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Smarcal1 SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1 [ Mus musculus (house mouse) ]

Gene ID: 54380, updated on 9-Mar-2023

Summary

Official Symbol
Smarcal1provided by MGI
Official Full Name
SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1provided by MGI
Primary source
MGI:MGI:1859183
See related
Ensembl:ENSMUSG00000039354 AllianceGenome:MGI:1859183
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Mharp; 6030401P21Rik
Summary
Enables ATP-dependent activity, acting on DNA. Predicted to be involved in DNA metabolic process and regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm and site of double-strand break. Predicted to be part of DNA replication factor A complex. Predicted to be active in nuclear replication fork. Is expressed in genitourinary system. Used to study Schimke immuno-osseous dysplasia. Human ortholog(s) of this gene implicated in Schimke immuno-osseous dysplasia. Orthologous to human SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in frontal lobe adult (RPKM 6.3), CNS E18 (RPKM 6.3) and 28 other tissues See more
Orthologs
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Genomic context

See Smarcal1 in Genome Data Viewer
Location:
1 C3; 1 36.72 cM
Exon count:
23
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (72575593..72675949)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (72536695..72636790)

Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 39661 Neighboring gene membrane associated ring-CH-type finger 4 Neighboring gene ribosomal protein L17 pseudogene Neighboring gene predicted gene, 39662 Neighboring gene ankyrin and armadillo repeat containing Neighboring gene ribosomal protein L19 pseudogene

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (3)  1 citation
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
 
enables ATP-dependent DNA/DNA annealing activity ISO
Inferred from Sequence Orthology
more info
 
enables ATP-dependent activity, acting on DNA IDA
Inferred from Direct Assay
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 nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in DNA damage response ISO
Inferred from Sequence Orthology
more info
 
involved_in DNA repair IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in double-strand break repair via nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in replication fork processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in replication fork processing ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
part_of DNA replication factor A complex ISO
Inferred from Sequence Orthology
more info
 
is_active_in nuclear replication fork IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in site of double-strand break ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
Names
hepA-related protein
sucrose nonfermenting protein 2-like 1
NP_061287.2
XP_006496204.1
XP_006496205.1
XP_006496206.1
XP_006496207.1
XP_011236859.1
XP_030111404.1
XP_036008323.1

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.

mRNA and Protein(s)

  1. NM_018817.2NP_061287.2  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

    See identical proteins and their annotated locations for NP_061287.2

    Status: VALIDATED

    Source sequence(s)
    AC163484, AK083488, AK146767, BY739344
    Consensus CDS
    CCDS35609.1
    UniProtKB/Swiss-Prot
    Q8BJL0, Q9QYC4
    Related
    ENSMUSP00000047589.9, ENSMUST00000047615.15
    Conserved Domains (3) summary
    cd18793
    Location:666791
    SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
    cd18010
    Location:395604
    DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
    pfam07443
    Location:214268
    HARP; HepA-related protein (HARP)

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000067.7 Reference GRCm39 C57BL/6J

    Range
    72575593..72675949
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006496141.5XP_006496204.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006496204.1

    UniProtKB/Swiss-Prot
    Q8BJL0, Q9QYC4
    Conserved Domains (3) summary
    cd18793
    Location:666791
    SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
    cd18010
    Location:395604
    DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
    pfam07443
    Location:214268
    HARP; HepA-related protein (HARP)
  2. XM_006496143.5XP_006496206.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006496206.1

    UniProtKB/Swiss-Prot
    Q8BJL0, Q9QYC4
    Conserved Domains (3) summary
    cd18793
    Location:666791
    SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
    cd18010
    Location:395604
    DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
    pfam07443
    Location:214268
    HARP; HepA-related protein (HARP)
  3. XM_011238557.4XP_011236859.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X2

    Related
    ENSMUST00000136498.8
    Conserved Domains (3) summary
    cd18793
    Location:666791
    SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
    cd18010
    Location:395604
    DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
    pfam07443
    Location:214267
    HARP; HepA-related protein (HARP)
  4. XM_036152430.1XP_036008323.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X3

    Conserved Domains (3) summary
    cd18793
    Location:420545
    SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
    cd18010
    Location:149358
    DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
    pfam07443
    Location:56110
    HARP; HepA-related protein (HARP)
  5. XM_030255544.2XP_030111404.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X4

    Conserved Domains (3) summary
    cd18793
    Location:372497
    SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
    cd18010
    Location:101310
    DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
    pfam07443
    Location:861
    HARP; HepA-related protein (HARP)
  6. XM_006496142.5XP_006496205.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006496205.1

    UniProtKB/Swiss-Prot
    Q8BJL0, Q9QYC4
    Related
    ENSMUSP00000137833.2, ENSMUST00000152225.2
    Conserved Domains (3) summary
    cd18793
    Location:666791
    SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
    cd18010
    Location:395604
    DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
    pfam07443
    Location:214268
    HARP; HepA-related protein (HARP)
  7. XM_006496144.1XP_006496207.1  SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

    See identical proteins and their annotated locations for XP_006496207.1

    UniProtKB/Swiss-Prot
    Q8BJL0, Q9QYC4
    Conserved Domains (3) summary
    cd18793
    Location:666791
    SF2_C_SNF; C-terminal helicase domain of the SNF family helicases
    cd18010
    Location:395604
    DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1
    pfam07443
    Location:214268
    HARP; HepA-related protein (HARP)