Seroatlas · Human Serome Atlas

SF1

Splicing factor 1

Also known as: SF01_HUMAN, ZCCHC25, ZFM1, ZNF162

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q15637
Gene: SF1
Ensembl: ENSG00000168066
Chromosome: 11
Canonical length: 639 aa
Protein class: Plasma proteins, Predicted intracellular proteins
Subcellular location: Nucleoplasm

OverviewNCBI Gene

This gene encodes a nuclear pre-mRNA splicing factor. The encoded protein specifically recognizes the intron branch point sequence at the 3' splice site, together with the large subunit of U2 auxiliary factor (U2AF), and is required for the early stages of spliceosome assembly. It also plays a role in nuclear pre-mRNA retention and transcriptional repression. The encoded protein contains an N-terminal U2AF ligand motif, a central hnRNP K homology motif and quaking 2 region which bind a key branch-site adenosine within the branch point sequence, a zinc knuckles domain, and a C-terminal proline-rich domain. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]

Canonical amino-acid sequenceUniProt

639 residues, UniProt reviewed canonical sequence.

>Q15637|SF1
     1  MATGANATPL DFPSKKRKRS RWNQDTMEQK TVIPGMPTVI PPGLTREQER AYIVQLQIED
    61  LTRKLRTGDL GIPPNPEDRS PSPEPIYNSE GKRLNTREFR TRKKLEEERH NLITEMVALN
   121  PDFKPPADYK PPATRVSDKV MIPQDEYPEI NFVGLLIGPR GNTLKNIEKE CNAKIMIRGK
   181  GSVKEGKVGR KDGQMLPGED EPLHALVTAN TMENVKKAVE QIRNILKQGI ETPEDQNDLR
   241  KMQLRELARL NGTLREDDNR ILRPWQSSET RSITNTTVCT KCGGAGHIAS DCKFQRPGDP
   301  QSAQDKARMD KEYLSLMAEL GEAPVPASVG STSGPATTPL ASAPRPAAPA NNPPPPSLMS
   361  TTQSRPPWMN SGPSESRPYH GMHGGGPGGP GGGPHSFPHP LPSLTGGHGG HPMQHNPNGP
   421  PPPWMQPPPP PMNQGPHPPG HHGPPPMDQY LGSTPVGSGV YRLHQGKGMM PPPPMGMMPP
   481  PPPPPSGQPP PPPSGPLPPW QQQQQQPPPP PPPSSSMASS TPLPWQQNTT TTTTSAGTGS
   541  IPPWQQQQAA AAASPGAPQM QGNPTMVPLP PGVQPPLPPG APPPPPPPPP GSAGMMYAPP
   601  PPPPPPMDPS NFVTMMGMGV AGMPPFGMPP APPPPPPQN

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SF1 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.59
Highest tissue expression: 185 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 185 nTPM
skeletal muscle: 144 nTPM
ovary: 140 nTPM
cerebellum: 138 nTPM
spleen: 131 nTPM
fallopian tube: 111 nTPM

Single-cell type

neutrophils: 437 nCPM
neutrophil progenitors: 380 nCPM
pituicytes/fscs: 314 nCPM
b-cells: 289 nCPM
innate lymphoid cells: 282 nCPM
t-cells: 245 nCPM

Immune cell

neutrophil: 14 nTPM
MAIT T-cell: 13 nTPM
gdT-cell: 13 nTPM
memory CD8 T-cell: 13 nTPM
naive CD8 T-cell: 12 nTPM
naive CD4 T-cell: 11 nTPM

Brain region

cerebral cortex: 168 nTPM
cerebellum: 152 nTPM
white matter: 145 nTPM
hypothalamus: 135 nTPM
thalamus: 134 nTPM
medulla oblongata: 131 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SF1.

Disease | GeneticClinVar

2 pathogenic / likely-pathogenic of 122 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Neurodevelopmental disorder
SF1-related neurodevelopmental disorder

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.18
gnomAD pLI: 1
gnomAD missense Z: 3.62
DepMap mean gene effect: -2.37
DepMap dependency class: pan

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

Zinc finger, CCHC-type
K Homology domain
K Homology domain, type 1 superfamily
KH domain-containing BBP-like
KHDC4/BBP-like, KH-domain type I
Zinc knuckle
KHDC4/BBP-like, KH-domain type I
Splicing factor 1, helix-hairpin domain
Splicing factor 1, helix-hairpin domain superfamily
Splicing factor 1 helix-hairpin domain

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of SF1 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads SF1 as an antibody target. Whether an autoantibody or antibody against SF1 could matter depends on whether native SF1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SF1 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label SF1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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