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Aliases for SMC1B Gene

Aliases for SMC1B Gene

  • Structural Maintenance Of Chromosomes 1B 2 3 5
  • SMC1 (Structural Maintenance Of Chromosomes 1, Yeast)-Like 1 2 3
  • SMC Protein 1B 3 4
  • SMC1L2 3 4
  • Mitosis-Specific Chromosome Segregation Protein Like Protein Beta 3
  • SMC1 Structural Maintenance Of Chromosomes 1-Like 2 (Yeast) 2
  • SMC1 Structural Maintenance Of Chromosomes 1-Like 2 3
  • Structural Maintenance Of Chromosomes Protein 1B 3
  • SMC-1-Beta 4
  • SMC1BETA 3
  • SMC-1B 4

External Ids for SMC1B Gene

Previous HGNC Symbols for SMC1B Gene

  • SMC1L2

Previous GeneCards Identifiers for SMC1B Gene

  • GC22M044118
  • GC22M045739
  • GC22M028686

Summaries for SMC1B Gene

Entrez Gene Summary for SMC1B Gene

  • 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]

GeneCards Summary for SMC1B Gene

SMC1B (Structural Maintenance Of Chromosomes 1B) is a Protein Coding gene. Among its related pathways are Oocyte meiosis and Cell Cycle, Mitotic. An important paralog of this gene is SMC1A.

UniProtKB/Swiss-Prot for SMC1B Gene

  • Meiosis-specific component of cohesin complex. Required for the maintenance of meiotic cohesion, but not, or only to a minor extent, for its establishment. Contributes to axial element (AE) formation and the organization of chromatin loops along the AE. Plays a key role in synapsis, recombination and chromosome movements. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The meiosis-specific cohesin complex probably replaces mitosis specific cohesin complex when it dissociates from chromatin during prophase I (By similarity).

Gene Wiki entry for SMC1B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMC1B Gene

Genomics for SMC1B Gene

Regulatory Elements for SMC1B Gene

Enhancers for SMC1B Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22G045244 1.9 FANTOM5 Ensembl ENCODE dbSUPER 10.6 +166.3 166304 5.6 HNRNPUL1 PKNOX1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF48 YY1 TCF12 MIR1249 NUP50 NUP50-AS1 UPK3A SMC1B RIBC2 LINC01589 ENSG00000273243 KIAA0930 ENSG00000273287
GH22G045271 1.7 FANTOM5 Ensembl ENCODE dbSUPER 11.3 +140.4 140368 3.7 FOXA2 MLX ZFP64 ARID4B DMAP1 ZNF48 YY1 SP5 MXD4 NFYC FAM118A KIAA0930 SMC1B RIBC2 LINC01589 UPK3A PHF21B RPS10P31 ENSG00000273287
GH22G045536 1.4 Ensembl ENCODE dbSUPER 11 -124.3 -124285 2.3 FEZF1 ZNF2 ZNF121 GLIS2 FOS TSHZ1 ZNF592 ZNF579 MAFF ZNF610 LINC01589 SMC1B RIBC2 GC22P045526 GC22M045550
GH22G045267 1.4 Ensembl ENCODE dbSUPER 10.9 +144.3 144349 2.8 RB1 ARID4B KLF17 DMAP1 ZNF48 RAD21 GLIS2 GATA4 EGR1 SCRT2 KIAA0930 MIR1249 RIBC2 SMC1B LINC01589 FAM118A RPS10P31 ENSG00000273287
GH22G045435 1.2 Ensembl ENCODE 12.3 -22.2 -22166 1.3 SIN3A ARID4B ZNF2 ZNF48 ZNF143 FOS ZNF263 SP5 MXD4 NFYC RIBC2 SMC1B UPK3A FAM118A NUP50 NUP50-AS1 ENSG00000232363
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SMC1B on UCSC Golden Path with GeneCards custom track

Genomic Location for SMC1B Gene

Chromosome:
22
Start:
45,344,063 bp from pter
End:
45,413,629 bp from pter
Size:
69,567 bases
Orientation:
Minus strand

Genomic View for SMC1B Gene

Genes around SMC1B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMC1B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMC1B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMC1B Gene

Proteins for SMC1B Gene

  • Protein details for SMC1B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8NDV3-SMC1B_HUMAN
    Recommended name:
    Structural maintenance of chromosomes protein 1B
    Protein Accession:
    Q8NDV3
    Secondary Accessions:
    • A0AV46
    • B0QY23
    • B0QY24
    • Q5TIC3
    • Q6ZUF9
    • Q9Y3G5

    Protein attributes for SMC1B Gene

    Size:
    1235 amino acids
    Molecular mass:
    143908 Da
    Quaternary structure:
    • Forms a heterodimer with SMC3. Component of a meiosis-specific cohesin complex, probably composed of the SMC1B and SMC3 heterodimer attached via their hinge domain, RAD21 (or its meiosis-specific related protein REC8), which link them, and STAG3, which interacts with RAD21 or REC8 (By similarity).
    SequenceCaution:
    • Sequence=BAC86266.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Alternative splice isoforms for SMC1B Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SMC1B Gene

