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

    Gene ID: 27127, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See SMC1B in Genome Data Viewer
    Location:
    22q13.31
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (45344063..45413599, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (45828963..45898486, complement)
    RS_2024_09 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 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. Cohesin component dynamics during meiotic prophase I in mammalian oocytes. Prieto I, et al. Chromosome Res, 2004. PMID 15125634
    3. 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
    4. 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
    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_2024_08

    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

    Gene LinkOut

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