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SMC1A structural maintenance of chromosomes 1A [ Homo sapiens (human) ]

Gene ID: 8243, updated on 1-Jun-2020

Summary

Official Symbol
SMC1Aprovided by HGNC
Official Full Name
structural maintenance of chromosomes 1Aprovided by HGNC
Primary source
HGNC:HGNC:11111
See related
Ensembl:ENSG00000072501 MIM:300040
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SMC1; SMCB; CDLS2; SB1.8; EIEE85; SMC1L1; DXS423E; SMC1alpha
Summary
Proper cohesion of sister chromatids is a prerequisite for the correct segregation of chromosomes during cell division. The cohesin multiprotein complex is required for sister chromatid cohesion. This complex is composed partly of two structural maintenance of chromosomes (SMC) proteins, SMC3 and either SMC1B or the protein encoded by this gene. Most of the cohesin complexes dissociate from the chromosomes before mitosis, although those complexes at the kinetochore remain. Therefore, the encoded protein is thought to be an important part of functional kinetochores. In addition, this protein interacts with BRCA1 and is phosphorylated by ATM, indicating a potential role for this protein in DNA repair. This gene, which belongs to the SMC gene family, is located in an area of the X-chromosome that escapes X inactivation. Mutations in this gene result in Cornelia de Lange syndrome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]
Expression
Ubiquitous expression in lymph node (RPKM 13.2), appendix (RPKM 13.1) and 25 other tissues See more
Orthologs

Genomic context

See SMC1A in Genome Data Viewer
Location:
Xp11.22
Exon count:
26
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (53374149..53422728, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (53401070..53449677, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein SA pseudogene 62 Neighboring gene MPV17L2 pseudogene 1 Neighboring gene microRNA 6857 Neighboring gene RIB43A domain with coiled-coils 1 Neighboring gene hydroxysteroid 17-beta dehydrogenase 10

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-07-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2018-07-23)

ClinGen Genome Curation PagePubMed

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify structural maintenance of chromosomes 1A (SMC1A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify structural maintenance of chromosomes 1A (SMC1A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify structural maintenance of chromosomes 1A (SMC1A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify structural maintenance of chromosomes 1A (SMC1A), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Vpr vpr HIV-1 Vpr decreases the amount of Smc1 and Smc3 proteins in the chromatin PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0178, MGC138332, DKFZp686L19178

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
RNA binding HDA PubMed 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
mediator complex binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA repair TAS
Traceable Author Statement
more info
PubMed 
cell division IEA
Inferred from Electronic Annotation
more info
 
meiotic cell cycle ISS
Inferred from Sequence or Structural Similarity
more info
 
mitotic sister chromatid cohesion TAS
Traceable Author Statement
more info
PubMed 
mitotic sister chromatid segregation TAS
Traceable Author Statement
more info
PubMed 
regulation of mitotic spindle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to DNA damage checkpoint signaling IDA
Inferred from Direct Assay
more info
PubMed 
response to radiation IEP
Inferred from Expression Pattern
more info
PubMed 
sister chromatid cohesion IMP
Inferred from Mutant Phenotype
more info
PubMed 
stem cell population maintenance IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
chromosome TAS
Traceable Author Statement
more info
 
chromosome, centromeric region TAS
Traceable Author Statement
more info
 
cohesin complex IDA
Inferred from Direct Assay
more info
PubMed 
cohesin complex TAS
Traceable Author Statement
more info
PubMed 
condensed chromosome kinetochore IEA
Inferred from Electronic Annotation
more info
 
condensed nuclear chromosome TAS
Traceable Author Statement
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
kinetochore IDA
Inferred from Direct Assay
more info
PubMed 
meiotic cohesin complex IDA
Inferred from Direct Assay
more info
PubMed 
mitotic spindle pole IDA
Inferred from Direct Assay
more info
PubMed 
nuclear matrix IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
structural maintenance of chromosomes protein 1A
Names
SMC protein 1A
SMC-1-alpha
SMC1 (structural maintenance of chromosomes 1, yeast)-like 1
epididymis secretory sperm binding protein
segregation of mitotic chromosomes 1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_006988.2 RefSeqGene

    Range
    4943..53522
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_773

mRNA and Protein(s)

  1. NM_001281463.1NP_001268392.1  structural maintenance of chromosomes protein 1A isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC233728
    Consensus CDS
    CCDS75985.1
    UniProtKB/TrEMBL
    G8JLG1
    Related
    ENSP00000364489.7, ENST00000375340.10
    Conserved Domains (1) summary
    pfam02463
    Location:151188
    SMC_N; RecF/RecN/SMC N terminal domain
  2. NM_006306.4NP_006297.2  structural maintenance of chromosomes protein 1A isoform 1

    See identical proteins and their annotated locations for NP_006297.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC233728, BC080185, D80000
    Consensus CDS
    CCDS14352.1
    UniProtKB/Swiss-Prot
    Q14683
    UniProtKB/TrEMBL
    Q68EN4
    Related
    ENSP00000323421.3, ENST00000322213.9
    Conserved Domains (1) summary
    pfam02463
    Location:31210
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    53374149..53422728 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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