Details for: SMARCAL1

Gene ID: 50485

Symbol: SMARCAL1

Ensembl ID: ENSG00000138375

Description: SNF2 related chromatin remodeling annealing helicase 1

Associated with

Cells (max top 100)

(Cell Significance Index and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: polychromatophilic erythroblast (CL0000550)
    Fold Change: 146.4526
    Cell Significance Index: -22.7800
  • Cell Name: hematopoietic oligopotent progenitor cell (CL0002032)
    Fold Change: 86.3811
    Cell Significance Index: -21.9100
  • Cell Name: mucosal type mast cell (CL0000485)
    Fold Change: 47.7038
    Cell Significance Index: -19.3800
  • Cell Name: ciliated cell of the bronchus (CL0002332)
    Fold Change: 20.3615
    Cell Significance Index: -19.4400
  • Cell Name: orthochromatic erythroblast (CL0000552)
    Fold Change: 19.2708
    Cell Significance Index: -23.7600
  • Cell Name: CD8-alpha-beta-positive, alpha-beta intraepithelial T cell (CL0000796)
    Fold Change: 8.4327
    Cell Significance Index: -22.5900
  • Cell Name: stromal cell of bone marrow (CL0010001)
    Fold Change: 6.0833
    Cell Significance Index: -24.0100
  • Cell Name: epidermal Langerhans cell (CL0002457)
    Fold Change: 4.5006
    Cell Significance Index: -9.8500
  • Cell Name: epithelial cell of pancreas (CL0000083)
    Fold Change: 1.7775
    Cell Significance Index: 29.2900
  • Cell Name: L2/3-6 intratelencephalic projecting glutamatergic neuron (CL4023040)
    Fold Change: 1.0448
    Cell Significance Index: 209.5900
  • Cell Name: colon goblet cell (CL0009039)
    Fold Change: 0.9738
    Cell Significance Index: 96.3400
  • Cell Name: neoplastic cell (CL0001063)
    Fold Change: 0.8450
    Cell Significance Index: 167.7000
  • Cell Name: tuft cell of colon (CL0009041)
    Fold Change: 0.8373
    Cell Significance Index: 755.9800
  • Cell Name: obsolete caudal ganglionic eminence derived GABAergic cortical interneuron (CL4023070)
    Fold Change: 0.6701
    Cell Significance Index: 240.3700
  • Cell Name: intestinal crypt stem cell of colon (CL0009043)
    Fold Change: 0.5934
    Cell Significance Index: 64.5500
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 0.5645
    Cell Significance Index: 91.8100
  • Cell Name: retinal progenitor cell (CL0002672)
    Fold Change: 0.5241
    Cell Significance Index: 29.4100
  • Cell Name: enteroendocrine cell of small intestine (CL0009006)
    Fold Change: 0.3756
    Cell Significance Index: 9.3900
  • Cell Name: preadipocyte (CL0002334)
    Fold Change: 0.3638
    Cell Significance Index: 7.1000
  • Cell Name: cortical cell of adrenal gland (CL0002097)
    Fold Change: 0.3635
    Cell Significance Index: 9.7400
  • Cell Name: forebrain neuroblast (CL1000042)
    Fold Change: 0.3303
    Cell Significance Index: 20.3000
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: 0.3036
    Cell Significance Index: 23.3000
  • Cell Name: microfold cell of epithelium of small intestine (CL1000353)
    Fold Change: 0.2802
    Cell Significance Index: 19.3800
  • Cell Name: skeletal muscle fiber (CL0008002)
    Fold Change: 0.2614
    Cell Significance Index: 6.7200
  • Cell Name: GABAergic interneuron (CL0011005)
    Fold Change: 0.2526
    Cell Significance Index: 174.6900
  • Cell Name: basal epithelial cell of tracheobronchial tree (CL0002329)
    Fold Change: 0.2437
    Cell Significance Index: 6.8100
  • Cell Name: conjunctival epithelial cell (CL1000432)
    Fold Change: 0.2389
    Cell Significance Index: 3.2600
  • Cell Name: paneth cell of colon (CL0009009)
    Fold Change: 0.1995
    Cell Significance Index: 2.9900
  • Cell Name: decidual cell (CL2000002)
    Fold Change: 0.1751
    Cell Significance Index: 2.8100
