Human Gene RANBP2 (uc002tem.4) Description and Page Index
  Description: Homo sapiens RAN binding protein 2 (RANBP2), mRNA.
RefSeq Summary (NM_006267): RAN is a small GTP-binding protein of the RAS superfamily that is associated with the nuclear membrane and is thought to control a variety of cellular functions through its interactions with other proteins. This gene encodes a very large RAN-binding protein that immunolocalizes to the nuclear pore complex. The protein is a giant scaffold and mosaic cyclophilin-related nucleoporin implicated in the Ran-GTPase cycle. The encoded protein directly interacts with the E2 enzyme UBC9 and strongly enhances SUMO1 transfer from UBC9 to the SUMO1 target SP100. These findings place sumoylation at the cytoplasmic filaments of the nuclear pore complex and suggest that, for some substrates, modification and nuclear import are linked events. This gene is partially duplicated in a gene cluster that lies in a hot spot for recombination on chromosome 2q. [provided by RefSeq, Jul 2008]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by transcript alignments. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: D42063.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000283195.11/ ENSP00000283195.6 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr2:109,335,937-109,402,267 Size: 66,331 Total Exon Count: 29 Strand: +
Coding Region
   Position: hg19 chr2:109,336,063-109,400,357 Size: 64,295 Coding Exon Count: 29 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:109,335,937-109,402,267)mRNA (may differ from genome)Protein (3224 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RBP2_HUMAN
DESCRIPTION: RecName: Full=E3 SUMO-protein ligase RanBP2; EC=6.3.2.-; AltName: Full=358 kDa nucleoporin; AltName: Full=Nuclear pore complex protein Nup358; AltName: Full=Nucleoporin Nup358; AltName: Full=Ran-binding protein 2; Short=RanBP2; AltName: Full=p270; Includes: RecName: Full=Putative peptidyl-prolyl cis-trans isomerase; Short=PPIase; EC=5.2.1.8; AltName: Full=Rotamase;
FUNCTION: E3 SUMO-protein ligase which facilitates SUMO1 and SUMO2 conjugation by UBE2I. Involved in transport factor (Ran-GTP, karyopherin)-mediated protein import via the F-G repeat-containing domain which acts as a docking site for substrates. Could also have isomerase or chaperone activity and may bind RNA or DNA. Component of the nuclear export pathway. Specific docking site for the nuclear export factor exportin-1.
CATALYTIC ACTIVITY: Peptidylproline (omega=180) = peptidylproline (omega=0).
PATHWAY: Protein modification; protein sumoylation.
SUBUNIT: Forms a tight complex with RANBP1 and UBE2I. Interacts with SUMO1 but not SUMO2. Interacts with PARK2. Interacts with sumoylated RANGAP1. Interacts with CDCA8.
INTERACTION: P04626:ERBB2; NbExp=3; IntAct=EBI-973138, EBI-641062; O60260:PARK2; NbExp=11; IntAct=EBI-973138, EBI-716346; Q53GG5:PDLIM3; NbExp=3; IntAct=EBI-973138, EBI-5658852;
SUBCELLULAR LOCATION: Nucleus, nuclear pore complex. Note=Cytoplasmic filaments.
DOMAIN: Contains F-X-F-G repeats.
PTM: Polyubiquitinated by PARK2, which leads to proteasomal degradation.
DISEASE: Defects in RANBP2 are the cause of encephalopathy acute infection-induced type 3 (IIAE3) [MIM:608033]. A rapidly progressive encephalopathy manifesting in susceptibile individuals with seizures and coma. It can occur within days in otherwise healthy children after common viral infections such as influenza and parainfluenza, without evidence of viral infection of the brain or inflammatory cell infiltration. Brain T2-weighted magnetic resonance imaging reveals characteristic symmetric lesions present in the thalami, pons and brainstem. Note=Mutations in the RANBP2 gene predispose to IIAE3, but by themselves are insufficient to make the phenotype fully penetrant; additional genetic and environmental factors are required (PubMed:19118815).
SIMILARITY: Contains 1 PPIase cyclophilin-type domain.
SIMILARITY: Contains 4 RanBD1 domains.
SIMILARITY: Contains 8 RanBP2-type zinc fingers.
SIMILARITY: Contains 1 TPR repeat.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/RANBP2ID483.html";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RANBP2
CDC HuGE Published Literature: RANBP2

