Human Gene RANBP6 (uc003zjr.3)
  Description: Homo sapiens RAN binding protein 6 (RANBP6), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:6,011,019-6,015,640 Size: 4,622 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg19 chr9:6,012,290-6,015,607 Size: 3,318 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:6,011,019-6,015,640)mRNA (may differ from genome)Protein (1105 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RNBP6_HUMAN
DESCRIPTION: RecName: Full=Ran-binding protein 6; Short=RanBP6;
FUNCTION: May function in nuclear protein import as nuclear transport receptor.
INTERACTION: Q76353:- (xeno); NbExp=2; IntAct=EBI-1055771, EBI-6248077;
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Nucleus (By similarity).
SIMILARITY: Belongs to the importin beta family.
SIMILARITY: Contains 7 HEAT repeats.
SEQUENCE CAUTION: Sequence=CAD97647.1; Type=Erroneous initiation;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RANBP6
CDC HuGE Published Literature: RANBP6
Positive Disease Associations: Asthma
Related Studies:
  1. Asthma
    Miriam F Moffatt et al. The New England journal of medicine 2010, A large-scale, consortium-based genomewide association study of asthma., The New England journal of medicine. [PubMed 20860503]
    Asthma is genetically heterogeneous. A few common alleles are associated with disease risk at all ages. Implicated genes suggest a role for communication of epithelial damage to the adaptive immune system and activation of airway inflammation. Variants at the ORMDL3/GSDMB locus are associated only with childhood-onset disease. Elevation of total serum IgE levels has a minor role in the development of asthma. (Funded by the European Commission and others.)
  2. Asthma
    Dara G Torgerson et al. Nature genetics 2011, Meta-analysis of genome-wide association studies of asthma in ethnically diverse North American populations., Nature genetics. [PubMed 21804549]

-  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: 10.90 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 279.37 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 -6.1033-0.185 Picture PostScript Text
3' UTR -333.151271-0.262 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
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR000357 - HEAT

Pfam Domains:
PF02985 - HEAT repeat
PF13513 - HEAT-like repeat
PF13646 - HEAT repeats

SCOP Domains:
48371 - ARM repeat
48431 - Lipovitellin-phosvitin complex, superhelical domain

ModBase Predicted Comparative 3D Structure on O60518
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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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008139 nuclear localization sequence binding
GO:0008565 protein transporter activity

Biological Process:
GO:0000060 protein import into nucleus, translocation
GO:0006607 NLS-bearing protein import into nucleus
GO:0006610 ribosomal protein import into nucleus
GO:0015031 protein transport

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0031965 nuclear membrane
GO:0034399 nuclear periphery


-  Descriptions from all associated GenBank mRNAs
  LF211301 - JP 2014500723-A/18804: Polycomb-Associated Non-Coding RNAs.
LF211302 - JP 2014500723-A/18805: Polycomb-Associated Non-Coding RNAs.
BX537405 - Homo sapiens mRNA; cDNA DKFZp686A1752 (from clone DKFZp686A1752).
BC098406 - Homo sapiens RAN binding protein 6, mRNA (cDNA clone MGC:104721 IMAGE:30347107), complete cds.
BC037423 - Homo sapiens RAN binding protein 6, mRNA (cDNA clone IMAGE:5496627), with apparent retained intron.
BC019838 - Homo sapiens RAN binding protein 6, mRNA (cDNA clone IMAGE:4480329), with apparent retained intron.
BC012805 - Homo sapiens RAN binding protein 6, mRNA (cDNA clone IMAGE:3507184), complete cds.
AK001982 - Homo sapiens cDNA FLJ11120 fis, clone PLACE1006119, highly similar to Homo sapiens Ran-GTP binding protein mRNA.
JD088044 - Sequence 69068 from Patent EP1572962.
LF345391 - JP 2014500723-A/152894: Polycomb-Associated Non-Coding RNAs.
JD416714 - Sequence 397738 from Patent EP1572962.
JD281067 - Sequence 262091 from Patent EP1572962.
JD089948 - Sequence 70972 from Patent EP1572962.
JD360822 - Sequence 341846 from Patent EP1572962.
LF345392 - JP 2014500723-A/152895: Polycomb-Associated Non-Coding RNAs.
JD083977 - Sequence 65001 from Patent EP1572962.
AK300408 - Homo sapiens cDNA FLJ54311 complete cds, highly similar to Ran-binding protein 6.
JD554192 - Sequence 535216 from Patent EP1572962.
AK304559 - Homo sapiens cDNA FLJ59084 complete cds, highly similar to Ran-binding protein 6.
JD273406 - Sequence 254430 from Patent EP1572962.
JD282438 - Sequence 263462 from Patent EP1572962.
KJ893581 - Synthetic construct Homo sapiens clone ccsbBroadEn_02975 RANBP6 gene, encodes complete protein.
AF039023 - Homo sapiens Ran-GTP binding protein mRNA, partial cds.
AK307840 - Homo sapiens cDNA, FLJ97788.
JD510231 - Sequence 491255 from Patent EP1572962.
LF345393 - JP 2014500723-A/152896: Polycomb-Associated Non-Coding RNAs.
JD424395 - Sequence 405419 from Patent EP1572962.
JD473246 - Sequence 454270 from Patent EP1572962.
JD309035 - Sequence 290059 from Patent EP1572962.
JD095718 - Sequence 76742 from Patent EP1572962.
LF345394 - JP 2014500723-A/152897: Polycomb-Associated Non-Coding RNAs.
JD489825 - Sequence 470849 from Patent EP1572962.
LF345395 - JP 2014500723-A/152898: Polycomb-Associated Non-Coding RNAs.
MA580968 - JP 2018138019-A/152894: Polycomb-Associated Non-Coding RNAs.
MA580969 - JP 2018138019-A/152895: Polycomb-Associated Non-Coding RNAs.
MA580970 - JP 2018138019-A/152896: Polycomb-Associated Non-Coding RNAs.
MA580971 - JP 2018138019-A/152897: Polycomb-Associated Non-Coding RNAs.
MA580972 - JP 2018138019-A/152898: Polycomb-Associated Non-Coding RNAs.
MA446878 - JP 2018138019-A/18804: Polycomb-Associated Non-Coding RNAs.
MA446879 - JP 2018138019-A/18805: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_012416, NP_036548, O60518, Q5T7X4, Q7Z3V2, Q96E78, RNBP6_HUMAN
UCSC ID: uc003zjr.3
RefSeq Accession: NM_012416
Protein: O60518 (aka RNBP6_HUMAN)
CCDS: CCDS6467.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012416.3
exon count: 1CDS single in 3' UTR: no RNA size: 4628
ORF size: 3318CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6836.00frame shift in genome: no % Coverage: 99.87
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # 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.