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

Gene ID: 8243, updated on 3-Dec-2017
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; Vega:OTTHUMG00000021614
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; 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
Location:
Xp11.22
Exon count:
26
Annotation release Status Assembly Chr Location
108 current GRCh38.p7 (GCF_000001405.33) 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 mpv17-like protein 2 Neighboring gene microRNA 6857 Neighboring gene RIB43A domain with coiled-coils 1 Neighboring gene hydroxysteroid 17-beta dehydrogenase 10

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Congenital muscular hypertrophy-cerebral syndrome
MedGen: C1802395 OMIM: 300590 GeneReviews: Cornelia de Lange Syndrome
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated (2012-09-06)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated (2012-09-06)

ClinGen Genome Curation Page

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

  • ATM Signaling Network in Development and Disease, organism-specific biosystem (from WikiPathways)
    ATM Signaling Network in Development and Disease, organism-specific biosystemThis pathway is modeled after Figure 4 in the article "The ATM signaling network in development and disease" (See Bibliography). When DNA is damaged, DDR begins to work on recuperating the damage th...
  • ATM Signaling Pathway, organism-specific biosystem (from WikiPathways)
    ATM Signaling Pathway, organism-specific biosystemAtaxia-telangiectasia (A-T) is a highly pleiotropic, autosomal recessive disease that leads to multisystem defects and has an intricate cellular phenotype, all linked to the functional inactivation o...
  • Cell Cycle, organism-specific biosystem (from WikiPathways)
    Cell Cycle, organism-specific biosystemThe cell cycle is the series of events that takes place in a cell leading to its division and duplication (replication). Regulation of the cell cycle involves processes crucial to the survival of a c...
  • Cell Cycle, organism-specific biosystem (from REACTOME)
    Cell Cycle, organism-specific biosystem
    Cell Cycle
  • Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
    Cell Cycle, Mitotic, organism-specific biosystemThe replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried o...
  • Cell cycle, organism-specific biosystem (from KEGG)
    Cell cycle, organism-specific biosystemMitotic cell cycle progression is accomplished through a reproducible sequence of events, DNA replication (S phase) and mitosis (M phase) separated temporally by gaps known as G1 and G2 phases. Cycli...
  • Cell cycle, conserved biosystem (from KEGG)
    Cell cycle, conserved biosystemMitotic cell cycle progression is accomplished through a reproducible sequence of events, DNA replication (S phase) and mitosis (M phase) separated temporally by gaps known as G1 and G2 phases. Cycli...
  • Cohesin Loading onto Chromatin, organism-specific biosystem (from REACTOME)
    Cohesin Loading onto Chromatin, organism-specific biosystemIn mitotic telophase, as chromosomes decondense, cohesin complex associated with PDS5 (PDS5A and PDS5B) and WAPAL (WAPL) proteins is loaded onto chromatin (Shintomi and Hirano, 2009, Kueng et al. 200...
  • Constitutive Androstane Receptor Pathway, organism-specific biosystem (from WikiPathways)
    Constitutive Androstane Receptor Pathway, organism-specific biosystemThe Constitutive Androstane Receptor (CAR) is a nuclear receptor and functions as a sensor for xenobiotics. It regulates transcription of genes encoding proteins in metabolism and excretion of xenobi...
  • DNA Damage Response, organism-specific biosystem (from WikiPathways)
    DNA Damage Response, organism-specific biosystemThis is the first pathway out of two pathways which deals with DNA damage response. It has two central gene products (ATM and ATR) which are connected to the sources of DNA damage (in blue). The two ...
  • Establishment of Sister Chromatid Cohesion, organism-specific biosystem (from REACTOME)
    Establishment of Sister Chromatid Cohesion, organism-specific biosystemThe cohesin complex loads onto chromatin in telophase, but its association with chromatin remains transient, dynamic until the S-phase of the cell cycle, presumably because the cohesin-bound NIPBL:MA...
  • M Phase, organism-specific biosystem (from REACTOME)
    M Phase, organism-specific biosystemMitosis, or the M phase, involves nuclear division and cytokinesis, where two identical daughter cells are produced. Mitosis involves prophase, prometaphase, metaphase, anaphase, and telophase. Fin...
  • Meiosis, organism-specific biosystem (from REACTOME)
    Meiosis, organism-specific biosystemDuring meiosis the replicated chromosomes of a single diploid cell are segregated into 4 haploid daughter cells by two successive divisions, meiosis I and meiosis II. In meiosis I, the distinguishing...
  • Meiotic synapsis, organism-specific biosystem (from REACTOME)
    Meiotic synapsis, organism-specific biosystemMeiotic synapsis is the stable physical pairing of homologous chromosomes that begins in leptonema of prophase I and lasts until anaphase of prophase I. First, short segments of axial elements form a...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Mitotic Anaphase, organism-specific biosystem (from REACTOME)
    Mitotic Anaphase, organism-specific biosystemIn anaphase, the paired chromosomes separate at the centromeres, and move to the opposite sides of the cell. The movement of the chromosomes is facilitated by a combination of kinetochore movement al...
  • Mitotic Metaphase and Anaphase, organism-specific biosystem (from REACTOME)
    Mitotic Metaphase and Anaphase, organism-specific biosystemMetaphase is marked by the formation of the metaphase plate. The metaphase plate is formed when the spindle fibers align the chromosomes along the middle of the cell. Such an organization helps to ...
  • Mitotic Prometaphase, organism-specific biosystem (from REACTOME)
    Mitotic Prometaphase, organism-specific biosystemThe dissolution of the nuclear membrane marks the beginning of the prometaphase. Kinetochores are created when proteins attach to the centromeres. Microtubules then attach at the kinetochores, and th...
  • Mitotic Telophase/Cytokinesis, organism-specific biosystem (from REACTOME)
    Mitotic Telophase/Cytokinesis, organism-specific biosystemIn this final phase of mitosis, new membranes are formed around two sets of chromatids and two daughter cells are formed. The chromosomes and the spindle fibers disperse, and the fiber ring around th...
  • Oocyte meiosis, organism-specific biosystem (from KEGG)
    Oocyte meiosis, organism-specific biosystemDuring meiosis, a single round of DNA replication is followed by two rounds of chromosome segregation, called meiosis I and meiosis II. At meiosis I, homologous chromosomes recombine and then segrega...
  • Oocyte meiosis, conserved biosystem (from KEGG)
    Oocyte meiosis, conserved biosystemDuring meiosis, a single round of DNA replication is followed by two rounds of chromosome segregation, called meiosis I and meiosis II. At meiosis I, homologous chromosomes recombine and then segrega...
  • Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystem (from WikiPathways)
    Pathways Affected in Adenoid Cystic Carcinoma, organism-specific biosystemProtein pathways altered by mutations in adenoid cystic carcinoma. Pathways include epigentic modification, DNA damage checkpoint signals, MYB/MYC signalling pathway, FGF/IGF/PI3K signalling, and not...
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Resolution of Sister Chromatid Cohesion, organism-specific biosystem (from REACTOME)
    Resolution of Sister Chromatid Cohesion, organism-specific biosystemThe resolution of sister chromatids in mitotic prometaphase involves removal of cohesin complexes from chromosomal arms, with preservation of cohesion at centromeres (Losada et al. 1998, Hauf et al. ...
  • Retinoblastoma (RB) in Cancer, organism-specific biosystem (from WikiPathways)
    Retinoblastoma (RB) in Cancer, organism-specific biosystemDescribes the role of retinoblastoma (RB) gene in cancer.
  • S Phase, organism-specific biosystem (from REACTOME)
    S Phase, organism-specific biosystemDNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of the chromosome are formed. As DNA replication continues,...
  • SUMO E3 ligases SUMOylate target proteins, organism-specific biosystem (from REACTOME)
    SUMO E3 ligases SUMOylate target proteins, organism-specific biosystemSUMO proteins are conjugated to lysine residues of target proteins via an isopeptide bond with the C-terminal glycine of SUMO (reviewed in Zhao 2007, Gareau and Lima 2010, Hannoun et al. 2010, Citro ...
  • SUMOylation, organism-specific biosystem (from REACTOME)
    SUMOylation, organism-specific biosystemSmall Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Ha...
  • SUMOylation of DNA damage response and repair proteins, organism-specific biosystem (from REACTOME)
    SUMOylation of DNA damage response and repair proteins, organism-specific biosystemSeveral factors that participate in DNA damage response and repair are SUMOylated (reviewed in Dou et al. 2011, Bekker-Jensen and Mailand 2011, Ulrich 2012, Psakhye and Jentsch 2012, Bologna and Ferr...
  • Separation of Sister Chromatids, organism-specific biosystem (from REACTOME)
    Separation of Sister Chromatids, organism-specific biosystemWhile sister chromatids resolve in prometaphase, separating along chromosomal arms, the cohesion of sister centromeres persists until anaphase. At the anaphase onset, the anaphase promoting complex/c...
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • miRNA Regulation of DNA Damage Response, organism-specific biosystem (from WikiPathways)
    miRNA Regulation of DNA Damage Response, organism-specific biosystemThis is the first out of two pathways which deals with the DNA damage response. It is comprised of two central gene products (ATM and ATR) influenced by different sources of DNA damage (in blue). The...
Products Interactant Other Gene Complex Source Pubs Description

