Human Gene SYF2 (ENST00000236273.9_8) from GENCODE V47lift37
  Description: SYF2 pre-mRNA splicing factor, transcript variant 1 (from RefSeq NM_015484.5)
Gencode Transcript: ENST00000236273.9_8
Gencode Gene: ENSG00000117614.10_10
Transcript (Including UTRs)
   Position: hg19 chr1:25,548,767-25,558,993 Size: 10,227 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr1:25,549,757-25,558,958 Size: 9,202 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:25,548,767-25,558,993)mRNA (may differ from genome)Protein (243 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SYF2_HUMAN
DESCRIPTION: RecName: Full=Pre-mRNA-splicing factor SYF2; AltName: Full=CCNDBP1-interactor; AltName: Full=p29;
FUNCTION: May be involved in pre-mRNA splicing (By similarity).
SUBUNIT: Identified in the spliceosome C complex. Interacts with CCNDBP1.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Abundantly expressed in the heart, skeletal muscle and kidney. Expressed at lower level other tissues.
SIMILARITY: Belongs to the SYF2 family.
SEQUENCE CAUTION: Sequence=CAI21417.1; Type=Erroneous gene model prediction;

-  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


-  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: 27.06 RPKM in Ovary
Total median expression: 773.46 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 -4.4035-0.126 Picture PostScript Text
3' UTR -227.70990-0.230 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
IPR013260 - mRNA_splic_SYF2

Pfam Domains:
PF08231 - SYF2 splicing factor

ModBase Predicted Comparative 3D Structure on O95926
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 orthologNo orthologNo orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

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

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0001701 in utero embryonic development
GO:0006397 mRNA processing
GO:0007095 mitotic G2 DNA damage checkpoint
GO:0007369 gastrulation
GO:0008284 positive regulation of cell proliferation
GO:0008380 RNA splicing
GO:0048568 embryonic organ development

Cellular Component:
GO:0000974 Prp19 complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0016607 nuclear speck
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071013 catalytic step 2 spliceosome
GO:0071014 post-mRNA release spliceosomal complex


-  Descriptions from all associated GenBank mRNAs
  AL080166 - Homo sapiens mRNA; cDNA DKFZp564O2082 (from clone DKFZp564O2082).
BC010862 - Homo sapiens SYF2 homolog, RNA splicing factor (S. cerevisiae), mRNA (cDNA clone MGC:9401 IMAGE:3877165), complete cds.
AF273089 - Homo sapiens P29 mRNA, complete cds.
JD088280 - Sequence 69304 from Patent EP1572962.
JD146810 - Sequence 127834 from Patent EP1572962.
JD112636 - Sequence 93660 from Patent EP1572962.
JD403730 - Sequence 384754 from Patent EP1572962.
JD510174 - Sequence 491198 from Patent EP1572962.
AK314859 - Homo sapiens cDNA, FLJ95758, highly similar to Homo sapiens GCIP-interacting protein p29 (P29), mRNA.
DQ890663 - Synthetic construct clone IMAGE:100003293; FLH164891.01X; RZPDo839D04158D SYF2 homolog, RNA splicing factor (S. cerevisiae) (SYF2) gene, encodes complete protein.
CU679829 - Synthetic construct Homo sapiens gateway clone IMAGE:100016869 5' read SYF2 mRNA.
KJ893496 - Synthetic construct Homo sapiens clone ccsbBroadEn_02890 SYF2 gene, encodes complete protein.
EU176475 - Synthetic construct Homo sapiens clone IMAGE:100011338; FLH164890.01L; RZPDo839C01253D SYF2 homolog, RNA splicing factor (S. cerevisiae) (SYF2) gene, encodes complete protein.
AK303582 - Homo sapiens cDNA FLJ58970 complete cds, highly similar to Homo sapiens SYF2 homolog, RNA splicing factor (SYF2), transcript variant 1, mRNA.
BC015824 - Homo sapiens SYF2 homolog, RNA splicing factor (S. cerevisiae), mRNA (cDNA clone IMAGE:4042910), with apparent retained intron.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95926 (Reactome details) participates in the following event(s):

R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
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: CBPIN, ENST00000236273.1, ENST00000236273.2, ENST00000236273.3, ENST00000236273.4, ENST00000236273.5, ENST00000236273.6, ENST00000236273.7, ENST00000236273.8, GCIPIP, NM_015484, O95926, Q5TH73, SYF2_HUMAN, uc317ebb.1, uc317ebb.2
UCSC ID: ENST00000236273.9_8
RefSeq Accession: NM_015484.5
Protein: O95926 (aka SYF2_HUMAN)

-  Gene Model Information
  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.