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    Smarcal1 SNF2 related chromatin remodeling ATPase like 1 [ Mus musculus (house mouse) ]

    Gene ID: 54380, updated on 30-Nov-2024

    Summary

    Official Symbol
    Smarcal1provided by MGI
    Official Full Name
    SNF2 related chromatin remodeling ATPase 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 double-strand break repair via nonhomologous end joining; regulation of transcription by RNA polymerase II; and replication fork processing. 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 cerebral cortex and 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, Nov 2024]
    Expression
    Ubiquitous expression in frontal lobe adult (RPKM 6.3), CNS E18 (RPKM 6.3) and 28 other tissues See more
    Orthologs
    NEW
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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
    RS_2024_02 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 STARR-seq mESC enhancer starr_01276 Neighboring gene predicted gene, 39661 Neighboring gene membrane associated ring-CH-type finger 4 Neighboring gene ribosomal protein L17 pseudogene Neighboring gene STARR-seq mESC enhancer starr_01277 Neighboring gene STARR-positive B cell enhancer ABC_E1548 Neighboring gene STARR-seq mESC enhancer starr_01281 Neighboring gene predicted gene, 39662 Neighboring gene ankyrin and armadillo repeat containing Neighboring gene STARR-seq mESC enhancer starr_01283 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)
    • Endonuclease-mediated (1) 
    • Targeted (3)  1 citation

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

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

    General protein information

    Preferred Names
    SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
    Names
    SWI/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1
    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)

    NEW Try the new Transcript table

    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
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, 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: GCF_000001635.27-RS_2024_02

    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
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, 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
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, 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
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, 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
      Q3TEQ9, Q3U4W0, Q3V3A8, Q8BJL0, Q8BVK7, Q8BXW4, Q8K309, Q9EQK8, 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)