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 IDA
Inferred from Direct Assay
more info
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 
negative regulation of DNA endoreduplication IMP
Inferred from Mutant Phenotype
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 
sister chromatid cohesion TAS
Traceable Author Statement
more info
 
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 
Preferred Names
structural maintenance of chromosomes protein 1A
Names
SMC protein 1A
SMC-1-alpha
SMC1 (structural maintenance of chromosomes 1, yeast)-like 1
segregation of mitotic chromosomes 1

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 (4) summary
    cd03275
    Location:10951198
    ABC_SMC1_euk; ATP-binding cassette domain of eukaryotic SMC1 proteins
    smart00968
    Location:491606
    SMC_hinge; SMC proteins Flexible Hinge Domain
    pfam02463
    Location:151186
    SMC_N; RecF/RecN/SMC N terminal domain
    pfam07851
    Location:403498
    TMPIT; TMPIT-like protein
  2. NM_006306.3NP_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, BP312805, D80000
    Consensus CDS
    CCDS14352.1
    UniProtKB/Swiss-Prot
    Q14683
    UniProtKB/TrEMBL
    Q68EN4
    Related
    ENSP00000323421.3, OTTHUMP00000023351, ENST00000322213.8, OTTHUMT00000056756
    Conserved Domains (1) summary
    pfam02463
    Location:31210
    SMC_N; RecF/RecN/SMC N terminal domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

Reference GRCh38.p7 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p7 Primary Assembly

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

Alternate CHM1_1.1

Genomic

  1. NC_018934.2 Alternate CHM1_1.1

    Range
    53391525..53440144 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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