Human Gene RBM17 (uc010qav.2)
  Description: Homo sapiens RNA binding motif protein 17 (RBM17), transcript variant 2, mRNA.
RefSeq Summary (NM_001145547): This gene encodes an RNA binding protein. The encoded protein is part of the spliceosome complex and functions in the second catalytic step of mRNA splicing. Alternatively spliced transcript variants have been described. Related pseudogenes exist on chromosomes 9 and 15. [provided by RefSeq, Mar 2009].
Transcript (Including UTRs)
   Position: hg19 chr10:6,131,309-6,159,422 Size: 28,114 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr10:6,139,029-6,157,519 Size: 18,491 Coding Exon Count: 11 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:6,131,309-6,159,422)mRNA (may differ from genome)Protein (401 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
H-INVHGNCLynxMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SPF45_HUMAN
DESCRIPTION: RecName: Full=Splicing factor 45; AltName: Full=45 kDa-splicing factor; AltName: Full=RNA-binding motif protein 17;
FUNCTION: Splice factor that binds to the single stranded 3'AG at the exon/intron border and promotes its utilization in the second catalytic step. Involved in the regulation of alternative splicing and the utilization of cryptic splice sites. Promotes the utilization of a cryptic splice site created by the beta-110 mutation in the HBB gene. The resulting frameshift leads to sickle cell anemia.
SUBUNIT: Binds SXL. Associates with the spliceosome.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Contains 1 G-patch domain.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  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): RBM17
CDC HuGE Published Literature: RBM17

-  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: 31.16 RPKM in Spleen
Total median expression: 947.98 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 -264.10644-0.410 Picture PostScript Text
3' UTR -482.801903-0.254 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
IPR000467 - G_patch_dom
IPR012677 - Nucleotide-bd_a/b_plait
IPR003954 - RRM_dom_euk
IPR016967 - Splicing_factor_SPF45

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF01585 - G-patch domain

SCOP Domains:
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2PE8 - X-ray MuPIT 2PEH - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96I25
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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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  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:0000380 alternative mRNA splicing, via spliceosome
GO:0000398 mRNA splicing, via spliceosome
GO:0006281 DNA repair
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0043484 regulation of RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0032991 macromolecular complex


-  Descriptions from all associated GenBank mRNAs
  AF542550 - Homo sapiens chromosome 10 map NT_033983.1 unknown mRNA.
AK314952 - Homo sapiens cDNA, FLJ95864.
BC007871 - Homo sapiens RNA binding motif protein 17, mRNA (cDNA clone MGC:14439 IMAGE:4303675), complete cds.
BC039322 - Homo sapiens RNA binding motif protein 17, mRNA (cDNA clone MGC:43415 IMAGE:5267008), complete cds.
JD128825 - Sequence 109849 from Patent EP1572962.
JD221427 - Sequence 202451 from Patent EP1572962.
JD495430 - Sequence 476454 from Patent EP1572962.
JD264388 - Sequence 245412 from Patent EP1572962.
JD420476 - Sequence 401500 from Patent EP1572962.
JD163992 - Sequence 145016 from Patent EP1572962.
JD398483 - Sequence 379507 from Patent EP1572962.
JD398482 - Sequence 379506 from Patent EP1572962.
JD396021 - Sequence 377045 from Patent EP1572962.
JD235550 - Sequence 216574 from Patent EP1572962.
JD453933 - Sequence 434957 from Patent EP1572962.
CU675847 - Synthetic construct Homo sapiens gateway clone IMAGE:100017191 5' read RBM17 mRNA.
AB528910 - Synthetic construct DNA, clone: pF1KE0688, Homo sapiens RBM17 gene for RNA binding motif protein 17, without stop codon, in Flexi system.
HQ448221 - Synthetic construct Homo sapiens clone IMAGE:100071622; CCSB005200_01 RNA binding motif protein 17 (RBM17) gene, encodes complete protein.
KJ899858 - Synthetic construct Homo sapiens clone ccsbBroadEn_09252 RBM17 gene, encodes complete protein.
KJ904931 - Synthetic construct Homo sapiens clone ccsbBroadEn_14325 RBM17 gene, encodes complete protein.
BC009064 - Homo sapiens RNA binding motif protein 17, mRNA (cDNA clone IMAGE:3868191), partial cds.
JD351305 - Sequence 332329 from Patent EP1572962.
JD501461 - Sequence 482485 from Patent EP1572962.
BX648288 - Homo sapiens mRNA; cDNA DKFZp686F13131 (from clone DKFZp686F13131).
FW340000 - Screening.
AK021863 - Homo sapiens cDNA FLJ11801 fis, clone HEMBA1006253, weakly similar to DNA-DAMAGE-REPAIR/TOLERATION PROTEIN DRT111 PRECURSOR.
JD137196 - Sequence 118220 from Patent EP1572962.
JD087549 - Sequence 68573 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein Q96I25 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: NM_001145547, NP_116294, Q96GY6, Q96I25, SPF45, SPF45_HUMAN
UCSC ID: uc010qav.2
RefSeq Accession: NM_001145547
Protein: Q96I25 (aka SPF45_HUMAN or SF45_HUMAN)
CCDS: CCDS7077.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001145547.1
exon count: 12CDS single in 3' UTR: no RNA size: 3760
ORF size: 1206CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2415.00frame shift in genome: no % Coverage: 99.81
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.