Safb scaffold attachment factor B [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Safbprovided by MGI
Official Full Name: scaffold attachment factor Bprovided by MGI
Primary source: MGI:MGI:2146974
See related: Ensembl:ENSMUSG00000071054 AllianceGenome:MGI:2146974
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: HAP; HET; SAFB1; SAF-B1; E130307D12; 3110021E02Rik; 5330423C17Rik
Summary: Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and chromatin binding activity. Involved in positive regulation of transcription by RNA polymerase II. Acts upstream of or within hormone metabolic process; intracellular estrogen receptor signaling pathway; and regulation of growth. Predicted to be located in midbody and nucleoplasm. Predicted to be active in nucleus. Is expressed in several structures, including central nervous system; future brain; olfactory epithelium; reproductive system; and retina layer. Orthologous to human SAFB (scaffold attachment factor B). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 64.7), CNS E14 (RPKM 34.2) and 28 other tissues See more
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Genomic context

Location:: 17 D; 17 29.4 cM

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (56891982..56913294)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (56584982..56606294)

Chromosome 17 - NC_000083.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells.
Title: SAFB associates with nascent RNAs and can promote gene expression in mouse embryonic stem cells.
despite a high degree of sequence similarity, SAFB1(-/-) and SAFB2(-/-) mice do not totally phenocopy each other
Title: Scaffold attachment factor B2 (SAFB2)-null mice reveal non-redundant functions of SAFB2 compared with its paralog, SAFB1.
Mice lacking SAFB1 exhibit developmental abnormalities in their lungs, high incidence of perinatal lethality, and adults develop different types of tumors. Mouse embryonic fibroblasts from Safb1-null animals are immortalized in culture.
Title: The Werner syndrome helicase protein is required for cell proliferation, immortalization, and tumorigenesis in Scaffold attachment factor B1 deficient mice.
Our data show that SAFB1 heterozygosity does not influence Wnt-1 induced tumorigenesis
Title: Scaffold Attachment Factor B1 (SAFB1) heterozygosity does not influence Wnt-1 or DMBA-induced tumorigenesis.
These results indicate a major role for SAFB1 in the activation of Srebp-1c through its interaction with RBMX.
Title: SAFB1, an RBMX-binding protein, is a newly identified regulator of hepatic SREBP-1c gene.
SAFB1 loss causes lack of contact inhibition, increased foci formation, and increased oncogene-induced anchorage-independent growth.
Title: Disruption of scaffold attachment factor B1 leads to TBX2 up-regulation, lack of p19ARF induction, lack of senescence, and cell immortalization.
SAFB1 plays a critical role in development, growth regulation, and reproduction.
Title: Scaffold attachment factor B1 functions in development, growth, and reproduction.
SAFB1 interacts in pull-down assays not only with PPARgamma but also with all nuclear receptors tested
Title: Scaffold attachment factor B1 directly interacts with nuclear receptors in living cells and represses transcriptional activity.
SAFB1 represses ERalpha activity via indirect association with histone deacetylation and interaction with the basal transcription machinery
Title: Structure-function analysis of the estrogen receptor alpha corepressor scaffold attachment factor-B1: identification of a potent transcriptional repression domain.

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Variation

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Alleles

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

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Safb (e-PCR), detects polymorphism
- UniSTS:470543

Safb (e-PCR), detects polymorphism
- UniSTS:470544

Safb (e-PCR), detects polymorphism
- UniSTS:470545

Safb (e-PCR), detects polymorphism
- UniSTS:479255

AU018122 (e-PCR)
- UniSTS:181039

D18386 (e-PCR)
- UniSTS:160675

Safb (e-PCR), detects polymorphism
- UniSTS:526023

MARC_16413-16414:1018631384:1 (e-PCR)
- UniSTS:268026

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within hormone metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular estrogen receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intracellular estrogen receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of mRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mRNA processing	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in midbody	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: scaffold attachment factor B1

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_001163300.1 → NP_001156772.1 scaffold attachment factor B1 isoform 2

See identical proteins and their annotated locations for NP_001156772.1

Status: VALIDATED

Source sequence(s)

CT485788

Consensus CDS

CCDS50152.1

UniProtKB/Swiss-Prot

D3YXK2

Related

ENSMUSP00000092849.4, ENSMUST00000095224.11

Conserved Domains (4) summary

smart00513
Location:31 → 65

SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation

PLN03124
Location:32 → 183

PLN03124; poly [ADP-ribose] polymerase; Provisional

COG0724
Location:368 → 527

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12679
Location:427 → 502

RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins
NM_001374619.1 → NP_001361548.1 scaffold attachment factor B1 isoform 1

Status: VALIDATED

Source sequence(s)

CT485788

UniProtKB/TrEMBL

S4R1M2

Related

ENSMUSP00000138277.2, ENSMUST00000182533.8

Conserved Domains (4) summary

smart00513
Location:31 → 65

SAP; Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation

PLN03124
Location:32 → 183

PLN03124; poly [ADP-ribose] polymerase; Provisional

COG0724
Location:368 → 527

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cd12679
Location:427 → 502

RRM_SAFB1_SAFB2; RNA recognition motif in scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), and similar proteins

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

NC_000083.7 Reference GRCm39 C57BL/6J

Range

56891982..56913294

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017317445.1 → XP_017172934.1 scaffold attachment factor B1 isoform X1

Conserved Domains (2) summary

COG0724
Location:211 → 370

RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]

cl17169
Location:270 → 345

RRM_SF; RNA recognition motif (RRM) superfamily