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SMARCAL1 SNF2 related chromatin remodeling annealing helicase 1 [ Homo sapiens (human) ]

Gene ID: 50485, updated on 4-Jan-2025

Summary

Official Symbol
SMARCAL1provided by HGNC
Official Full Name
SNF2 related chromatin remodeling annealing helicase 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_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (216412484..216483053)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (216894907..216965465)
RS_2024_09 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: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

General gene information

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding  
enables ATP-dependent DNA/DNA annealing activity PubMed 
enables ATP-dependent DNA/DNA annealing activity PubMed 
enables ATP-dependent activity, acting on DNA  
enables helicase activity  
enables hydrolase activity  
enables protein binding PubMed 
Component Evidence Code Pubs
part_of DNA replication factor A complex PubMed 
is_active_in nuclear replication fork  
located_in nucleoplasm  
located_in nucleus PubMed 
located_in site of double-strand break 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
SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1
sucrose nonfermenting protein 2-like 1
NP_001120679.1
NP_054859.2

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_2024_08

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)
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