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sf3b1 splicing factor 3b, subunit 1 [ Danio rerio (zebrafish) ]

Gene ID: 446117, updated on 17-Nov-2020

Summary

Official Symbol
sf3b1provided by ZNC
Official Full Name
splicing factor 3b, subunit 1provided by ZNC
Primary source
ZFIN:ZDB-GENE-040827-3
See related
Ensembl:ENSDARG00000056138
Gene type
protein coding
RefSeq status
MODEL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
ts; wu:fb99f09
Orthologs

Genomic context

See sf3b1 in Genome Data Viewer
Location:
chromosome: 9
Exon count:
26
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 9 NC_007120.7 (32161623..32177156, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 9 NC_007120.6 (32350877..32366395, complement)
103 previous assembly Zv9 (GCF_000002035.4) 9 NC_007120.5 (33195116..33210433, complement)

Chromosome 9 - NC_007120.7Genomic Context describing neighboring genes Neighboring gene phosphoinositide kinase, FYVE finger containing Neighboring gene ankyrin repeat domain 44 Neighboring gene coenzyme Q10B Neighboring gene uncharacterized LOC101884351

Genomic regions, transcripts, and products

Bibliography

Pathways from PubChem

General gene information

Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
RNA splicing IEA
Inferred from Electronic Annotation
more info
 
definitive hemopoiesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
hematopoietic stem cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
mRNA processing IEA
Inferred from Electronic Annotation
more info
 
melanocyte differentiation IGI
Inferred from Genetic Interaction
more info
PubMed 
melanocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
myeloid cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
neural crest cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of apoptotic process IGI
Inferred from Genetic Interaction
more info
PubMed 
spliceosomal complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spliceosomal complex assembly IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2-type prespliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
spliceosomal complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
splicing factor 3B subunit 1
Names
tst

NCBI Reference Sequences (RefSeq)

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_007120.7 Reference GRCz11 Primary Assembly

    Range
    32161623..32177156 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_679219.5XP_684311.1  splicing factor 3B subunit 1 isoform X1

    UniProtKB/TrEMBL
    F1QQZ1
    Related
    ENSDARP00000073029.5, ENSDART00000078568.5
    Conserved Domains (6) summary
    smart01104
    Location:231393
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
    COG5181
    Location:4571312
    HSH155; U2 snRNP spliceosome subunit [RNA processing and modification]
    cd00020
    Location:9911092
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam08920
    Location:343454
    SF3b1; Splicing factor 3B subunit 1
    pfam12815
    Location:269341
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
    sd00044
    Location:861885
    HEAT; HEAT repeat [structural motif]
  2. XM_005167787.3XP_005167844.1  splicing factor 3B subunit 1 isoform X2

    Conserved Domains (5) summary
    smart01104
    Location:231350
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
    COG5181
    Location:4141269
    HSH155; U2 snRNP spliceosome subunit [RNA processing and modification]
    cd00020
    Location:9481049
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam08920
    Location:300411
    SF3b1; Splicing factor 3B subunit 1
    sd00044
    Location:818842
    HEAT; HEAT repeat [structural motif]
  3. XM_005167788.4XP_005167845.1  splicing factor 3B subunit 1 isoform X3

    Conserved Domains (6) summary
    smart01104
    Location:77239
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
    COG5181
    Location:3031158
    HSH155; U2 snRNP spliceosome subunit [RNA processing and modification]
    cd00020
    Location:837938
    ARM; Armadillo/beta-catenin-like repeats. An approximately 40 amino acid long tandemly repeated sequence motif first identified in the Drosophila segment polarity gene armadillo; these repeats were also found in the mammalian armadillo homolog beta-catenin, ...
    pfam08920
    Location:189300
    SF3b1; Splicing factor 3B subunit 1
    pfam12815
    Location:115187
    CTD; Spt5 C-terminal nonapeptide repeat binding Spt4
    sd00044
    Location:707731
    HEAT; HEAT repeat [structural motif]
  4. XM_009304794.3XP_009303069.1  splicing factor 3B subunit 1 isoform X5

    See identical proteins and their annotated locations for XP_009303069.1

  5. XM_009304793.3XP_009303068.1  splicing factor 3B subunit 1 isoform X4

RNA

  1. XR_002459523.1 RNA Sequence

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