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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 7-Jun-2020

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
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

Genomic context

See SMARCAL1 in Genome Data Viewer
Location:
2q35
Exon count:
19
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (216412484..216483053)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (217277137..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 SMARCAL1 antisense RNA 1 Neighboring gene uncharacterized LOC107985984 Neighboring gene Sharpr-MPRA regulatory region 13820 Neighboring gene RPL37A divergent transcript Neighboring gene uncharacterized LOC101928156 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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
DNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-dependent ATPase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-dependent ATPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
annealing helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
annealing helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
annealing helicase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
DNA duplex unwinding IEA
Inferred from Electronic Annotation
more info
 
DNA metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA rewinding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA strand renaturation IEA
Inferred from Electronic Annotation
more info
 
cellular response to DNA damage stimulus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular response to DNA damage stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
replication fork processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
replication fork processing IMP
Inferred from Mutant Phenotype
more info
PubMed 
replication fork processing TAS
Traceable Author Statement
more info
PubMed 
replication fork protection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
t-circle formation TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
colocalizes_with DNA replication factor A complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
colocalizes_with DNA replication factor A complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear replication fork IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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
NP_001120679.1
NP_054859.2

NCBI Reference Sequences (RefSeq)

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
    Q9NZC9
    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
    Q9NZC9
    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: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

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