-  MalaCards Disease Associations
  MalaCards Gene Search: RANBP2
Diseases sorted by gene-association score: inflammatory myofibroblastic tumor* (265), infection-induced acute encephalopathy 3, susceptibility* (100), familial acute necrotizing encephalopathy* (68), acute necrotizing encephalopathy (29), encephalopathy, acute, infection-induced, 4* (18), encephalopathy (17), influenza (12), acute hemorrhagic leukoencephalitis (9), mesenchymal cell neoplasm (6)
* = Manually curated disease association

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 18.43 RPKM in Testis
Total median expression: 525.17 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 -58.20126-0.462 Picture PostScript Text
3' UTR -453.381910-0.237 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
IPR002130 - Cyclophilin-like_PPIase_dom
IPR020892 - Cyclophilin-type_PPIase_CS
IPR022011 - IR1-M
IPR011993 - PH_like_dom
IPR000156 - Ran_bind_dom
IPR001440 - TPR-1
IPR013026 - TPR-contain_dom
IPR011990 - TPR-like_helical
IPR019734 - TPR_repeat
IPR001876 - Znf_RanBP2

Pfam Domains:
PF00160 - Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
PF00638 - RanBP1 domain
PF00641 - Zn-finger in Ran binding protein and others
PF12185 - Nup358/RanBP2 E3 ligase domain
PF13181 - Tetratricopeptide repeat

SCOP Domains:
81901 - HCP-like
48439 - Protein prenylyltransferase
48452 - TPR-like
50729 - PH domain-like
50891 - Cyclophilin-like
90209 - Znf265, first zinc-finger domain

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

1RRP
- X-ray MuPIT

1XKE
- NMR MuPIT

1Z5S
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
3UIN - X-ray MuPIT 3UIO - X-ray MuPIT 3UIP - X-ray MuPIT
4GA0 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P49792
FrontTopSide
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
No orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008536 Ran GTPase binding
GO:0016740 transferase activity
GO:0019789 SUMO transferase activity
GO:0046872 metal ion binding
GO:0005096 GTPase activator activity
GO:0003755 peptidyl-prolyl cis-trans isomerase activity
GO:0016018 cyclosporin A binding

Biological Process:
GO:0000082 G1/S transition of mitotic cell cycle
GO:0000413 protein peptidyl-prolyl isomerization
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0006457 protein folding
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006607 NLS-bearing protein import into nucleus
GO:0007051 spindle organization
GO:0015031 protein transport
GO:0016032 viral process
GO:0016925 protein sumoylation
GO:0043547 positive regulation of GTPase activity
GO:0046604 positive regulation of mitotic centrosome separation
GO:0046907 intracellular transport
GO:0051028 mRNA transport
GO:0051642 centrosome localization

Cellular Component:
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005642 annulate lamellae
GO:0005643 nuclear pore
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005829 cytosol
GO:0016020 membrane
GO:0031965 nuclear membrane
GO:0042405 nuclear inclusion body
GO:0044614 nuclear pore cytoplasmic filaments
GO:0044615 nuclear pore nuclear basket


