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Aliases for SMARCAL1 Gene

Aliases for SMARCAL1 Gene

  • SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A-Like 1 2 3 5
  • HepA-Related Protein 2 3 4
  • Sucrose Nonfermenting Protein 2-Like 1 3 4
  • ATP-Driven Annealing Helicase 2 3
  • HHARP 3 4
  • HARP 3 4
  • SMARCA-Like Protein 1 3
  • EC 3.6.4.- 4
  • EC 3.6.1 63

External Ids for SMARCAL1 Gene

Previous GeneCards Identifiers for SMARCAL1 Gene

  • GC02P215378
  • GC02P215998
  • GC02P217241
  • GC02P217481
  • GC02P217102
  • GC02P216985
  • GC02P209131
  • GC02P217277

Summaries for SMARCAL1 Gene

Entrez Gene Summary for SMARCAL1 Gene

  • 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]

GeneCards Summary for SMARCAL1 Gene

SMARCAL1 (SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A-Like 1) is a Protein Coding gene. Diseases associated with SMARCAL1 include schimke immunoosseous dysplasia and neurodegeneration with brain iron accumulation 1. Among its related pathways are DNA Damage and AMPK Enzyme Complex Pathway. GO annotations related to this gene include helicase activity and annealing helicase activity. An important paralog of this gene is ZRANB3.

UniProtKB/Swiss-Prot for SMARCAL1 Gene

  • ATP-dependent annealing helicase that binds selectively to fork DNA relative to ssDNA or dsDNA and catalyzes the rewinding of the stably unwound DNA. Rewinds single-stranded DNA bubbles that are stably bound by replication protein A (RPA). Acts throughout the genome to reanneal stably unwound DNA, performing the opposite reaction of many enzymes, such as helicases and polymerases, that unwind DNA. May play an important role in DNA damage response by acting at stalled replication forks.

Gene Wiki entry for SMARCAL1 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SMARCAL1 Gene

Genomics for SMARCAL1 Gene

Regulatory Elements for SMARCAL1 Gene

Enhancers for SMARCAL1 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around SMARCAL1 on UCSC Golden Path with GeneCards custom track

Promoters for SMARCAL1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around SMARCAL1 on UCSC Golden Path with GeneCards custom track

Genomic Location for SMARCAL1 Gene

Chromosome:
2
Start:
216,412,414 bp from pter
End:
216,483,053 bp from pter
Size:
70,640 bases
Orientation:
Plus strand

Genomic View for SMARCAL1 Gene

Genes around SMARCAL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SMARCAL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SMARCAL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SMARCAL1 Gene

Proteins for SMARCAL1 Gene

  • Protein details for SMARCAL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NZC9-SMAL1_HUMAN
    Recommended name:
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
    Protein Accession:
    Q9NZC9
    Secondary Accessions:
    • A6NEH0
    • Q53R00
    • Q96AY1
    • Q9NXQ5
    • Q9UFH3
    • Q9UI93

    Protein attributes for SMARCAL1 Gene

    Size:
    954 amino acids
    Molecular mass:
    105938 Da
    Quaternary structure:
    • Interacts with RPA2; the interaction is direct and mediates the recruitment by the RPA complex of SMARCAL1 to sites of DNA damage.
    SequenceCaution:
    • Sequence=BAA90955.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SMARCAL1 Gene

neXtProt entry for SMARCAL1 Gene

Proteomics data for SMARCAL1 Gene at MOPED

Post-translational modifications for SMARCAL1 Gene

  • DNA damage-regulated phosphorylation by kinases that may include ATM, ATR and PRKDC.
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for SMARCAL1 (SMARCAL1)

Domains & Families for SMARCAL1 Gene

Protein Domains for SMARCAL1 Gene

Suggested Antigen Peptide Sequences for SMARCAL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NZC9

UniProtKB/Swiss-Prot:

SMAL1_HUMAN :
  • Contains 2 HARP domains.
  • Belongs to the SNF2/RAD54 helicase family. SMARCAL1 subfamily.
Domain:
  • Contains 2 HARP domains.
  • Contains 1 helicase ATP-binding domain.
  • Contains 1 helicase C-terminal domain.
Family:
  • Belongs to the SNF2/RAD54 helicase family. SMARCAL1 subfamily.
genes like me logo Genes that share domains with SMARCAL1: view

No data available for Gene Families for SMARCAL1 Gene

Function for SMARCAL1 Gene

Molecular function for SMARCAL1 Gene

UniProtKB/Swiss-Prot Function:
ATP-dependent annealing helicase that binds selectively to fork DNA relative to ssDNA or dsDNA and catalyzes the rewinding of the stably unwound DNA. Rewinds single-stranded DNA bubbles that are stably bound by replication protein A (RPA). Acts throughout the genome to reanneal stably unwound DNA, performing the opposite reaction of many enzymes, such as helicases and polymerases, that unwind DNA. May play an important role in DNA damage response by acting at stalled replication forks.

