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

Gene ID: 23347, updated on 1-Mar-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
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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)

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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.

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