-  Descriptions from all associated GenBank mRNAs
  D42063 - Homo sapiens mRNA for RanBP2 (Ran-binding protein 2), complete cds.
LP895392 - Sequence 256 from Patent EP3253886.
JD247658 - Sequence 228682 from Patent EP1572962.
JD490303 - Sequence 471327 from Patent EP1572962.
AB209483 - Homo sapiens mRNA for RAN binding protein 2 variant protein.
DQ578622 - Homo sapiens piRNA piR-46734, complete sequence.
JD168593 - Sequence 149617 from Patent EP1572962.
AK026993 - Homo sapiens cDNA: FLJ23340 fis, clone HEP13465, highly similar to HUMRANBP2 Human mRNA for RanBP2.
U19240 - Human Ran binding protein mRNA, partial cds.
AK025711 - Homo sapiens cDNA: FLJ22058 fis, clone HEP10089, highly similar to HUMRANBP2 Human mRNA for RanBP2 (Ran-binding protein 2).
U19248 - Human Ran binding protein mRNA, partial cds.
AY170822 - Homo sapiens transformation-related protein 1 mRNA, complete cds.
JD023731 - Sequence 4755 from Patent EP1572962.
AY170823 - Homo sapiens transformation-related protein 2 mRNA, complete cds.
AK025462 - Homo sapiens cDNA: FLJ21809 fis, clone HEP00942, highly similar to HUMRANBP2 Human mRNA for RanBP2 (Ran-binding protein 2).
JD555229 - Sequence 536253 from Patent EP1572962.
JD284030 - Sequence 265054 from Patent EP1572962.
JD509460 - Sequence 490484 from Patent EP1572962.
JD285158 - Sequence 266182 from Patent EP1572962.
JD548185 - Sequence 529209 from Patent EP1572962.
JD411633 - Sequence 392657 from Patent EP1572962.
JD299460 - Sequence 280484 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_npcPathway - Mechanism of Protein Import into the Nucleus
h_ranbp2Pathway - Sumoylation by RanBP2 Regulates Transcriptional Repression
h_ranPathway - Cycling of Ran in nucleocytoplasmic transport

Reactome (by CSHL, EBI, and GO)

Protein P49792 (Reactome details) participates in the following event(s):

