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Ssb small RNA binding exonuclease protection factor La [ Mus musculus (house mouse) ]

Gene ID: 20823, updated on 1-Mar-2024

Summary

Official Symbol
Ssbprovided by MGI
Official Full Name
small RNA binding exonuclease protection factor Laprovided by MGI
Primary source
MGI:MGI:98423
See related
Ensembl:ENSMUSG00000068882 AllianceGenome:MGI:98423
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
SS-B
Summary
Enables RNA binding activity. Predicted to be involved in several processes, including IRES-dependent viral translational initiation; RNA metabolic process; and protein localization to cytoplasmic stress granule. Located in nucleus. Is expressed in several structures, including central nervous system; early conceptus; gonad; sensory organ; and spleen. Orthologous to human SSB (small RNA binding exonuclease protection factor La). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in CNS E11.5 (RPKM 93.7), liver E14 (RPKM 50.9) and 11 other tissues See more
Orthologs
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Genomic context

See Ssb in Genome Data Viewer
Location:
2 C2; 2 40.95 cM
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (69691963..69702185)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (69861562..69871846)

Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene predicted gene, 39841 Neighboring gene STARR-positive B cell enhancer mm9_chr2:69698414-69698714 Neighboring gene STARR-positive B cell enhancer ABC_E4462 Neighboring gene kelch-like 23 Neighboring gene STARR-positive B cell enhancer ABC_E11134 Neighboring gene STARR-seq mESC enhancer starr_04746 Neighboring gene STARR-positive B cell enhancer ABC_E508 Neighboring gene methyltransferase 5, N6-adenosine Neighboring gene STARR-seq mESC enhancer starr_04748 Neighboring gene STARR-positive B cell enhancer ABC_E9515 Neighboring gene STARR-seq mESC enhancer starr_04749 Neighboring gene ubiquitin protein ligase E3 component n-recognin 3 Neighboring gene STARR-seq mESC enhancer starr_04750 Neighboring gene STARR-positive B cell enhancer ABC_E4463 Neighboring gene myosin IIIB Neighboring gene STARR-seq mESC enhancer starr_04751 Neighboring gene STARR-seq mESC enhancer starr_04752 Neighboring gene STARR-seq mESC enhancer starr_04756 Neighboring gene STARR-seq mESC enhancer starr_04757

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (2) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC118101

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA binding ISO
Inferred from Sequence Orthology
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
 
enables poly(U) RNA binding ISO
Inferred from Sequence Orthology
more info
 
enables sequence-specific mRNA binding ISO
Inferred from Sequence Orthology
more info
 
enables tRNA binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in IRES-dependent viral translational initiation ISO
Inferred from Sequence Orthology
more info
 
involved_in RNA processing IEA
Inferred from Electronic Annotation
more info
 
involved_in nuclear histone mRNA catabolic process ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in protein localization to cytoplasmic stress granule ISO
Inferred from Sequence Orthology
more info
 
involved_in tRNA 3'-end processing ISO
Inferred from Sequence Orthology
more info
 
involved_in tRNA 5'-leader removal ISO
Inferred from Sequence Orthology
more info
 
involved_in tRNA export from nucleus ISO
Inferred from Sequence Orthology
more info
 
involved_in tRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in tRNA processing ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
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 IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
part_of ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
lupus La protein homolog
Names
La protein
Lupus LA protein homolog (LA ribonucleoprotein) (LA autoantigen homolog)
Sjogren syndrome antigen B
autoantigen La
la autoantigen homolog
la ribonucleoprotein

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_001110145.2NP_001103615.1  lupus La protein homolog isoform a

    See identical proteins and their annotated locations for NP_001103615.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 5, 6, and 7 all encode the same isoform (a).
    Source sequence(s)
    AL845261, AL929249, BX322634
    Consensus CDS
    CCDS16101.1
    UniProtKB/Swiss-Prot
    P32067
    UniProtKB/TrEMBL
    Q3TG93, Q564E6, Q8BTU4
    Related
    ENSMUSP00000088365.5, ENSMUST00000090852.11
    Conserved Domains (3) summary
    cd08028
    Location:1091
    LARP_3; La RNA-binding domain of La-related protein 3
    cd12291
    Location:112183
    RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
    pfam08777
    Location:230333
    RRM_3; RNA binding motif
  2. NM_001355265.2NP_001342194.1  lupus La protein homolog isoform b

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and uses an alternate in-frame splice junction in the 3' end compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is 1 aa shorter compared to isoform a. Variants 3, 8, and 9 all encode the same isoform (b).
    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/TrEMBL
    Q3TG93, Q8BTU4
    Conserved Domains (3) summary
    cd08028
    Location:1091
    LARP_3; La RNA-binding domain of La-related protein 3
    cd12291
    Location:112183
    RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
    cd12541
    Location:230306
    RRM2_La; RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins
  3. NM_001421043.1NP_001407972.1  lupus La protein homolog isoform a

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/Swiss-Prot
    P32067
    UniProtKB/TrEMBL
    Q3TG93, Q564E6, Q8BTU4
  4. NM_001421044.1NP_001407973.1  lupus La protein homolog isoform a

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/Swiss-Prot
    P32067
    UniProtKB/TrEMBL
    Q3TG93, Q564E6, Q8BTU4
  5. NM_001421045.1NP_001407974.1  lupus La protein homolog isoform a

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/Swiss-Prot
    P32067
    UniProtKB/TrEMBL
    Q3TG93, Q564E6, Q8BTU4
  6. NM_001421046.1NP_001407975.1  lupus La protein homolog isoform b

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/TrEMBL
    Q3TG93, Q8BTU4
  7. NM_001421049.1NP_001407978.1  lupus La protein homolog isoform b

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/TrEMBL
    Q3TG93, Q8BTU4
  8. NM_001421050.1NP_001407979.1  lupus La protein homolog isoform c

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/TrEMBL
    Q3TG93, Q8BTU4
  9. NM_001421052.1NP_001407981.1  lupus La protein homolog isoform c

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/TrEMBL
    Q3TG93, Q8BTU4
  10. NM_001421053.1NP_001407982.1  lupus La protein homolog isoform c

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/TrEMBL
    Q3TG93, Q8BTU4
  11. NM_001421054.1NP_001407983.1  lupus La protein homolog isoform d

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
    UniProtKB/TrEMBL
    Q3TG93, Q8BTU4
  12. NM_009278.5NP_033304.1  lupus La protein homolog isoform a

    See identical proteins and their annotated locations for NP_033304.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1, 2, 5, 6, and 7 all encode the same isoform (a).
    Source sequence(s)
    AL845261, AL929249, BX322634
    Consensus CDS
    CCDS16101.1
    UniProtKB/Swiss-Prot
    P32067
    UniProtKB/TrEMBL
    Q3TG93, Q564E6, Q8BTU4
    Related
    ENSMUSP00000130313.2, ENSMUST00000166411.8
    Conserved Domains (3) summary
    cd08028
    Location:1091
    LARP_3; La RNA-binding domain of La-related protein 3
    cd12291
    Location:112183
    RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins
    pfam08777
    Location:230333
    RRM_3; RNA binding motif

RNA

  1. NR_149321.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and lacks an alternate exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AL845261, AL929249, BX322634
  2. NR_185233.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634
  3. NR_185234.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL845261, AL929249, BX322634

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    69691963..69702185
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)