.
JD078814 - Sequence 59838 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RAT8, NM_003624, O60405, O75759, O75760, Q9BT47, Q9H6Z4, Q9UG74, RANB3_HUMAN, uc002mdx.1, uc002mdx.2, uc002mdx.3, uc002mdx.4
UCSC ID: uc002mdx.4
RefSeq Accession: NM_003624
Protein: Q9H6Z4 (aka RANB3_HUMAN or RBP3_HUMAN)
CCDS: CCDS42478.1, CCDS45935.1

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