Aliases for SNRPF Gene

Aliases for SNRPF Gene

  • Small Nuclear Ribonucleoprotein Polypeptide F 2 3 5
  • Sm-F 2 3 4
  • Small Nuclear Ribonucleoprotein F 3 4
  • Sm Protein F 3 4
  • SnRNP-F 3 4
  • SNRPF 5
  • PBSCF 4
  • SMF 3
  • SmF 4

External Ids for SNRPF Gene

Previous GeneCards Identifiers for SNRPF Gene

  • GC12P095685
  • GC12P096616
  • GC12P096185
  • GC12P094755
  • GC12P094776
  • GC12P093317
  • GC12P096252

Summaries for SNRPF Gene

GeneCards Summary for SNRPF Gene

SNRPF (Small Nuclear Ribonucleoprotein Polypeptide F) is a Protein Coding gene. Among its related pathways are Processing of Capped Intronless Pre-mRNA and mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include RNA binding.

UniProtKB/Swiss-Prot Summary for SNRPF Gene

  • Plays role in pre-mRNA splicing as core component of the SMN-Sm complex that mediates spliceosomal snRNP assembly and as component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346). Is also a component of the minor U12 spliceosome (PubMed:15146077). As part of the U7 snRNP it is involved in histone 3'-end processing (PubMed:12975319).

Gene Wiki entry for SNRPF Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SNRPF Gene

Genomics for SNRPF Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SNRPF Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12J095858 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 269.9 +0.5 473 3.6 BCLAF1 SP1 ZNF207 MYC SIX5 POLR2A YY1 MXD4 CTCF CEBPB SNRPF-DT SNRPF piR-54033 AMDHD1 CCDC38 MK280269-015 lnc-CCDC38-2
GH12J095652 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 30.3 -205.2 -205196 2.4 IKZF1 CEBPA ATF3 ZBTB10 YY1 CEBPB MAX ZNF217 EP300 FOXA2 NR2C1 ELK3 METAP2 SNRPF NTN4 USP44 VEZT LTA4H piR-34822-070 lnc-USP44-2
GH12J095857 Enhancer 0.2 ENCODE 250.7 -1.6 -1570 0.2 SNRPF SNRPF-DT piR-32677-110 MK280269-015 NTN4 lnc-CCDC38-2
GH12J096486 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 18.7 +629.7 629711 3.6 ZNF654 ZNF207 MYC ZBTB10 YY1 MXD4 REST CEBPB CTCF SIN3A CFAP54 SNRPF CDK17 ELK3 LTA4H ENSG00000258272
GH12J096414 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.6 +564.5 564464 17.6 BCLAF1 ZNF654 JUND ZNF580 ATF2 CEBPA ZNF223 BRCA1 CEBPB ZNF639 CDK17 RF00017-1104 piR-42491-049 ELK3 USP44 METAP2 CFAP54 LTA4H SNRPF HSALNG0093302
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Top Transcription factor binding sites by QIAGEN in the SNRPF gene promoter:
  • Brachyury
  • CBF(2)
  • CBF-A
  • CBF-B
  • CBF-C
  • CP1A
  • CP1C
  • E47
  • N-Myc
  • Tal-1beta

Genomic Locations for SNRPF Gene

Latest Assembly
chr12:95,858,928-95,903,828
(GRCh38/hg38)
Size:
44,901 bases
Orientation:
Plus strand

Previous Assembly
chr12:96,252,730-96,260,883
(GRCh37/hg19 by Entrez Gene)
Size:
8,154 bases
Orientation:
Plus strand

chr12:96,252,706-96,297,606
(GRCh37/hg19 by Ensembl)
Size:
44,901 bases
Orientation:
Plus strand

Genomic View for SNRPF Gene

Genes around SNRPF on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SNRPF Gene

Proteins for SNRPF Gene

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

    Protein Symbol:
    P62306-RUXF_HUMAN
    Recommended name:
    Small nuclear ribonucleoprotein F
    Protein Accession:
    P62306
    Secondary Accessions:
    • A2VCR2
    • B2R498
    • Q15356
    • Q6IBQ1
    • Q6P4I0

