Human Gene RBM39 (uc002xeb.3) Description and Page Index
  Description: Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA.
RefSeq Summary (NM_184234): This gene encodes a member of the U2AF65 family of proteins. The encoded protein is found in the nucleus, where it co-localizes with core spliceosomal proteins. It has been shown to play a role in both steroid hormone receptor-mediated transcription and alternative splicing, and it is also a transcriptional coregulator of the viral oncoprotein v-Rel. Multiple transcript variants have been observed for this gene. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Aug 2011].
Transcript (Including UTRs)
   Position: hg19 chr20:34,291,531-34,330,258 Size: 38,728 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr20:34,292,403-34,328,796 Size: 36,394 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:34,291,531-34,330,258)mRNA (may differ from genome)Protein (530 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: RBM39_HUMAN
DESCRIPTION: RecName: Full=RNA-binding protein 39; AltName: Full=Hepatocellular carcinoma protein 1; AltName: Full=RNA-binding motif protein 39; AltName: Full=RNA-binding region-containing protein 2; AltName: Full=Splicing factor HCC1;
FUNCTION: Transcriptional coactivator for steroid nuclear receptors ESR1/ER-alpha and ESR2/ER-beta, and JUN/AP-1 (By similarity). May be involved in pre-mRNA splicing process.
SUBUNIT: Interacts with NCOA6 (By similarity). Interacts with RSRC1 (via Arg/Ser-rich domain).
SUBCELLULAR LOCATION: Nucleus speckle. Note=Concentrated in nuclear speckles. Colocalizes with the core spliceosomal snRNP proteins.
TISSUE SPECIFICITY: Widely expressed. Highly expressed in pancreas, skeletal muscle, lung and brain. Expressed at intermediate level in kidney, liver and heart.
MISCELLANEOUS: Antibodies against RNPC2 are present in sera from a patient with hepatocellular carcinoma who developed several autoantibodies.
SIMILARITY: Belongs to the splicing factor SR family.
SIMILARITY: Contains 3 RRM (RNA recognition motif) domains.

-  MalaCards Disease Associations
  MalaCards Gene Search: RBM39
Diseases sorted by gene-association score: colorectal adenoma (3), hepatocellular carcinoma (3)

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 89.17 RPKM in Ovary
Total median expression: 2561.60 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 -172.44409-0.422 Picture PostScript Text
3' UTR -212.09872-0.243 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
IPR006509 - CC1_SF
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF13893 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF15519 - linker between RRM2 and RRM3 domains in RBM39 protein

SCOP Domains:
54928 - RNA-binding domain, RBD

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

2JRS
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q14498
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 orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005815 microtubule organizing center
GO:0015630 microtubule cytoskeleton
GO:0016607 nuclear speck
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  L10911 - Homo sapiens splicing factor (CC1.4) mRNA, complete cds.
L10910 - Homo sapiens splicing factor (CC1.3) mRNA, complete cds.
BC107886 - Homo sapiens RNA-binding region (RNP1, RRM) containing 2, mRNA (cDNA clone IMAGE:6668060).
BC141835 - Homo sapiens RNA binding motif protein 39, mRNA (cDNA clone MGC:165071 IMAGE:40148871), complete cds.
BC158172 - Homo sapiens RNA binding motif protein 39, mRNA (cDNA clone MGC:164941 IMAGE:40148190), complete cds.
GQ900961 - Homo sapiens clone HEL-T-73 epididymis secretory sperm binding protein mRNA, complete cds.
AL833168 - Homo sapiens mRNA; cDNA DKFZp686N0118 (from clone DKFZp686N0118).
BX640812 - Homo sapiens mRNA; cDNA DKFZp686C17209 (from clone DKFZp686C17209).
CR749443 - Homo sapiens mRNA; cDNA DKFZp781C0423 (from clone DKFZp781C0423).
JD486567 - Sequence 467591 from Patent EP1572962.
JD090711 - Sequence 71735 from Patent EP1572962.
JD563954 - Sequence 544978 from Patent EP1572962.
AK299678 - Homo sapiens cDNA FLJ59214 complete cds, highly similar to RNA-binding region-containing protein 2.
JD486741 - Sequence 467765 from Patent EP1572962.
JD260493 - Sequence 241517 from Patent EP1572962.
AK303910 - Homo sapiens cDNA FLJ58465 complete cds, highly similar to RNA-binding region-containing protein 2.
BC131543 - Homo sapiens RNA binding motif protein 39, mRNA (cDNA clone MGC:141906 IMAGE:40085367), complete cds.
AK297520 - Homo sapiens cDNA FLJ59035 complete cds, highly similar to RNA-binding region-containing protein 2.
JD527370 - Sequence 508394 from Patent EP1572962.
BX640714 - Homo sapiens mRNA; cDNA DKFZp686A11192 (from clone DKFZp686A11192).
BX537770 - Homo sapiens mRNA; cDNA DKFZp781I1140 (from clone DKFZp781I1140); complete cds.
AK126158 - Homo sapiens cDNA FLJ44170 fis, clone THYMU2035319, highly similar to RNA-binding region-containing protein 2.
AK297060 - Homo sapiens cDNA FLJ60296 complete cds, highly similar to RNA-binding region-containing protein 2.
AK299165 - Homo sapiens cDNA FLJ58459 complete cds, highly similar to RNA-binding region-containing protein 2.
AK130283 - Homo sapiens cDNA FLJ26773 fis, clone PRS03513.
KJ906002 - Synthetic construct Homo sapiens clone ccsbBroadEn_15672 RBM39 gene, encodes complete protein.
AB590896 - Synthetic construct DNA, clone: pFN21AE1966, Homo sapiens RBM39 gene for RNA binding motif protein 39, without stop codon, in Flexi system.
BC008204 - Homo sapiens RNA-binding region (RNP1, RRM) containing 2, mRNA (cDNA clone IMAGE:3867490), with apparent retained intron.
JD066864 - Sequence 47888 from Patent EP1572962.
DQ656052 - Homo sapiens clone UGL062-A-H5, mRNA sequence.
JD167747 - Sequence 148771 from Patent EP1572962.
U92990 - Homo sapiens clone DT1P1F10 mRNA, CAG repeat region.

-  Other Names for This Gene
  Alternate Gene Symbols: A2RRD3, A5D8W2, B0BLV3, E1P5S0, E1P5S1, HCC1, NM_184234, NP_909122, Q14498, Q14499, RBM39_HUMAN, RNPC2
UCSC ID: uc002xeb.3
RefSeq Accession: NM_184234
Protein: Q14498 (aka RBM39_HUMAN)
CCDS: CCDS13265.1, CCDS13266.1, CCDS56186.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_184234.2
exon count: 17CDS single in 3' UTR: no RNA size: 2881
ORF size: 1593CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3003.50frame shift in genome: no % Coverage: 99.76
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: 344# 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.