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Smarcal1 Gene Detail
Summary
  • Symbol
    Smarcal1
  • Name
    SNF2 related chromatin remodeling ATPase like 1
  • Synonyms
    6030401P21Rik, Mharp
  • Feature Type
    protein coding gene
  • IDs
    MGI:1859183
    NCBI Gene: 54380
  • Alliance
    gene page
  • Transcription Start Sites
    2 TSS
Location &
Maps
more
  • Sequence Map
    Chr1:72622410-72672293 bp, + strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 1, 36.72 cM
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    1765 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1859183
 protein coding gene Chr1:72575593-72675949 (+)
129S1/SvImJ MGP_129S1SvImJ_G0016133
 protein coding gene Chr1:73101579-73155531 (+)
A/J MGP_AJ_G0016116
 protein coding gene Chr1:70473771-70524769 (+)
AKR/J MGP_AKRJ_G0016073
 protein coding gene Chr1:72500776-72552374 (+)
BALB/cJ MGP_BALBcJ_G0016071
 protein coding gene Chr1:70607476-70660414 (+)
C3H/HeJ MGP_C3HHeJ_G0015902
 protein coding gene Chr1:72811453-72870653 (+)
C57BL/6NJ MGP_C57BL6NJ_G0016524
 protein coding gene Chr1:75921559-75977070 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0014245
 protein coding gene Chr1:66193026-66242179 (+)
CAST/EiJ MGP_CASTEiJ_G0015486
 protein coding gene Chr1:72108664-72160840 (+)
CBA/J MGP_CBAJ_G0015875
 protein coding gene Chr1:78407767-78458739 (+)
DBA/2J MGP_DBA2J_G0015976
 protein coding gene Chr1:69879057-69928279 (+)
FVB/NJ MGP_FVBNJ_G0015979
 protein coding gene Chr1:69059484-69110467 (+)
LP/J MGP_LPJ_G0016048
 protein coding gene Chr1:74155521-74209146 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0015999
 protein coding gene Chr1:81877239-81928739 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0016571
 protein coding gene Chr1:72535714-72591933 (+)
PWK/PhJ MGP_PWKPhJ_G0015273
 protein coding gene Chr1:69324211-69375821 (+)
SPRET/EiJ MGP_SPRETEiJ_G0015052
 protein coding gene Chr1:71902562-71952247 (+)
WSB/EiJ MGP_WSBEiJ_G0015548
 protein coding gene Chr1:72352599-72404835 (+)



Homology
more
  • Human Ortholog
    SMARCAL1, SNF2 related chromatin remodeling annealing helicase 1
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SMARCAL1, SNF2 related chromatin remodeling annealing helicase 1
  • Synonyms
    HARP, HHARP
  • Links
    NCBI Gene ID: 50485
    neXtProt AC: NX_Q9NZC9
    UniProt: Q9NZC9

  • Chr Location
    2q35; chr2:216412383-216483053 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with Smarcal1 mouse models; 1 with human SMARCAL1 associations

Human Disease Mouse Models
      
IDs
 View 1 model
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    1 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    15 phenotypes from 2 alleles in 2 genetic backgrounds
    19 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Mice homozygous for a null allele display reduced B cell counts and increased susceptibility to heat induced mortality. Treatment of homozygous null mice with alpha-amanitin results in phenotypes similar to Schimke Type Immunoosseous Dysplasia.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    25
  • GO References
    6
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    734
  • Tissues
    17
  • cDNA Data
    96
  • Literature Summary
    3
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000039354 Ensembl Gene Model | MGI Sequence Detail 49884 C57BL/6J ±  kb
    transcript ENSMUST00000047615 Ensembl | MGI Sequence Detail 3059 Not Applicable  
    polypeptide ENSMUSP00000047589 Ensembl | MGI Sequence Detail 910 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      3 Sequences
    • Protein Ontology
      PR:000015261 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1
      (term hierarchy)
    • PDB
      4O66
    • EC
      3.6.4.-
    • InterPro Domains
      IPR010003 HARP domain
      IPR001650 Helicase, C-terminal domain-like
      IPR014001 Helicase superfamily 1/2, ATP-binding domain
      IPR027417 P-loop containing nucleoside triphosphate hydrolase
      IPR038718 SNF2-like, N-terminal domain superfamily
      IPR000330 SNF2, N-terminal
      IPR049730 SNF2/RAD5-like, C-terminal helicase domain
    • GlyGen
      Q8BJL0 1 site, 1 N-linked glycan (1 site)
    Molecular
    Reagents
    less
    • All nucleic 96
      cDNA 96

      Microarray probesets 5
    Other
    Accession IDs
    less
    MGI:2138358, MGI:2445177
    References
    more
    • Summaries
      All 53
      Developmental Gene Expression 3
      Diseases 1
      Gene Ontology 6
      Phenotypes 19
    • Earliest
      J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
    • Latest
      J:348335 Georgieva D, et al., BRCA1 and 53BP1 regulate reprogramming efficiency by mediating DNA repair pathway choice at replication-associated double-strand breaks. Cell Rep. 2024 Apr 23;43(4):114006
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    11/19/2024
    MGI 6.24     		The Jackson Laboratory