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SMARCAL1 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1 [ Homo sapiens (human) ]

Gene ID: 50485, updated on 10-Jun-2024

Summary

Official Symbol
SMARCAL1provided by HGNC
Official Full Name
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1provided by HGNC
Primary source
HGNC:HGNC:11102
See related
Ensembl:ENSG00000138375 MIM:606622; AllianceGenome:HGNC:11102
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
HARP; HHARP
Summary
The protein encoded by this gene is a member of the SWI/SNF family of proteins. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein shows sequence similarity to the E. coli RNA polymerase-binding protein HepA. Mutations in this gene are a cause of Schimke immunoosseous dysplasia (SIOD), an autosomal recessive disorder with the diagnostic features of spondyloepiphyseal dysplasia, renal dysfunction, and T-cell immunodeficiency. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in ovary (RPKM 7.5), testis (RPKM 7.2) and 25 other tissues See more
Orthologs
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Genomic context

See SMARCAL1 in Genome Data Viewer
Location:
2q35
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (216412484..216483053)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (216894907..216965465)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (217277207..217347776)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene membrane associated ring-CH-type finger 4 Neighboring gene uncharacterized LOC107985983 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:217180211-217181410 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:217183431-217184162 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr2:217184163-217184894 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:217205324-217206036 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:217214111-217214808 Neighboring gene SMARCAL1 antisense RNA 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:217256655-217257184 Neighboring gene uncharacterized LOC107985984 Neighboring gene Sharpr-MPRA regulatory region 13820 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17096 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:217339556-217340056 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17098 Neighboring gene RPL37A divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12305 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17099 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17100 Neighboring gene ribosomal protein L37a

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?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables ATP-dependent DNA/DNA annealing activity IDA
Inferred from Direct Assay
more info
PubMed 
enables ATP-dependent DNA/DNA annealing activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables ATP-dependent chromatin remodeler activity IEA
Inferred from Electronic Annotation
more info
 
enables helicase activity IEA
Inferred from Electronic Annotation
more info
 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in chromatin remodeling IEA
Inferred from Electronic Annotation
more info
 
involved_in double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in replication fork processing IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in replication fork processing IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in replication fork processing TAS
Traceable Author Statement
more info
PubMed 
involved_in t-circle formation TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
part_of DNA replication factor A complex IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nuclear replication fork IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus 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
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
Names
ATP-driven annealing helicase
HepA-related protein
SMARCA-like protein 1
sucrose nonfermenting protein 2-like 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_009771.1 RefSeqGene

    Range
    5001..75640
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_108

mRNA and Protein(s)

  1. NM_001127207.2NP_001120679.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

    See identical proteins and their annotated locations for NP_001120679.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC043341, BX104166, DA856812
    Consensus CDS
    CCDS2403.1
    UniProtKB/Swiss-Prot
    A6NEH0, Q53R00, Q96AY1, Q9NXQ5, Q9NZC9, Q9UFH3, Q9UI93
    UniProtKB/TrEMBL
    A0A8V8TLD4
    Related
    ENSP00000350940.5, ENST00000358207.9
    Conserved Domains (3) summary
    COG0553
    Location:417889
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    pfam07443
    Location:248301
    HARP; HepA-related protein (HARP)
    pfam15759
    Location:85303
    TMEM108; TMEM108 family
  2. NM_014140.4NP_054859.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

    See identical proteins and their annotated locations for NP_054859.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript. Variants 1 and 2 encode the same protein.
    Source sequence(s)
    BC043341, BX104166, DB099423
    Consensus CDS
    CCDS2403.1
    UniProtKB/Swiss-Prot
    A6NEH0, Q53R00, Q96AY1, Q9NXQ5, Q9NZC9, Q9UFH3, Q9UI93
    UniProtKB/TrEMBL
    A0A8V8TLD4
    Related
    ENSP00000349823.4, ENST00000357276.9
    Conserved Domains (3) summary
    COG0553
    Location:417889
    HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]
    pfam07443
    Location:248301
    HARP; HepA-related protein (HARP)
    pfam15759
    Location:85303
    TMEM108; TMEM108 family

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_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    216412484..216483053
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    216894907..216965465
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)