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    SMCHD1 structural maintenance of chromosomes flexible hinge domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 23347, updated on 17-Jun-2024

    Summary

    Official Symbol
    SMCHD1provided by HGNC
    Official Full Name
    structural maintenance of chromosomes flexible hinge domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:29090
    See related
    Ensembl:ENSG00000101596 MIM:614982; AllianceGenome:HGNC:29090
    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
    BAMS; FSHD2
    Summary
    This gene encodes a protein which contains a hinge region domain found in members of the SMC (structural maintenance of chromosomes) protein family. [provided by RefSeq, Dec 2011]
    Expression
    Ubiquitous expression in lymph node (RPKM 16.1), bone marrow (RPKM 16.1) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SMCHD1 in Genome Data Viewer
    Location:
    18p11.32
    Exon count:
    51
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (2655726..2805017)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (2811308..2960649)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (2655725..2805015)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:2653904-2654533 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9246 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9247 Neighboring gene Sharpr-MPRA regulatory region 12050 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13027 Neighboring gene RNA, U6 small nuclear 340, pseudogene Neighboring gene CBX3 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:2716737-2717237 Neighboring gene uncharacterized LOC124904372 Neighboring gene Sharpr-MPRA regulatory region 3375 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9249 Neighboring gene Sharpr-MPRA regulatory region 4434 Neighboring gene elastin microfibril interfacer 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:2919273-2920004 Neighboring gene lipin 2 Neighboring gene CHORDC1 pseudogene 4

    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?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0650, DKFZp686O0631

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    is_active_in Barr body IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in Barr body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with chromosome, telomeric region IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in site of double-strand break IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    structural maintenance of chromosomes flexible hinge domain-containing protein 1
    Names
    SMC hinge domain-containing protein 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_031972.2 RefSeqGene

      Range
      5002..154293
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_015295.3NP_056110.2  structural maintenance of chromosomes flexible hinge domain-containing protein 1

      See identical proteins and their annotated locations for NP_056110.2

      Status: REVIEWED

      Source sequence(s)
      AB014550, AI904018, AP001011, AP005061, AW503637, BC006008, BP872870, BU153211, BU509173, DA283721, DA675822, DB071574, DN913642
      Consensus CDS
      CCDS45822.1
      UniProtKB/Swiss-Prot
      A6NHR9, O75141, Q6AHX6, Q6ZTQ8, Q9H6Q2, Q9UG39
      UniProtKB/TrEMBL
      A0A8I5KRS9
      Related
      ENSP00000326603.7, ENST00000320876.11
      Conserved Domains (3) summary
      smart00968
      Location:17201846
      SMC_hinge; SMC proteins Flexible Hinge Domain
      pfam15898
      Location:16401703
      PRKG1_interact; cGMP-dependent protein kinase interacting domain
      cl00075
      Location:143275
      HATPase_c; Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      2655726..2805017
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011525642.2XP_011523944.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I5KRS9
      Conserved Domains (3) summary
      smart00968
      Location:17201846
      SMC_hinge; SMC proteins Flexible Hinge Domain
      pfam15898
      Location:16401703
      PRKG1_interact; cGMP-dependent protein kinase interacting domain
      cl00075
      Location:143275
      HATPase_c; Histidine kinase-like ATPases; This family includes several ATP-binding proteins for example: histidine kinase, DNA gyrase B, topoisomerases, heat shock protein HSP90, phytochrome-like ATPases and DNA mismatch repair proteins
    2. XM_047437427.1XP_047293383.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A8I5KRS9
    3. XM_047437426.1XP_047293382.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I5KRS9
    4. XM_047437428.1XP_047293384.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X5

    5. XM_047437429.1XP_047293385.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X6

    6. XM_047437425.1XP_047293381.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I5KRS9

    RNA

    1. XR_001753172.2 RNA Sequence

    2. XR_935055.3 RNA Sequence

    3. XR_007066135.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      2811308..2960649
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318425.1XP_054174400.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8I5KRS9
    2. XM_054318428.1XP_054174403.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A8I5KRS9
    3. XM_054318427.1XP_054174402.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8I5KRS9
    4. XM_054318429.1XP_054174404.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X5

    5. XM_054318430.1XP_054174405.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X6

    6. XM_054318426.1XP_054174401.1  structural maintenance of chromosomes flexible hinge domain-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A8I5KRS9

    RNA

    1. XR_008484992.1 RNA Sequence

    2. XR_008484994.1 RNA Sequence

    3. XR_008484993.1 RNA Sequence