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sf1 splicing factor 1 [ Danio rerio (zebrafish) ]

Gene ID: 572785, updated on 27-Mar-2024

Summary

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Official Symbol
sf1provided by ZNC
Official Full Name
splicing factor 1provided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-2492
See related
Ensembl:ENSDARG00000008188 AllianceGenome:ZFIN:ZDB-GENE-030131-2492
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
znf162; wu:fc09f06
Summary
Predicted to enable mRNA binding activity. Acts upstream of or within retina development in camera-type eye. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Orthologous to human SF1 (splicing factor 1). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs
human mouse all
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Genomic context

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Location:
chromosome: 7
Exon count:
12
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (22809895..22820816)
105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (22538737..22549659)

Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein 4.2 Neighboring gene RNA binding motif protein 4.1 Neighboring gene phosphorylase, glycogen, muscle b Neighboring gene chloride channel, voltage-sensitive 5b

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Targeted Disruption of Aromatase Reveals Dual Functions of cyp19a1a During Sex Differentiation in Zebrafish. Yin Y, et al. Endocrinology, 2017 Sep 1. PMID 28575219
  2. The tissue-specific RNA binding protein T-STAR controls regional splicing patterns of neurexin pre-mRNAs in the brain. Ehrmann I, et al. PLoS Genet, 2013 Apr. PMID 23637638, Free PMC Article
  3. Rx3 and Shh direct anisotropic growth and specification in the zebrafish tuberal/anterior hypothalamus. Muthu V, et al. Development, 2016 Jul 15. PMID 27317806, Free PMC Article
  4. Identification of zebrafish insertional mutants with defects in visual system development and function. Gross JM, et al. Genetics, 2005 May. PMID 15716491, Free PMC Article
  5. Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo. Lemeer S, et al. J Proteome Res, 2008 Apr. PMID 18307296

See all (15) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables pre-mRNA branch point binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA splicing IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA splicing, via spliceosome IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within retina development in camera-type eye IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of spliceosomal complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
splicing factor 1
Names
zinc finger protein 162

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_212653.1 → NP_997818.1  splicing factor 1

    See identical proteins and their annotated locations for NP_997818.1

    Status: PROVISIONAL

    Source sequence(s)
    AY391459
    UniProtKB/TrEMBL
    Q6TNQ8
    Related
    ENSDARP00000105365.2, ENSDART00000126037.4
    Conserved Domains (2) summary
    cd02395
    Location:137 → 255
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16275
    Location:18 → 130
    SF1-HH; Splicing factor 1 helix-hairpin domain

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007118.7 Reference GRCz11 Primary Assembly

    Range
    22809895..22820816
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009303076.2 → XP_009301351.1  splicing factor 1 isoform X2

    UniProtKB/TrEMBL
    A0A8M3AU14
    Conserved Domains (2) summary
    cd02395
    Location:209 → 327
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16275
    Location:90 → 202
    SF1-HH; Splicing factor 1 helix-hairpin domain

  2. XM_021477588.1 → XP_021333263.1  splicing factor 1 isoform X3

    UniProtKB/TrEMBL
    A0A8M9Q1R8
    Conserved Domains (2) summary
    smart00343
    Location:279 → 293
    ZnF_C2HC; zinc finger
    cl25681
    Location:36 → 257
    SF1-HH; Splicing factor 1 helix-hairpin domain

  3. XM_009303077.3 → XP_009301352.1  splicing factor 1 isoform X4

    UniProtKB/TrEMBL
    A0A8M3B3Z3
    Conserved Domains (1) summary
    cd02395
    Location:22 → 140
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...

  4. XM_021477589.1 → XP_021333264.1  splicing factor 1 isoform X4

    UniProtKB/TrEMBL
    A0A8M3B3Z3
    Conserved Domains (1) summary
    cd02395
    Location:22 → 140
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...

  5. XM_009303075.2 → XP_009301350.1  splicing factor 1 isoform X1

    UniProtKB/TrEMBL
    A0A0R4IBT0, A0A8M3BAW2
    Related
    ENSDARP00000130303.1, ENSDART00000166900.3
    Conserved Domains (2) summary
    cd02395
    Location:209 → 327
    SF1_like-KH; Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 ...
    pfam16275
    Location:90 → 202
    SF1-HH; Splicing factor 1 helix-hairpin domain
Nucleotide Protein Strain
Heading Accession and Version

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