    Protein attributes for SNRPF Gene

    Size:
    86 amino acids
    Molecular mass:
    9725 Da
    Quaternary structure:
    • Core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Most spliceosomal snRNPs contain a common set of Sm proteins, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG that assemble in a heptameric protein ring on the Sm site of the small nuclear RNA to form the core snRNP (PubMed:19325628, PubMed:21516107, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of the U1 snRNP (PubMed:19325628, PubMed:25555158). The U1 snRNP is composed of the U1 snRNA and the 7 core Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG, and at least three U1 snRNP-specific proteins SNRNP70/U1-70K, SNRPA/U1-A and SNRPC/U1-C (PubMed:19325628, PubMed:25555158). Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF, SNRPG, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39, plus LSM2, LSM3, LSM4, LSM5, LSM6, LSM7 and LSM8 (PubMed:26912367). Component of the U7 snRNP complex, or U7 Sm protein core complex, that is composed of the U7 snRNA and at least LSM10, LSM11, SNRPB, SNRPD3, SNRPE, SNRPF and SNRPG; the complex does not contain SNRPD1 and SNRPD2 (PubMed:11574479). Component of the U11/U12 snRNPs that are part of the U12-type spliceosome (PubMed:15146077). Part of the SMN-Sm complex that contains SMN1, GEMIN2/SIP1, DDX20/GEMIN3, GEMIN4, GEMIN5, GEMIN6, GEMIN7, GEMIN8, STRAP/UNRIP and the Sm proteins SNRPB, SNRPD1, SNRPD2, SNRPD3, SNRPE, SNRPF and SNRPG; catalyzes core snRNPs assembly (PubMed:18984161). Forms a 6S pICln-Sm complex composed of CLNS1A/pICln, SNRPD1, SNRPD2, SNRPE, SNRPF and SNRPG; ring-like structure where CLNS1A/pICln mimics additional Sm proteins and which is unable to assemble into the core snRNP (PubMed:18984161, PubMed:23333303).

    Three dimensional structures from OCA and Proteopedia for SNRPF Gene

neXtProt entry for SNRPF Gene

Post-translational modifications for SNRPF Gene

  • Ubiquitination at Lys8, Lys17, and Lys24
  • Modification sites at PhosphoSitePlus

Other Protein References for SNRPF Gene

No data available for DME Specific Peptides for SNRPF Gene

Domains & Families for SNRPF Gene

Gene Families for SNRPF Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for SNRPF Gene

InterPro:
Blocks:
  • Like-Sm ribonucleoprotein-related, core

Suggested Antigen Peptide Sequences for SNRPF Gene

GenScript: Design optimal peptide antigens:
  • Sm protein F (RUXF_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P62306

UniProtKB/Swiss-Prot:

RUXF_HUMAN :
  • Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily.
Family:
  • Belongs to the snRNP Sm proteins family. SmF/LSm6 subfamily.
genes like me logo Genes that share domains with SNRPF: view

Function for SNRPF Gene

Molecular function for SNRPF Gene

UniProtKB/Swiss-Prot Function:
Plays role in pre-mRNA splicing as core component of the SMN-Sm complex that mediates spliceosomal snRNP assembly and as component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome (PubMed:11991638, PubMed:18984161, PubMed:19325628, PubMed:23333303, PubMed:25555158, PubMed:26912367, PubMed:28502770, PubMed:28781166, PubMed:28076346). Component of both the pre-catalytic spliceosome B complex and activated spliceosome C complexes (PubMed:11991638, PubMed:28502770, PubMed:28781166, PubMed:28076346). Is also a component of the minor U12 spliceosome (PubMed:15146077). As part of the U7 snRNP it is involved in histone 3'-end processing (PubMed:12975319).

Phenotypes From GWAS Catalog for SNRPF Gene

Gene Ontology (GO) - Molecular Function for SNRPF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IBA,IMP 7744013
GO:0005515 protein binding IPI 9417867
genes like me logo Genes that share ontologies with SNRPF: view
genes like me logo Genes that share phenotypes with SNRPF: view

miRNA for SNRPF Gene

miRTarBase miRNAs that target SNRPF

Inhibitory RNAs for research

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

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

Localization for SNRPF Gene

Subcellular locations from UniProtKB/Swiss-Prot for SNRPF Gene

Cytoplasm, cytosol. Nucleus. Note=SMN-mediated assembly into core snRNPs occurs in the cytosol before SMN-mediated transport to the nucleus to be included in spliceosomes. {ECO:0000305}.