Post-translational modifications for SMC1B Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SMC1B Gene

No data available for DME Specific Peptides for SMC1B Gene

Domains & Families for SMC1B Gene

Protein Domains for SMC1B Gene

Suggested Antigen Peptide Sequences for SMC1B Gene

Graphical View of Domain Structure for InterPro Entry

Q8NDV3

UniProtKB/Swiss-Prot:

SMC1B_HUMAN :
  • The flexible hinge domain, which separates the large intramolecular coiled coil regions, allows the heterotypic interaction with the corresponding domain of SMC3, forming a V-shaped heterodimer. The two heads of the heterodimer are then connected by different ends of the cleavable RAD21 or REC8 protein, forming a ring structure (By similarity).
  • Belongs to the SMC family. SMC1 subfamily.
Domain:
  • The flexible hinge domain, which separates the large intramolecular coiled coil regions, allows the heterotypic interaction with the corresponding domain of SMC3, forming a V-shaped heterodimer. The two heads of the heterodimer are then connected by different ends of the cleavable RAD21 or REC8 protein, forming a ring structure (By similarity).
Family:
  • Belongs to the SMC family. SMC1 subfamily.
genes like me logo Genes that share domains with SMC1B: view

Function for SMC1B Gene

Molecular function for SMC1B Gene

UniProtKB/Swiss-Prot Function:
Meiosis-specific component of cohesin complex. Required for the maintenance of meiotic cohesion, but not, or only to a minor extent, for its establishment. Contributes to axial element (AE) formation and the organization of chromatin loops along the AE. Plays a key role in synapsis, recombination and chromosome movements. The cohesin complex is required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The meiosis-specific cohesin complex probably replaces mitosis specific cohesin complex when it dissociates from chromatin during prophase I (By similarity).

Gene Ontology (GO) - Molecular Function for SMC1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding IEA --
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with SMC1B: view
genes like me logo Genes that share phenotypes with SMC1B: view

Animal Models for SMC1B Gene

MGI Knock Outs for SMC1B:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for SMC1B Gene

Localization for SMC1B Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMC1B Gene

Nucleus. Chromosome. Chromosome, centromere. Note=Associates with chromatin. In prophase I stage of meiosis, localizes along the AE of synaptonemal complexes. In late-pachytene-diplotene, the bulk of protein dissociates from the chromosome arms probably because of phosphorylation by PLK, except at centromeres, where cohesin complexes remain. Remains chromatin associated at the centromeres up to metaphase II. At anaphase II, dissociates from centromeres, allowing chromosomes segregation (By similarity). {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SMC1B gene
Compartment Confidence
nucleus 5
cytosol 5
cytoskeleton 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for SMC1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000775 chromosome, centromeric region IEA --
GO:0000794 condensed nuclear chromosome IEA --
GO:0000795 synaptonemal complex IEA --
GO:0000800 lateral element IEA --
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with SMC1B: view

Pathways & Interactions for SMC1B Gene

genes like me logo Genes that share pathways with SMC1B: view

Pathways by source for SMC1B Gene

3 Reactome pathways for SMC1B Gene
2 KEGG pathways for SMC1B Gene
1 Qiagen pathway for SMC1B Gene

Gene Ontology (GO) - Biological Process for SMC1B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007049 cell cycle IEA --
GO:0007062 sister chromatid cohesion IEA --
GO:0007126 meiotic nuclear division IEA --
GO:0051276 chromosome organization IEA --
GO:0051321 meiotic cell cycle IEA --
genes like me logo Genes that share ontologies with SMC1B: view

No data available for SIGNOR curated interactions for SMC1B Gene

Drugs & Compounds for SMC1B Gene

(4) Drugs for SMC1B Gene - From: ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
KPT-185 Pharma CRM1 inhibitor,selective and irrversible 0
KPT-276 Pharma 0
KPT-330 Pharma 0
Verdinexor (KPT-335) Pharma 0

(4) ApexBio Compounds for SMC1B Gene

Compound Action Cas Number
KPT-185 CRM1 inhibitor,selective and irrversible 1333151-73-7
KPT-276 1421919-75-6
KPT-330 1393477-72-9
Verdinexor (KPT-335) 1392136-43-4
genes like me logo Genes that share compounds with SMC1B: view

Drug Products

Transcripts for SMC1B Gene

mRNA/cDNA for SMC1B Gene

Unigene Clusters for SMC1B Gene

Structural maintenance of chromosomes 1B:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for SMC1B Gene

No ASD Table

Relevant External Links for SMC1B Gene

GeneLoc Exon Structure for
SMC1B
ECgene alternative splicing isoforms for
SMC1B

Expression for SMC1B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SMC1B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SMC1B Gene

This gene is overexpressed in Testis (x47.9).