R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-165043 Rev multimer-bound HIV mRNA:Crm1:Ran:GTP complex associates with the NPC
R-HSA-180622 Vpr binds nucleoporins
R-HSA-180710 Rev:importin beta:B23 recruited to the nuclear pore
R-HSA-2990882 CDK1 phosphorylates NUP98
R-HSA-75098 mRNP complex dissociates from cytosolic face of NPC
R-HSA-165047 Translocation of nuclear RNA transport complex to cytoplasm
R-HSA-180732 Translocation of Rev:importin-beta:B23 to the nucleus
R-HSA-141409 Mad1 binds kinetochore
R-HSA-375302 Kinetochore capture of astral microtubules
R-HSA-5666129 CDC42:GTP recruits DIAPH2-2 to kinetochores
R-HSA-5666169 Kinetochore capture of astral microtubules is positively regulated by CDC42:GTP:p-S196-DIAPH2-2
R-HSA-2990880 NEK6/NEK7 phosphorylates NUP98
R-HSA-170796 NPC transports GCK1:GKRP from cytosol to nucleoplasm
R-HSA-5578744 Importin-8 imports AGO2:miRNA into the nucleus
R-HSA-6783483 tRNA:XPOT:RAN:GTP translocates from the nucleus to the cytosol
R-HSA-3000348 RANBP2 SUMOylates SP100 with SUMO2
R-HSA-3000399 RANBP2 SUMOylates SP100 with SUMO1
R-HSA-3000411 RANBP2 SUMOylates PML with SUMO2
R-HSA-4570493 RANBP2 (NUP358) SUMOylates HNRNPC with SUMO1
R-HSA-4615872 RANBP2 SUMOylates HDAC4 with SUMO1
R-HSA-4615987 RANBP2 SUMOylates HDAC4 with SUMO2,3
R-HSA-5228508 RANBP2 SUMOylates PML with SUMO1
R-HSA-5228525 RANBP2 SUMOylates TOP2A with SUMO1
R-HSA-192627 Viral mRNA Export
R-HSA-192925 Export of Spliced Viral mRNA
R-HSA-5252041 NPC transports Hikeshi:HSP70s:ATP from cytosol to nucleoplasm
R-HSA-141431 MAD2 associates with the Mad1 kinetochore complex
R-HSA-141439 Release of activated MAD2 from kinetochores
R-HSA-2467811 Separation of sister chromatids
R-HSA-2467809 ESPL1 (Separase) cleaves centromeric cohesin
R-HSA-5666160 AURKB phosphorylates DIAPH2-2 at kinetochores
R-HSA-141422 MAD2 converted to an inhibitory state via interaction with Mad1
R-HSA-1638821 PP2A-B56 dephosphorylates centromeric cohesin
R-HSA-1638803 Phosphorylation of cohesin by PLK1 at centromeres
R-HSA-2468287 CDK1 phosphorylates CDCA5 (Sororin) at centromeres
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-165054 Rev-mediated nuclear export of HIV RNA
R-HSA-180910 Vpr-mediated nuclear import of PICs
R-HSA-180746 Nuclear import of Rev protein
R-HSA-3301854 Nuclear Pore Complex (NPC) Disassembly
R-HSA-141444 Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
R-HSA-68877 Mitotic Prometaphase
R-HSA-5663220 RHO GTPases Activate Formins
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-177243 Interactions of Rev with host cellular proteins
R-HSA-176033 Interactions of Vpr with host cellular proteins
R-HSA-2980766 Nuclear Envelope Breakdown
R-HSA-170822 Regulation of Glucokinase by Glucokinase Regulatory Protein
R-HSA-168276 NS1 Mediated Effects on Host Pathways
R-HSA-1169408 ISG15 antiviral mechanism
R-HSA-5578749 Transcriptional regulation by small RNAs
R-HSA-6784531 tRNA processing in the nucleus
R-HSA-3108214 SUMOylation of DNA damage response and repair proteins
R-HSA-4570464 SUMOylation of RNA binding proteins
R-HSA-4551638 SUMOylation of chromatin organization proteins
R-HSA-4615885 SUMOylation of DNA replication proteins
R-HSA-168325 Viral Messenger RNA Synthesis
R-HSA-3371453 Regulation of HSF1-mediated heat shock response
R-HSA-2500257 Resolution of Sister Chromatid Cohesion
R-HSA-2467813 Separation of Sister Chromatids
R-HSA-141424 Amplification of signal from the kinetochores
R-HSA-68886 M Phase
R-HSA-195258 RHO GTPase Effectors
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-162587 HIV Life Cycle
R-HSA-162909 Host Interactions of HIV factors
R-HSA-68875 Mitotic Prophase
R-HSA-70171 Glycolysis
R-HSA-168253 Host Interactions with Influenza Factors
R-HSA-1169410 Antiviral mechanism by IFN-stimulated genes
R-HSA-211000 Gene Silencing by RNA
R-HSA-72306 tRNA processing
R-HSA-3108232 SUMO E3 ligases SUMOylate target proteins
R-HSA-168273 Influenza Viral RNA Transcription and Replication
R-HSA-3371556 Cellular response to heat stress
R-HSA-68882 Mitotic Anaphase
R-HSA-69618 Mitotic Spindle Checkpoint
R-HSA-69278 Cell Cycle (Mitotic)
R-HSA-194315 Signaling by Rho GTPases
R-HSA-8953854 Metabolism of RNA
R-HSA-162906 HIV Infection
R-HSA-70326 Glucose metabolism
R-HSA-168254 Influenza Infection
R-HSA-913531 Interferon Signaling
R-HSA-74160 Gene expression (Transcription)
R-HSA-2990846 SUMOylation
R-HSA-168255 Influenza Life Cycle
R-HSA-2262752 Cellular responses to stress
R-HSA-2555396 Mitotic Metaphase and Anaphase
R-HSA-69620 Cell Cycle Checkpoints
R-HSA-1640170 Cell Cycle
R-HSA-162582 Signal Transduction
R-HSA-5663205 Infectious disease
R-HSA-71387 Metabolism of carbohydrates
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-597592 Post-translational protein modification
R-HSA-8953897 Cellular responses to external stimuli
R-HSA-1643685 Disease
R-HSA-1430728 Metabolism
R-HSA-168256 Immune System
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: NM_006267, NP_006258, NUP358, P49792, Q13074, Q15280, Q53TE2, Q59FH7, RBP2_HUMAN
UCSC ID: uc002tem.4
RefSeq Accession: NM_006267
Protein: P49792 (aka RBP2_HUMAN)
CCDS: CCDS2079.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene RANBP2:
iiae3 (Susceptibility to Infection-Induced Acute Encephalopathy 3)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006267.4
exon count: 29CDS single in 3' UTR: no RNA size: 11711
ORF size: 9675CDS single in intron: no Alignment % ID: 99.99
txCdsPredict score: 17984.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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