This gene encodes a nuclear protein that interacts with cyclin D-type binding-protein 1, which is thought to be a cell cycle regulator at the G1/S transition. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008] See more...

Aliases for SYF2 Gene

Aliases for SYF2 Gene

  • SYF2 Pre-MRNA Splicing Factor 2 3 5
  • P29 2 3 4
  • Functional Spliceosome-Associated Protein 29 2 3
  • Pre-MRNA-Splicing Factor SYF2 3 4
  • CCNDBP1 Interactor 2 3
  • FSAP29 2 3
  • CBPIN 3 4
  • NTC31 2 3
  • SYF2 Homolog, RNA Splicing Factor (S. Cerevisiae) 2
  • SYF2 Homolog, RNA Splicing Factor 3
  • GCIP-Interacting Protein P29 3
  • CCNDBP1-Interactor 4
  • DKFZp564O2082 2
  • GCIPIP 4
  • SYF2 5

External Ids for SYF2 Gene

Previous HGNC Symbols for SYF2 Gene

  • CBPIN

Previous GeneCards Identifiers for SYF2 Gene

  • GC01M025296
  • GC01M025421
  • GC01M025548
  • GC01M023802

Summaries for SYF2 Gene

Entrez Gene Summary for SYF2 Gene

  • This gene encodes a nuclear protein that interacts with cyclin D-type binding-protein 1, which is thought to be a cell cycle regulator at the G1/S transition. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

GeneCards Summary for SYF2 Gene

SYF2 (SYF2 Pre-MRNA Splicing Factor) is a Protein Coding gene. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway.

UniProtKB/Swiss-Prot Summary for SYF2 Gene

  • Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28076346).

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYF2 Gene

Genomics for SYF2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SYF2 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYF2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYF2

Top Transcription factor binding sites by QIAGEN in the SYF2 gene promoter:
  • AML1a
  • CUTL1
  • Ik-2
  • IRF-1
  • IRF-7A
  • NF-1
  • NF-1/L
  • Pax-6
  • POU2F1
  • POU2F1a

Genomic Locations for SYF2 Gene

Genomic Locations for SYF2 Gene
chr1:25,222,276-25,232,502
(GRCh38/hg38)
Size:
10,227 bases
Orientation:
Minus strand
chr1:25,548,767-25,559,013
(GRCh37/hg19)
Size:
10,247 bases
Orientation:
Minus strand

Genomic View for SYF2 Gene

Genes around SYF2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYF2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYF2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYF2 Gene

Proteins for SYF2 Gene

  • Protein details for SYF2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95926-SYF2_HUMAN
    Recommended name:
    Pre-mRNA-splicing factor SYF2
    Protein Accession:
    O95926
    Secondary Accessions:
    • Q5TH73

    Protein attributes for SYF2 Gene

    Size:
    243 amino acids
    Molecular mass:
    28722 Da
    Quaternary structure:
    • Identified in the spliceosome C complex (PubMed:11991638, PubMed:28502770, PubMed:28076346). Interacts with CCNDBP1 (PubMed:11118353).

    Three dimensional structures from OCA and Proteopedia for SYF2 Gene

    Alternative splice isoforms for SYF2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SYF2 Gene

Post-translational modifications for SYF2 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYF2 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SYF2 Gene

Domains & Families for SYF2 Gene

Gene Families for SYF2 Gene

Protein Domains for SYF2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYF2 Gene

GenScript: Design optimal peptide antigens:
  • p29 (SYF2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O95926

UniProtKB/Swiss-Prot:

SYF2_HUMAN :
  • Belongs to the SYF2 family.
Family:
  • Belongs to the SYF2 family.
genes like me logo Genes that share domains with SYF2: view

Function for SYF2 Gene

Molecular function for SYF2 Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28076346).

Phenotypes From GWAS Catalog for SYF2 Gene

Gene Ontology (GO) - Molecular Function for SYF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding HDA 22658674
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with SYF2: view
genes like me logo Genes that share phenotypes with SYF2: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYF2

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SYF2 Gene

Localization for SYF2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYF2 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYF2 gene
Compartment Confidence
nucleus 5
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000974 Prp19 complex IBA 21873635
GO:0005634 nucleus NAS 11118353
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0016607 nuclear speck IDA --
genes like me logo Genes that share ontologies with SYF2: view

Pathways & Interactions for SYF2 Gene

genes like me logo Genes that share pathways with SYF2: view

Pathways by source for SYF2 Gene

Gene Ontology (GO) - Biological Process for SYF2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0001701 in utero embryonic development IEA --
GO:0006397 mRNA processing IEA --
GO:0007095 mitotic G2 DNA damage checkpoint IEA --
GO:0007369 gastrulation IEA --
genes like me logo Genes that share ontologies with SYF2: view

