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SMC1B structural maintenance of chromosomes 1B [ Homo sapiens (human) ]

Gene ID: 27127, updated on 5-Mar-2024

Summary

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Official Symbol
SMC1Bprovided by HGNC
Official Full Name
structural maintenance of chromosomes 1Bprovided by HGNC
Primary source
HGNC:HGNC:11112
See related
Ensembl:ENSG00000077935 MIM:608685; AllianceGenome:HGNC:11112
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SMC1L2; SMC1BETA
Summary
SMC1L2 belongs to a family of proteins required for chromatid cohesion and DNA recombination during meiosis and mitosis (3:Revenkova et al., 2001 [PubMed 11564881]).[supplied by OMIM, Mar 2008]
Expression
Restricted expression toward testis (RPKM 20.7) See more
Orthologs
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Genomic context

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Location:
22q13.31
Exon count:
26
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (45344063..45413599, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (45828963..45898486, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (45739944..45809480, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13880 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45686240-45686773 Neighboring gene uroplakin 3A Neighboring gene Sharpr-MPRA regulatory region 10691 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13881 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45706877-45707685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19226 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19227 Neighboring gene family with sequence similarity 118 member A Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:45809563-45810395 Neighboring gene RIB43A domain with coiled-coils 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:45838232-45838794 Neighboring gene uncharacterized LOC107985537

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. SMC1B is present in mammalian somatic cells and interacts with mitotic cohesin proteins. Mannini L, et al. Sci Rep, 2015 Dec 17. PMID 26673124, Free PMC Article
  2. RNA immunoprecipitation identifies novel targets of DAZL in human foetal ovary. Rosario R, et al. Mol Hum Reprod, 2017 Mar 1. PMID 28364521, Free PMC Article
  3. Protein deep sequencing applied to biobank samples from patients with pancreatic cancer. Ansari D, et al. J Cancer Res Clin Oncol, 2015 Feb. PMID 25216700
  4. Cohesin component dynamics during meiotic prophase I in mammalian oocytes. Prieto I, et al. Chromosome Res, 2004. PMID 15125634
  5. Novel meiosis-specific isoform of mammalian SMC1. Revenkova E, et al. Mol Cell Biol, 2001 Oct. PMID 11564881, Free PMC Article

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Through the translational regulation of novel RNA targets SMC1B and TEX11, DAZL may have a key role in regulating chromosome cohesion and DNA recombination; two processes fundamental in determining oocyte quality and whose establishment in foetal life may support lifelong fertility.
    Title: RNA immunoprecipitation identifies novel targets of DAZL in human foetal ovary.
  2. Data show that structural maintenance of chromosomes protein 1B (SMC1B) is expressed in primary fibroblasts.
    Title: SMC1B is present in mammalian somatic cells and interacts with mitotic cohesin proteins.
  3. High SMC1B expression is associated with pancreatic cancer.
    Title: Protein deep sequencing applied to biobank samples from patients with pancreatic cancer.
  4. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ43748

Gene Ontology Provided by GOA

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
  
Process Evidence Code Pubs
involved_in meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in sister chromatid cohesion IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromosome, centromeric region IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in lateral element IEA
Inferred from Electronic Annotation
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 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
structural maintenance of chromosomes protein 1B
Names
SMC protein 1B
SMC1 (structural maintenance of chromosomes 1, yeast)-like 1
SMC1 structural maintenance of chromosomes 1-like 2
mitosis-specific chromosome segregation protein like protein beta

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)

  1. NM_001291501.2 → NP_001278430.1  structural maintenance of chromosomes protein 1B isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two alternate in-frame exons in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AJ504806, BC126208, BG194018
    Consensus CDS
    CCDS74876.1
    UniProtKB/Swiss-Prot
    Q8NDV3
    Related
    ENSP00000385902.3, ENST00000404354.3
    Conserved Domains (5) summary
    cd03275
    Location:4 → 148
    ABC_SMC1_euk; ATP-binding cassette domain of eukaryotic SMC1 proteins
    smart00968
    Location:513 → 628
    SMC_hinge; SMC proteins Flexible Hinge Domain
    COG1196
    Location:3 → 1092
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cl19219
    Location:421 → 492
    DUF342; Protein of unknown function (DUF342)
    cl21455
    Location:1088 → 1142
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. NM_148674.5 → NP_683515.4  structural maintenance of chromosomes protein 1B isoform 1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AJ504806, AK125736, BC126208, BG194018
    Consensus CDS
    CCDS43027.1
    UniProtKB/Swiss-Prot
    A0AV46, B0QY23, B0QY24, Q5TIC3, Q6ZUF9, Q8NDV3, Q9Y3G5
    Related
    ENSP00000350036.4, ENST00000357450.9
    Conserved Domains (4) summary
    cd03275
    Location:4 → 148
    ABC_SMC1_euk; ATP-binding cassette domain of eukaryotic SMC1 proteins
    smart00968
    Location:513 → 628
    SMC_hinge; SMC proteins Flexible Hinge Domain
    COG1196
    Location:3 → 1219
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cl19219
    Location:421 → 492
    DUF342; Protein of unknown function (DUF342)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    45344063..45413599 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011530144.3 → XP_011528446.1  structural maintenance of chromosomes protein 1B isoform X1

    Conserved Domains (5) summary
    cd03275
    Location:1072 → 1175
    ABC_SMC1_euk; ATP-binding cassette domain of eukaryotic SMC1 proteins
    smart00968
    Location:472 → 587
    SMC_hinge; SMC proteins Flexible Hinge Domain
    COG1196
    Location:1 → 1178
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cl19219
    Location:380 → 451
    DUF342; Protein of unknown function (DUF342)
    cl21455
    Location:1 → 107
    P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

  2. XM_011530145.3 → XP_011528447.1  structural maintenance of chromosomes protein 1B isoform X3

    Conserved Domains (4) summary
    cd03275
    Location:4 → 148
    ABC_SMC1_euk; ATP-binding cassette domain of eukaryotic SMC1 proteins
    smart00968
    Location:513 → 628
    SMC_hinge; SMC proteins Flexible Hinge Domain
    pfam02463
    Location:3 → 1092
    SMC_N; RecF/RecN/SMC N terminal domain
    cl19219
    Location:421 → 492
    DUF342; Protein of unknown function (DUF342)

  3. XM_047441333.1 → XP_047297289.1  structural maintenance of chromosomes protein 1B isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    45828963..45898486 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054325546.1 → XP_054181521.1  structural maintenance of chromosomes protein 1B isoform X1

  2. XM_054325548.1 → XP_054181523.1  structural maintenance of chromosomes protein 1B isoform X3

  3. XM_054325547.1 → XP_054181522.1  structural maintenance of chromosomes protein 1B isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NDV3.3 GenPept UniProtKB/Swiss-Prot:Q8NDV3

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