Protein differential expression in normal tissues from HIPED for SMC1B Gene

This gene is overexpressed in Testis (24.7) and Fetal ovary (24.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SMC1B Gene



NURSA nuclear receptor signaling pathways regulating expression of SMC1B Gene:

SMC1B

SOURCE GeneReport for Unigene cluster for SMC1B Gene:

Hs.334176
genes like me logo Genes that share expression patterns with SMC1B: view

Primer Products

No data available for Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SMC1B Gene

Orthologs for SMC1B Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for SMC1B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SMC1B 34 35
  • 99.54 (n)
cow
(Bos Taurus)
Mammalia SMC1B 34 35
  • 90.16 (n)
dog
(Canis familiaris)
Mammalia SMC1B 34 35
  • 90.04 (n)
mouse
(Mus musculus)
Mammalia Smc1b 34 16 35
  • 85.76 (n)
rat
(Rattus norvegicus)
Mammalia Smc1b 34
  • 85.76 (n)
oppossum
(Monodelphis domestica)
Mammalia SMC1B 35
  • 74 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 72 (a)
OneToMany
-- 35
  • 63 (a)
OneToMany
chicken
(Gallus gallus)
Aves SMC1B 34 35
  • 70.74 (n)
lizard
(Anolis carolinensis)
Reptilia SMC1B 35
  • 65 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smc1b 34
  • 64.18 (n)
zebrafish
(Danio rerio)
Actinopterygii smc1b 34 35
  • 58.58 (n)
fruit fly
(Drosophila melanogaster)
Insecta SMC1 35
  • 40 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea him-1 35
  • 37 (a)
ManyToMany
C44C10.4 35
  • 26 (a)
ManyToMany
C44C10.5 35
  • 24 (a)
ManyToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SMC1 35
  • 26 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.5929 35
  • 43 (a)
OneToMany
Species where no ortholog for SMC1B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMC1B Gene

ENSEMBL:
Gene Tree for SMC1B (if available)
TreeFam:
Gene Tree for SMC1B (if available)

Paralogs for SMC1B Gene

Paralogs for SMC1B Gene

(2) SIMAP similar genes for SMC1B Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SMC1B: view

Variants for SMC1B Gene

Sequence variations from dbSNP and Humsavar for SMC1B Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1000044848 -- 45,398,817(+) AGAGC(A/G)AAACT intron-variant
rs1000050334 -- 45,407,048(+) GTCTC(C/T)TTTAC intron-variant
rs1000077293 -- 45,399,079(+) CCCTA(A/T)GTTGT intron-variant
rs1000110235 -- 45,410,025(+) TGGTG(A/G)GCAAC intron-variant, upstream-variant-2KB
rs1000120097 -- 45,410,311(+) ATAAT(G/T)TTCTC intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for SMC1B Gene

Variant ID Type Subtype PubMed ID
dgv2468n106 CNV deletion 24896259
esv2758843 CNV gain 17122850
esv34218 CNV gain 17911159
esv3558242 CNV deletion 23714750
esv3568444 CNV loss 25503493
esv3647921 CNV gain 21293372
esv3647931 CNV gain 21293372
nsv1066204 CNV gain 25217958
nsv1120448 CNV tandem duplication 24896259
nsv1150203 CNV deletion 26484159
nsv3651 CNV insertion 18451855
nsv471210 CNV gain 18288195
nsv515690 CNV gain+loss 19592680
nsv834221 CNV loss 17160897
nsv955470 CNV deletion 24416366
nsv9921 CNV gain+loss 18304495

Variation tolerance for SMC1B Gene

Residual Variation Intolerance Score: 43.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 14.39; 96.36% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMC1B Gene

Human Gene Mutation Database (HGMD)
SMC1B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SMC1B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMC1B Gene

Disorders for SMC1B Gene

Relevant External Links for SMC1B

Genetic Association Database (GAD)
SMC1B
Human Genome Epidemiology (HuGE) Navigator
SMC1B
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMC1B

No disorders were found for SMC1B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SMC1B Gene

Publications for SMC1B Gene

  1. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I. … Wright H. (Nature 1999) 2 3 4 64
  2. MicroRNA-related genetic variations as predictors for risk of second primary tumor and/or recurrence in patients with early-stage head and neck cancer. (PMID: 20819778) Zhang X. … Wu X. (Carcinogenesis 2010) 3 46 64
  3. The evolution of SMC proteins: phylogenetic analysis and structural implications. (PMID: 14660695) Cobbe N. … Heck M.M.S. (Mol. Biol. Evol. 2004) 3 4 64
  4. Novel meiosis-specific isoform of mammalian SMC1. (PMID: 11564881) Revenkova E. … Jessberger R. (Mol. Cell. Biol. 2001) 2 3 64
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64

Products for SMC1B Gene

Sources for SMC1B Gene

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