Human Gene SRSF5 (uc001xll.3) Description and Page Index
  Description: Homo sapiens serine/arginine-rich splicing factor 5 (SRSF5), transcript variant 1, mRNA.
RefSeq Summary (NM_006925): The protein encoded by this gene is a member of the serine/arginine (SR)-rich family of pre-mRNA splicing factors, which constitute part of the spliceosome. Each of these factors contains an RNA recognition motif (RRM) for binding RNA and an RS domain for binding other proteins. The RS domain is rich in serine and arginine residues and facilitates interaction between different SR splicing factors. In addition to being critical for mRNA splicing, the SR proteins have also been shown to be involved in mRNA export from the nucleus and in translation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016].
Transcript (Including UTRs)
   Position: hg19 chr14:70,193,619-70,238,722 Size: 45,104 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr14:70,234,874-70,238,178 Size: 3,305 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr14:70,193,619-70,238,722)mRNA (may differ from genome)Protein (272 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SRSF5_HUMAN
DESCRIPTION: RecName: Full=Serine/arginine-rich splicing factor 5; AltName: Full=Delayed-early protein HRS; AltName: Full=Pre-mRNA-splicing factor SRP40; AltName: Full=Splicing factor, arginine/serine-rich 5;
FUNCTION: Plays a role in constitutive splicing and can modulate the selection of alternative splice sites.
SUBUNIT: Interacts (via RS domain) with PHF5A (via N-terminus) (By similarity). Found in a pre-mRNA splicing complex with SRSF4/SFRS4, SRSF5/SFRS5, SNRNP70, SNRPA1, SRRM1 and SRRM2.
SUBCELLULAR LOCATION: Nucleus.
PTM: Extensively phosphorylated on serine residues in the RS domain (By similarity).
SIMILARITY: Belongs to the splicing factor SR family.
SIMILARITY: Contains 2 RRM (RNA recognition motif) domains.
SEQUENCE CAUTION: Sequence=AAC39543.1; Type=Frameshift; Positions=113, 140;

-  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: 218.52 RPKM in Pituitary
Total median expression: 5700.38 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 -565.201451-0.390 Picture PostScript Text
3' UTR -146.02544-0.268 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
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

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

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q13243
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0043422 protein kinase B binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0001889 liver development
GO:0006376 mRNA splice site selection
GO:0006397 mRNA processing
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0008380 RNA splicing
GO:0031124 mRNA 3'-end processing
GO:0032868 response to insulin
GO:0032869 cellular response to insulin stimulus
GO:0033120 positive regulation of RNA splicing
GO:0051726 regulation of cell cycle
GO:0097421 liver regeneration

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005829 cytosol
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  BC040209 - Homo sapiens splicing factor, arginine/serine-rich 5, mRNA (cDNA clone MGC:42507 IMAGE:4823314), complete cds.
JD558398 - Sequence 539422 from Patent EP1572962.
JD320236 - Sequence 301260 from Patent EP1572962.
BX640605 - Homo sapiens mRNA; cDNA DKFZp686L2175 (from clone DKFZp686L2175); complete cds.
BC095420 - Homo sapiens splicing factor, arginine/serine-rich 5, mRNA (cDNA clone IMAGE:30520500), with apparent retained intron.
AK311805 - Homo sapiens cDNA, FLJ92066, Homo sapiens splicing factor, arginine/serine-rich 5 (SFRS5), mRNA.
AK296113 - Homo sapiens cDNA FLJ57379 complete cds, highly similar to Splicing factor, arginine/serine-rich 5.
AK300560 - Homo sapiens cDNA FLJ57437 complete cds, highly similar to Splicing factor, arginine/serine-rich 5.
JD019929 - Sequence 953 from Patent EP1572962.
BC018823 - Homo sapiens splicing factor, arginine/serine-rich 5, mRNA (cDNA clone MGC:1236 IMAGE:3346982), complete cds.
BX247988 - human full-length cDNA clone CS0DF038YO05 of Fetal brain of Homo sapiens (human).
AB209804 - Homo sapiens premature mRNA for CS0DF038YO05 variant.
U30884 - Human splicing factor SRp40-2 (SRp40) mRNA, complete cds.
U30826 - Human splicing factor SRp40-1 (SRp40) mRNA, complete cds.
U30827 - Human splicing factor SRp40-3 (SRp40) mRNA, complete cds.
JD033381 - Sequence 14405 from Patent EP1572962.
AB464246 - Synthetic construct DNA, clone: pF1KB6381, Homo sapiens SFRS5 gene for splicing factor, arginine/serine-rich 5, without stop codon, in Flexi system.
KJ892130 - Synthetic construct Homo sapiens clone ccsbBroadEn_01524 SRSF5 gene, encodes complete protein.
AB451374 - Homo sapiens SFRS5 mRNA for splicing factor arginine/serine-rich 5, partial cds, clone: FLJ08060AAAF.
CR542182 - Homo sapiens full open reading frame cDNA clone RZPDo834F0224D for gene SFRS5, splicing factor, arginine/serine-rich 5; complete cds, without stopcodon.
AB451250 - Homo sapiens SFRS5 mRNA for splicing factor arginine/serine-rich 5, complete cds, clone: FLJ08060AAAN.
CR542167 - Homo sapiens full open reading frame cDNA clone RZPDo834C0624D for gene SFRS5, splicing factor, arginine/serine-rich 5; complete cds, incl. stopcodon.
BT007089 - Homo sapiens splicing factor, arginine/serine-rich 5 mRNA, complete cds.
BC029984 - Homo sapiens splicing factor, arginine/serine-rich 5, mRNA (cDNA clone IMAGE:4214118).
AF070562 - Homo sapiens clone 24529 mRNA sequence.
JD526450 - Sequence 507474 from Patent EP1572962.
JD396231 - Sequence 377255 from Patent EP1572962.
JD396783 - Sequence 377807 from Patent EP1572962.
JD043655 - Sequence 24679 from Patent EP1572962.
JD306159 - Sequence 287183 from Patent EP1572962.
JD426856 - Sequence 407880 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein Q13243 (Reactome details) participates in the following event(s):

R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally
R-HSA-72185 mRNA polyadenylation
R-HSA-72180 Cleavage of mRNA at the 3'-end
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72187 mRNA 3'-end processing
R-HSA-109688 Cleavage of Growing Transcript in the Termination Region
R-HSA-72172 mRNA Splicing
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-73856 RNA Polymerase II Transcription Termination
R-HSA-8953854 Metabolism of RNA
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: BC040209, HRS, NM_006925, NP_008856, O14797, Q13243, Q16662, Q49AD6, Q6FGE0, SFRS5, SRP40, SRSF5_HUMAN
UCSC ID: uc001xll.3
RefSeq Accession: NM_006925
Protein: Q13243 (aka SRSF5_HUMAN)
CCDS: CCDS32109.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: BC040209.1
exon count: 9CDS single in 3' UTR: no RNA size: 2832
ORF size: 819CDS single in intron: no Alignment % ID: 99.93
txCdsPredict score: 1497.00frame shift in genome: no % Coverage: 99.36
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.