No data available for SIGNOR curated interactions for SYF2 Gene

Drugs & Compounds for SYF2 Gene

No Compound Related Data Available

Transcripts for SYF2 Gene

mRNA/cDNA for SYF2 Gene

2 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYF2

Alternative Splicing Database (ASD) splice patterns (SP) for SYF2 Gene

ExUns: 1a · 1b ^ 2a · 2b · 2c ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b
SP1: - -
SP2: - - -
SP3: -
SP4: -

Relevant External Links for SYF2 Gene

GeneLoc Exon Structure for
SYF2

Expression for SYF2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYF2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SYF2 Gene

This gene is overexpressed in CD8 Tcells (9.4), Testis (8.7), and Fetal Brain (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SYF2 Gene



Protein tissue co-expression partners for SYF2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYF2

SOURCE GeneReport for Unigene cluster for SYF2 Gene:

Hs.20013

mRNA Expression by UniProt/SwissProt for SYF2 Gene:

O95926-SYF2_HUMAN
Tissue specificity: Abundantly expressed in the heart, skeletal muscle and kidney. Expressed at lower level other tissues.

Evidence on tissue expression from TISSUES for SYF2 Gene

  • Nervous system(4.5)
  • Lung(4.4)
  • Skin(2.2)
  • Blood(2)
  • Lymph node(2)
genes like me logo Genes that share expression patterns with SYF2: view

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYF2 Gene

Orthologs for SYF2 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SYF2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SYF2 30 31
  • 98.35 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia -- 31
  • 93 (a)
OneToMany
SYF2 30
  • 90.91 (n)
-- 31
  • 87 (a)
OneToMany
Cow
(Bos Taurus)
Mammalia SYF2 30 31
  • 91.49 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SYF2 31
  • 90 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SYF2 31
  • 87 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Syf2 30 17 31
  • 83.61 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Syf2 30
  • 83.4 (n)
Chicken
(Gallus gallus)
Aves SYF2 30 31
  • 77.96 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 86 (a)
OneToMany
-- 31
  • 77 (a)
OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia syf2 30
  • 73.96 (n)
Str.6933 30
African clawed frog
(Xenopus laevis)
Amphibia MGC53740 30
Zebrafish
(Danio rerio)
Actinopterygii syf2 30 31
  • 70.76 (n)
OneToOne
hmzeh0031 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.8518 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG12343 30 31
  • 57.24 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010515 30
  • 55.25 (n)
Worm
(Caenorhabditis elegans)
Secernentea K04G7.11 30 31
  • 57.26 (n)
OneToOne
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT2G16860 30
  • 50.64 (n)
Rice
(Oryza sativa)
Liliopsida Os06g0711600 30
  • 50.56 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.10576 31
  • 50 (a)
OneToOne
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes syf2 30
  • 48.29 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU00361 30
  • 42.48 (n)
Species where no ortholog for SYF2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SYF2 Gene

ENSEMBL:
Gene Tree for SYF2 (if available)
TreeFam:
Gene Tree for SYF2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYF2: view image

Paralogs for SYF2 Gene

Pseudogenes.org Pseudogenes for SYF2 Gene

genes like me logo Genes that share paralogs with SYF2: view

No data available for Paralogs for SYF2 Gene

Variants for SYF2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYF2 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
rs35324907 - p.Ala89Val

Additional dbSNP identifiers (rs#s) for SYF2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SYF2 Gene

Variant ID Type Subtype PubMed ID
dgv132n100 CNV gain 25217958
dgv133n100 CNV gain 25217958
dgv134n100 CNV gain 25217958
esv3576582 CNV gain 25503493
nsv1160388 CNV duplication 26073780
nsv475560 CNV novel sequence insertion 20440878
nsv7187 CNV insertion 18451855

Variation tolerance for SYF2 Gene

Residual Variation Intolerance Score: 63.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.32; 53.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYF2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYF2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYF2 Gene

Disorders for SYF2 Gene

No disorders were found for SYF2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SYF2 Gene

Publications for SYF2 Gene

  1. p29, a novel GCIP-interacting protein, localizes in the nucleus. (PMID: 11118353) Chang MS … Yang YC (Biochemical and biophysical research communications 2000) 2 3 4
  2. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. (PMID: 28076346) Bertram K … Lührmann R (Nature 2017) 3 4
  3. The DNA sequence and biological annotation of human chromosome 1. (PMID: 16710414) Gregory SG … Prigmore E (Nature 2006) 3 4
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  5. Purification and characterization of native spliceosomes suitable for three-dimensional structural analysis. (PMID: 11991638) Jurica MS … Moore MJ (RNA (New York, N.Y.) 2002) 3 4

Products for SYF2 Gene

Sources for SYF2 Gene