Smc1a structural maintenance of chromosomes 1A [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smc1aprovided by MGI
Official Full Name: structural maintenance of chromosomes 1Aprovided by MGI
Primary source: MGI:MGI:1344345
See related: Ensembl:ENSMUSG00000041133 AllianceGenome:MGI:1344345
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: Smc1; Smcb; Sb1.8; SMC-1A; Smc1l1; Smc1alpha; mKIAA0178; 5830426I24Rik
Summary: Enables chromatin binding activity and mediator complex binding activity. Acts upstream of or within meiotic cell cycle and stem cell population maintenance. Located in nucleus. Part of meiotic cohesin complex. Is expressed in several structures, including alimentary system; genitourinary system; integumental system; nervous system; and sensory organ. Human ortholog(s) of this gene implicated in Cornelia de Lange syndrome 2 and developmental and epileptic encephalopathy. Orthologous to human SMC1A (structural maintenance of chromosomes 1A). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 47.7), liver E14 (RPKM 30.8) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: X F3; X 68.46 cM

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	X	NC_000086.8 (150799386..150844969)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	X	NC_000086.7 (152016428..152061973)

Chromosome X - NC_000086.8 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?

Effects of SMC1A on immune microenvironment and cancer stem cells in colon adenocarcinoma.
Title: Effects of SMC1A on immune microenvironment and cancer stem cells in colon adenocarcinoma.
Whereas SMC1alpha can substitute for SMC1beta in many functions, the protection of telomere integrity requires SMC1beta.
Title: SMC1α Substitutes for Many Meiotic Functions of SMC1β but Cannot Protect Telomeres from Damage.
To decipher the functions of the two meiosis-specific kleisins, REC8 or RAD21L, together with the only meiosis-specific SMC protein SMC1b, we generated Smc1b-/-Rec8-/- and Smc1b-/-Rad21L-/- mouse mutants.
Title: Distinct Roles of Meiosis-Specific Cohesin Complexes in Mammalian Spermatogenesis.
expression analysis of Smc1a and Nipbl in developing mouse embryos reveals a specific pattern in the hindbrain
Title: CyclinD1 Down-Regulation and Increased Apoptosis Are Common Features of Cohesinopathies.
SMC1A participates in tissue-specific enhancer-promoter interactions and interactions that demarcate regions of correlated regulatory output.
Title: The genomic landscape of cohesin-associated chromatin interactions.
Point mutation at the Nbs1 Threonine 278 site does not affect mouse development, but compromises the Chk2 and Smc1 phosphorylation after DNA damage.
Title: Point mutation at the Nbs1 Threonine 278 site does not affect mouse development, but compromises the Chk2 and Smc1 phosphorylation after DNA damage.
A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion.
Title: A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion.
SMC1alpha is mainly associated with homologous or non-homologous synapsed regions. The protein also localizes along meiotic chromosome cores of Spo11 null spermatocytes.
Title: Differential association of SMC1alpha and SMC3 proteins with meiotic chromosomes in wild-type and SPO11-deficient male mice.
observations suggest that many of the abnormal stress responses seen in cells lacking ATM, NBS1, or BRCA1 result from a failure of ATM migration to sites of DNA breaks and a resultant lack of SMC1 phosphorylation.
Title: Phosphorylation of SMC1 is a critical downstream event in the ATM-NBS1-BRCA1 pathway.
SMC1beta was found along the axial elements of synaptonemal complexes in prophase I of testis sections and chromosome spreads . Thus, SMC1beta and not SMC1alpha is likely involved in maintaining cohesion between sister centromeres until anaphase II.
Title: Novel meiosis-specific isoform of mammalian SMC1.

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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 (2)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

DXHXS423 (e-PCR), detects polymorphism
- UniSTS:142889

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables mediator complex binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA repair	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell cycle	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cell division	IEA Inferred from Electronic Annotation more info
involved_in chromosome organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within meiotic cell cycle	IPI Inferred from Physical Interaction more info	PubMed
involved_in meiotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in mitotic spindle assembly	ISO Inferred from Sequence Orthology more info
involved_in response to DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in sister chromatid cohesion	IBA Inferred from Biological aspect of Ancestor more info
involved_in sister chromatid cohesion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somatic stem cell population maintenance	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromosome	IEA Inferred from Electronic Annotation more info
located_in chromosome, centromeric region	IEA Inferred from Electronic Annotation more info
part_of cohesin complex	IDA Inferred from Direct Assay more info	PubMed
part_of cohesin complex	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in kinetochore	ISO Inferred from Sequence Orthology more info
located_in lateral element	ISO Inferred from Sequence Orthology more info
part_of meiotic cohesin complex	IBA Inferred from Biological aspect of Ancestor more info
part_of meiotic cohesin complex	IDA Inferred from Direct Assay more info	PubMed
part_of meiotic cohesin complex	ISO Inferred from Sequence Orthology more info
part_of mitotic cohesin complex	ISO Inferred from Sequence Orthology more info
located_in mitotic spindle pole	ISO Inferred from Sequence Orthology more info
located_in nuclear matrix	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	TAS Traceable Author Statement 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
located_in synaptonemal complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: structural maintenance of chromosomes protein 1A

Names: SMC (segregation of mitotic chromosomes 1)-like 1; SMC protein 1A; SMC-1-alpha; chromosome segregation protein SmcB; segregation of mitotic chromosomes b

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_019710.2 → NP_062684.2 structural maintenance of chromosomes protein 1A

See identical proteins and their annotated locations for NP_062684.2

Status: VALIDATED

Source sequence(s)

AL672180, AW045560, BC131667

Consensus CDS

CCDS30473.1

UniProtKB/Swiss-Prot

A2AFQ5, Q3V480, Q9CU62, Q9CUX9, Q9D959, Q9WTU1

Related

ENSMUSP00000044645.6, ENSMUST00000045312.6

Conserved Domains (1) summary

pfam02463
Location:3 → 1210

SMC_N; RecF/RecN/SMC N terminal domain

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_000086.8 Reference GRCm39 C57BL/6J

Range

150799386..150844969

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036161950.1 → XP_036017843.1 structural maintenance of chromosomes protein 1A isoform X2

Conserved Domains (1) summary

pfam02463
Location:3 → 1000

SMC_N; RecF/RecN/SMC N terminal domain
XM_036161951.1 → XP_036017844.1 structural maintenance of chromosomes protein 1A isoform X3

Conserved Domains (1) summary

pfam02463
Location:3 → 854

SMC_N; RecF/RecN/SMC N terminal domain
XM_006528840.4 → XP_006528903.1 structural maintenance of chromosomes protein 1A isoform X1

Conserved Domains (1) summary

pfam02463
Location:4 → 1076

SMC_N; RecF/RecN/SMC N terminal domain