Enzyme Numbers (IUBMB) for SMARCAL1 Gene

Gene Ontology (GO) - Molecular Function for SMARCAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with SMARCAL1: view
genes like me logo Genes that share phenotypes with SMARCAL1: view

Human Phenotype Ontology for SMARCAL1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SMARCAL1 Gene

MGI Knock Outs for SMARCAL1:

Animal Model Products

CRISPR Products

miRNA for SMARCAL1 Gene

miRTarBase miRNAs that target SMARCAL1

No data available for Transcription Factor Targets and HOMER Transcription for SMARCAL1 Gene

Localization for SMARCAL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SMARCAL1 Gene

Nucleus. Note=Recruited to damaged DNA regions.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SMARCAL1 Gene COMPARTMENTS Subcellular localization image for SMARCAL1 gene
Compartment Confidence
nucleus 5
cytosol 2

No data available for Gene Ontology (GO) - Cellular Components for SMARCAL1 Gene

Pathways & Interactions for SMARCAL1 Gene

genes like me logo Genes that share pathways with SMARCAL1: view

Pathways by source for SMARCAL1 Gene

1 Cell Signaling Technology pathway for SMARCAL1 Gene

Gene Ontology (GO) - Biological Process for SMARCAL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000733 DNA strand renaturation IMP 18974355
GO:0031297 replication fork processing IMP 19793862
genes like me logo Genes that share ontologies with SMARCAL1: view

No data available for SIGNOR curated interactions for SMARCAL1 Gene

Drugs & Compounds for SMARCAL1 Gene

No Compound Related Data Available

Transcripts for SMARCAL1 Gene

Unigene Clusters for SMARCAL1 Gene

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for SMARCAL1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18
SP1: -
SP2: - -
SP3:

Relevant External Links for SMARCAL1 Gene

GeneLoc Exon Structure for
SMARCAL1
ECgene alternative splicing isoforms for
SMARCAL1

Expression for SMARCAL1 Gene

mRNA expression in normal human tissues for SMARCAL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SMARCAL1 Gene

This gene is overexpressed in CD8 Tcells (16.7), Peripheral blood mononuclear cells (16.1), Blymphocyte (10.3), CD4 Tcells (7.9), and Monocytes (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for SMARCAL1 Gene



SOURCE GeneReport for Unigene cluster for SMARCAL1 Gene Hs.516674

mRNA Expression by UniProt/SwissProt for SMARCAL1 Gene

Q9NZC9-SMAL1_HUMAN
Tissue specificity: Ubiquitously expressed, with high levels in testis.
genes like me logo Genes that share expression patterns with SMARCAL1: view

Protein tissue co-expression partners for SMARCAL1 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for SMARCAL1 Gene

Orthologs for SMARCAL1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SMARCAL1 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia SMARCAL1 35
  • 81.96 (n)
  • 77.87 (a)
SMARCAL1 36
  • 77 (a)
OneToOne
dog
(Canis familiaris)
Mammalia SMARCAL1 35
  • 84.77 (n)
  • 79.98 (a)
SMARCAL1 36
  • 79 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Smarcal1 35
  • 80.16 (n)
  • 75.66 (a)
Smarcal1 16
Smarcal1 36
  • 75 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia SMARCAL1 35
  • 99.69 (n)
  • 99.79 (a)
SMARCAL1 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Smarcal1 35
  • 80.68 (n)
  • 77.88 (a)
oppossum
(Monodelphis domestica)
Mammalia SMARCAL1 36
  • 59 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SMARCAL1 36
  • 57 (a)
OneToOne
chicken
(Gallus gallus)
Aves SMARCAL1 35
  • 61.32 (n)
  • 59.65 (a)
SMARCAL1 36
  • 53 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SMARCAL1 36
  • 53 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia smarcal1 35
  • 61.19 (n)
  • 60.32 (a)
Str.11392 35
zebrafish
(Danio rerio)
Actinopterygii smarcal1 35
  • 66 (n)
  • 64.68 (a)
smarcal1 36
  • 60 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG3753 37
  • 40 (a)
Marcal1 35
  • 50.26 (n)
  • 42.12 (a)
Marcal1 36
  • 34 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008426 35
  • 51.52 (n)
  • 41.83 (a)
worm
(Caenorhabditis elegans)
Secernentea C16A3.1a 37
  • 37 (a)
C16A3.1b 37
  • 37 (a)
C16A3.1c 37
  • 37 (a)
C16A3.1 35
  • 48.94 (n)
  • 40.45 (a)
C16A3.1 36
  • 35 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes MOT1 36
  • 10 (a)
OneToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons CHR18 35
  • 49.07 (n)
  • 41.83 (a)
rice
(Oryza sativa)
Liliopsida Os07g0636200 35
  • 48.3 (n)
  • 41.97 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.8418 35
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2015 36
  • 44 (a)
OneToOne
Species with no ortholog for SMARCAL1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SMARCAL1 Gene

