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ssb small RNA binding exonuclease protection factor La [ Danio rerio (zebrafish) ]

Gene ID: 321504, updated on 2-Nov-2024

Summary

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Official Symbol
ssbprovided by ZNC
Official Full Name
small RNA binding exonuclease protection factor Laprovided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-223
See related
Ensembl:ENSDARG00000029252 AllianceGenome:ZFIN:ZDB-GENE-030131-223
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
zgc:55588; wu:fb17f11
Summary
Predicted to enable mRNA binding activity. Predicted to be involved in positive regulation of translation and tRNA processing. Predicted to act upstream of or within RNA processing. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus. Is expressed in several structures, including digestive system; immature eye; mesoderm; musculature system; and nervous system. Orthologous to human SSB (small RNA binding exonuclease protection factor La). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See ssb in Genome Data Viewer
Location:
chromosome: 6
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (3715497..3728632)
105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (3552595..3567812)

Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene peptidylprolyl isomerase G (cyclophilin G) Neighboring gene phosphatase, orphan 2 Neighboring gene Sp5 transcription factor b Neighboring gene glutamate-rich 2

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 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. Proteomic profile and toxicity pathway analysis in zebrafish embryos exposed to bisphenol A and di-n-butyl phthalate at environmentally relevant levels. Dong X, et al. Chemosphere, 2018 Feb. PMID 29145093
  2. A novel chemical screening strategy in zebrafish identifies common pathways in embryogenesis and rhabdomyosarcoma development. Le X, et al. Development, 2013 Jun. PMID 23615277, Free PMC Article
  3. Incomplete splicing, cell division defects, and hematopoietic blockage in dhx8 mutant zebrafish. English MA, et al. Dev Dyn, 2012 May. PMID 22411201, Free PMC Article
  4. Structure, evolution and expression of collagen XXVIII: Lessons from the zebrafish. Gebauer JM, et al. Matrix Biol, 2016 Jan. PMID 26235539
  5. Single cell transcriptomics of the developing zebrafish lens and identification of putative controllers of lens development. Farnsworth DR, et al. Exp Eye Res, 2021 May. PMID 33705730, Free PMC Article

See all (12) 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 nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within RNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytoplasmic stress granule IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
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 ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
lupus La protein
Names
Sjogren syndrome antigen B (autoantigen La)

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_199547.1 → NP_955841.1  lupus La protein

    See identical proteins and their annotated locations for NP_955841.1

    Status: PROVISIONAL

    Source sequence(s)
    BC045392
    UniProtKB/TrEMBL
    A0A8N7XJ07, B2GRX6, F6NWT8, Q7ZTI0
    Related
    ENSDARP00000041626.5, ENSDART00000041627.5
    Conserved Domains (3) summary
    cd08028
    Location:7 → 88
    LARP_3; La RNA-binding domain of La-related protein 3
    cd12291
    Location:109 → 181
    RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
    pfam08777
    Location:229 → 326
    RRM_3; RNA binding motif

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007117.7 Reference GRCz11 Primary Assembly

    Range
    3715497..3728632
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005172073.5 → XP_005172130.1  lupus La protein isoform X1

    See identical proteins and their annotated locations for XP_005172130.1

    UniProtKB/TrEMBL
    A0A8N7XJ07, B2GRX6, F6NWT8, Q7ZTI0
    Conserved Domains (3) summary
    cd08028
    Location:7 → 88
    LARP_3; La RNA-binding domain of La-related protein 3
    cd12291
    Location:109 → 181
    RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
    pfam08777
    Location:229 → 326
    RRM_3; RNA binding motif

  2. XM_009302102.4 → XP_009300377.1  lupus La protein isoform X1

    See identical proteins and their annotated locations for XP_009300377.1

    UniProtKB/TrEMBL
    A0A8N7XJ07, B2GRX6, F6NWT8, Q7ZTI0
    Conserved Domains (3) summary
    cd08028
    Location:7 → 88
    LARP_3; La RNA-binding domain of La-related protein 3
    cd12291
    Location:109 → 181
    RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
    pfam08777
    Location:229 → 326
    RRM_3; RNA binding motif
Nucleotide Protein Strain
Heading Accession and Version

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