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 SNRPF gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 3
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SNRPF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 28076346
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA,IDA 7744013
GO:0005683 U7 snRNP IDA 11574479
GO:0005685 U1 snRNP IBA,IDA 21113136
genes like me logo Genes that share ontologies with SNRPF: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SNRPF Gene

Pathways & Interactions for SNRPF Gene

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

Pathways by source for SNRPF Gene

Gene Ontology (GO) - Biological Process for SNRPF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000387 spliceosomal snRNP assembly IEA,TAS --
GO:0000398 mRNA splicing, via spliceosome IEA,TAS --
GO:0006369 termination of RNA polymerase II transcription TAS --
GO:0006397 mRNA processing IEA --
GO:0008334 histone mRNA metabolic process TAS --
genes like me logo Genes that share ontologies with SNRPF: view

No data available for SIGNOR curated interactions for SNRPF Gene

Drugs & Compounds for SNRPF Gene

No Compound Related Data Available

Transcripts for SNRPF Gene

mRNA/cDNA for SNRPF Gene

1 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

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

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

No ASD Table

Relevant External Links for SNRPF Gene

GeneLoc Exon Structure for
SNRPF

Expression for SNRPF Gene

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

Protein differential expression in normal tissues from HIPED for SNRPF Gene

This gene is overexpressed in Nasal epithelium (8.3) and Adrenal (7.8).

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



Protein tissue co-expression partners for SNRPF Gene

- Elite partner

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

SOURCE GeneReport for Unigene cluster for SNRPF Gene:

Hs.105465

Evidence on tissue expression from TISSUES for SNRPF Gene

  • Nervous system(4.4)
  • Liver(4.4)
  • Intestine(4.4)
  • Blood(4.3)
  • Kidney(2.1)
  • Lung(2)
genes like me logo Genes that share expression patterns with SNRPF: view

Primer products for research

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SNRPF Gene

Orthologs for SNRPF Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SNRPF Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SNRPF 29 30
  • 100 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SNRPF 30
  • 100 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia SNRPF 29 30
  • 94.19 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Snrpf 29
  • 93.41 (n)
Dog
(Canis familiaris)
Mammalia SNRPF 29 30
  • 93.02 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Snrpf 29 16 30
  • 90.31 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia SNRPF 30
  • 75 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SNRPF 29 30
  • 84.11 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SNRPF 30
  • 97 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia snrpf 29
  • 82.56 (n)
Str.2969 29
Zebrafish
(Danio rerio)
Actinopterygii snrpf 29 30
  • 80 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta DebB 31
  • 79 (a)
SmF 30
  • 75 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea snr-5 30
  • 66 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMX3 30 32
  • 49 (a)
OneToMany
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.8951 29
Soybean
(Glycine max)
eudicotyledons Gma.8349 29
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.865 30
  • 84 (a)
OneToOne
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes smf1 29
  • 63.81 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU01614 29
  • 58.22 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.4735 29
Species where no ortholog for SNRPF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SNRPF Gene

ENSEMBL:
Gene Tree for SNRPF (if available)
TreeFam:
Gene Tree for SNRPF (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SNRPF: view image
Alliance of Genome Resources:
Additional Orthologs for SNRPF

Paralogs for SNRPF Gene

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

No data available for Paralogs for SNRPF Gene

Variants for SNRPF Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SNRPF Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
nsv455693 CNV loss 19166990
nsv559834 CNV loss 21841781
nsv559835 CNV loss 21841781
nsv7234 OTHER inversion 18451855

Variation tolerance for SNRPF Gene

Residual Variation Intolerance Score: 55.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.15; 3.40% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SNRPF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SNRPF
Leiden Open Variation Database (LOVD)
SNRPF

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SNRPF Gene

Disorders for SNRPF Gene

Additional Disease Information for SNRPF

No disorders were found for SNRPF Gene.

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

Publications for SNRPF Gene

  1. snRNP Sm proteins share two evolutionarily conserved sequence motifs which are involved in Sm protein-protein interactions. (PMID: 7744013) Hermann H … Lührmann R (The EMBO journal 1995) 2 3 4
  2. Cryo-EM Structure of a Pre-catalytic Human Spliceosome Primed for Activation. (PMID: 28781166) Bertram K … Stark H (Cell 2017) 3 4
  3. Cryo-EM structure of a human spliceosome activated for step 2 of splicing. (PMID: 28076346) Bertram K … Lührmann R (Nature 2017) 3 4
  4. Molecular architecture of the human U4/U6.U5 tri-snRNP. (PMID: 26912367) Agafonov DE … Stark H (Science (New York, N.Y.) 2016) 3 4
  5. Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition. (PMID: 25555158) Kondo Y … Nagai K (eLife 2015) 3 4

Products for SNRPF Gene

Sources for SNRPF Gene