ENSEMBL:
Gene Tree for SMARCAL1 (if available)
TreeFam:
Gene Tree for SMARCAL1 (if available)

Paralogs for SMARCAL1 Gene

Paralogs for SMARCAL1 Gene

(1) SIMAP similar genes for SMARCAL1 Gene using alignment to 9 proteins:

genes like me logo Genes that share paralogs with SMARCAL1: view

Variants for SMARCAL1 Gene

Sequence variations from dbSNP and Humsavar for SMARCAL1 Gene

SNP ID Clin Chr 02 pos Sequence Context AA Info Type
rs2066524 - 216,414,831(+) CCATT(A/G)CTGGC reference, missense
rs11555797 - 216,415,045(+) TCCAC(A/G)TAGTC reference, missense
VAR_021365 -
rs6734114 - 216,415,323(+) CTTAC(A/T)TCCAT reference, missense
rs2066522 - 216,420,381(+) ACCAG(C/G)AGTGA reference, missense

Structural Variations from Database of Genomic Variants (DGV) for SMARCAL1 Gene

Variant ID Type Subtype PubMed ID
nsv834537 CNV Loss 17160897
nsv875845 CNV Gain 21882294
nsv524480 CNV Loss 19592680
nsv875846 CNV Gain 21882294
nsv3161 CNV Insertion 18451855

Variation tolerance for SMARCAL1 Gene

Residual Variation Intolerance Score: 50.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.18; 75.88% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SMARCAL1 Gene

HapMap Linkage Disequilibrium report
SMARCAL1
Human Gene Mutation Database (HGMD)
SMARCAL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SMARCAL1 Gene

Disorders for SMARCAL1 Gene

MalaCards: The human disease database

(8) MalaCards diseases for SMARCAL1 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
schimke immunoosseous dysplasia
  • schimke immuno-osseous dysplasia
neurodegeneration with brain iron accumulation 1
  • pantothenate kinase-associated neurodegeneration
harp syndrome
  • hypoprebetalipoproteinemia, acanthocytosis, retinitis pigmentosa, and pallidal degeneration
spondyloepiphyseal dysplasia with congenital joint dislocations
  • mucopolysaccharidosis iv
nezelof syndrome
  • nezelof's syndrome
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

SMAL1_HUMAN
  • Schimke immuno-osseous dysplasia (SIOD) [MIM:242900]: Causes spondyloepiphyseal dysplasia, renal dysfunction and T-cell immunodeficiency. Approximately half of all patients also exhibit hyperthyroidism, while around half also exhibit episodal cerebral ischemia. {ECO:0000269 PubMed:11799392}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SMARCAL1

Genetic Association Database (GAD)
SMARCAL1
Human Genome Epidemiology (HuGE) Navigator
SMARCAL1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SMARCAL1
genes like me logo Genes that share disorders with SMARCAL1: view

No data available for Genatlas for SMARCAL1 Gene

Publications for SMARCAL1 Gene

  1. Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA- related SNF2 helicase protein from human and mouse. (PMID: 10857751) Coleman M.A. … Mohrenweiser H.W. (Genomics 2000) 2 3 4 23 67
  2. Novel compound mutations of SMARCAL1 associated with severe Schimke immuno-osseous dysplasia in a Chinese patient. (PMID: 20179009) Yue Z. … Wang Y. (Nephrol. Dial. Transplant. 2010) 3 23
  3. Schimke immuno-osseous dysplasia: SMARCAL1 loss-of-function and phenotypic correlation. (PMID: 18805831) Elizondo L.I. … Boerkoel C.F. (J. Med. Genet. 2009) 3 23
  4. SMARCAL1 mutations: a cause of prepubertal idiopathic steroid-resistant nephrotic syndrome. (PMID: 19127206) Zivicnjak M. … Ehrich J.H. (Pediatr. Res. 2009) 3 23
  5. The annealing helicase SMARCAL1 maintains genome integrity at stalled replication forks. (PMID: 19793861) Bansbach C.E. … Cortez D. (Genes Dev. 2009) 3 23

Products for SMARCAL1 Gene

Sources for SMARCAL1 Gene

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