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

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: human all
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Genomic context

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_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The lupus autoantigen La/Ssb is an Xist-binding protein involved in Xist folding and cloud formation.
Title: The lupus autoantigen La/Ssb is an Xist-binding protein involved in Xist folding and cloud formation.
La deletion is associated with Neuron Death and Reactive Astrocytosis.
Title: La Deletion from Mouse Brain Alters Pre-tRNA Metabolism and Accumulation of Pre-5.8S rRNA, with Neuron Death and Reactive Astrocytosis.
Data indicate that La antigen (Sjogren's syndrome antigen B) is essential in different cell types and required for normal development of various tissue types.
Title: Targeted deletion of the gene encoding the La autoantigen (Sjögren's syndrome antigen B) in B cells or the frontal brain causes extensive tissue loss.
Overexpression of mouse or human La enhanced M-MuLV particle release in the absence of glycosylated gag.
Title: The cellular protein La functions in enhancement of virus release through lipid rafts facilitated by murine leukemia virus glycosylated Gag.
La appears to be an important contributor to Akt-mediated translational regulation of these transcripts in murine glial cells.
Title: Akt phosphorylation of La regulates specific mRNA translation in glial progenitors.
Overexpression of La autoantigen is associated with lymphoma
Title: In vivo targeting of dead tumor cells in a murine tumor model using a monoclonal antibody specific for the La autoantigen.
truncation of La alters the immunodominance hierarchy of T cell responsiveness to hLa and may be a factor in the initiation or maintenance of anti-La autoimmunity.
Title: T cell epitopes of the La/SSB autoantigen in humanized transgenic mice expressing the HLA class II haplotype DRB1*0301/DQB1*0201.
Restricted specificity of intermolecular spreading to endogenous La (SS-B) and 60 kDa Ro (SS-A) in experimental autoimmunity.
Title: Restricted specificity of intermolecular spreading to endogenous La (SS-B) and 60 kDa Ro (SS-A) in experimental autoimmunity.
Blastocysts derived from La+/- intercrosses yielded 38 La+/+ and La+/- embryonic stem (ES) cell lines but no La-/- ES cell lines, suggesting that La contributes a critical function toward the establishment or survival of ES cells.
Title: The multifunctional RNA-binding protein La is required for mouse development and for the establishment of embryonic stem cells.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (2)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

UniSTS:479281 (e-PCR)
- UniSTS:479281

Ssb (e-PCR), detects polymorphism
- UniSTS:479281

Ssb (e-PCR), detects polymorphism
- UniSTS:496729

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

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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)

NM_001110145.2 → NP_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:10 → 91

LARP_3; La RNA-binding domain of La-related protein 3

cd12291
Location:112 → 183

RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

pfam08777
Location:230 → 333

RRM_3; RNA binding motif
NM_001355265.2 → NP_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:10 → 91

LARP_3; La RNA-binding domain of La-related protein 3

cd12291
Location:112 → 183

RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

cd12541
Location:230 → 306

RRM2_La; RNA recognition motif 2 in La autoantigen (La or LARP3) and similar proteins
NM_001421043.1 → NP_001407972.1 lupus La protein homolog isoform a

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634

UniProtKB/Swiss-Prot

P32067

UniProtKB/TrEMBL

Q564E6
NM_001421044.1 → NP_001407973.1 lupus La protein homolog isoform a

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634

UniProtKB/Swiss-Prot

P32067

UniProtKB/TrEMBL

Q564E6
NM_001421045.1 → NP_001407974.1 lupus La protein homolog isoform a

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634

UniProtKB/Swiss-Prot

P32067

UniProtKB/TrEMBL

Q564E6
NM_001421046.1 → NP_001407975.1 lupus La protein homolog isoform b

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634
NM_001421049.1 → NP_001407978.1 lupus La protein homolog isoform b

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634
NM_001421050.1 → NP_001407979.1 lupus La protein homolog isoform c

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634
NM_001421052.1 → NP_001407981.1 lupus La protein homolog isoform c

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634
NM_001421053.1 → NP_001407982.1 lupus La protein homolog isoform c

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634
NM_001421054.1 → NP_001407983.1 lupus La protein homolog isoform d

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634
NM_009278.5 → NP_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:10 → 91

LARP_3; La RNA-binding domain of La-related protein 3

cd12291
Location:112 → 183

RRM1_La; RNA recognition motif 1 in La autoantigen (La or LARP3) and similar proteins

pfam08777
Location:230 → 333

RRM_3; RNA binding motif

RNA

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
NR_185233.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634
NR_185234.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AL845261, AL929249, BX322634