  • Cell Name: indirect pathway medium spiny neuron (CL4023029)
    Fold Change: 0.1644
    Cell Significance Index: 7.2700
  • Cell Name: paneth cell of epithelium of small intestine (CL1000343)
    Fold Change: 0.1357
    Cell Significance Index: 2.9400
  • Cell Name: intermediate cell of urothelium (CL4030055)
    Fold Change: 0.1350
    Cell Significance Index: 24.3400
  • Cell Name: bladder urothelial cell (CL1001428)
    Fold Change: 0.1342
    Cell Significance Index: 6.9700
  • Cell Name: enterocyte of epithelium of small intestine (CL1000334)
    Fold Change: 0.1308
    Cell Significance Index: 3.7700
  • Cell Name: direct pathway medium spiny neuron (CL4023026)
    Fold Change: 0.1096
    Cell Significance Index: 4.1500
  • Cell Name: cell in vitro (CL0001034)
    Fold Change: 0.0864
    Cell Significance Index: 47.1700
  • Cell Name: hippocampal granule cell (CL0001033)
    Fold Change: 0.0852
    Cell Significance Index: 5.7300
  • Cell Name: enteroendocrine cell of colon (CL0009042)
    Fold Change: 0.0757
    Cell Significance Index: 14.4100
  • Cell Name: cortical interneuron (CL0008031)
    Fold Change: 0.0755
    Cell Significance Index: 1.8100
  • Cell Name: enterocyte of epithelium of large intestine (CL0002071)
    Fold Change: 0.0631
    Cell Significance Index: 2.8600
  • Cell Name: stromal cell of ovary (CL0002132)
    Fold Change: 0.0531
    Cell Significance Index: 7.2900
  • Cell Name: pigmented epithelial cell (CL0000529)
    Fold Change: 0.0527
    Cell Significance Index: 99.2800
  • Cell Name: basal cell of urothelium (CL1000486)
    Fold Change: 0.0521
    Cell Significance Index: 6.4100
  • Cell Name: hair follicular keratinocyte (CL2000092)
    Fold Change: 0.0426
    Cell Significance Index: 18.8600
  • Cell Name: anterior lens cell (CL0002223)
    Fold Change: 0.0362
    Cell Significance Index: 66.6900
  • Cell Name: lens epithelial cell (CL0002224)
    Fold Change: 0.0362
    Cell Significance Index: 55.6600
  • Cell Name: secondary lens fiber (CL0002225)
    Fold Change: 0.0244
    Cell Significance Index: 33.2200
  • Cell Name: acinar cell of salivary gland (CL0002623)
    Fold Change: 0.0129
    Cell Significance Index: 0.6000
  • Cell Name: non-pigmented ciliary epithelial cell (CL0002304)
    Fold Change: 0.0116
    Cell Significance Index: 7.3600
  • Cell Name: Purkinje cell (CL0000121)
    Fold Change: 0.0011
    Cell Significance Index: 0.0300
  • Cell Name: ciliary muscle cell (CL1000443)
    Fold Change: -0.0055
    Cell Significance Index: -2.4900
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: -0.0196
    Cell Significance Index: -0.6900
  • Cell Name: early pro-B cell (CL0002046)
    Fold Change: -0.0204
    Cell Significance Index: -1.3200
  • Cell Name: kidney loop of Henle cortical thick ascending limb epithelial cell (CL1001109)
    Fold Change: -0.0236
    Cell Significance Index: -17.2700
  • Cell Name: odontoblast (CL0000060)
    Fold Change: -0.0264
    Cell Significance Index: -3.3800
  • Cell Name: pancreatic A cell (CL0000171)
    Fold Change: -0.0281
    Cell Significance Index: -20.8100
  • Cell Name: pulmonary alveolar epithelial cell (CL0000322)
    Fold Change: -0.0307
    Cell Significance Index: -23.2600
  • Cell Name: pigmented ciliary epithelial cell (CL0002303)
    Fold Change: -0.0341
    Cell Significance Index: -4.9600
  • Cell Name: eye photoreceptor cell (CL0000287)
    Fold Change: -0.0393
    Cell Significance Index: -2.4800
  • Cell Name: type B pancreatic cell (CL0000169)
    Fold Change: -0.0401
    Cell Significance Index: -22.6100
  • Cell Name: pancreatic PP cell (CL0002275)
    Fold Change: -0.0407
    Cell Significance Index: -25.4300
  • Cell Name: tonsil germinal center B cell (CL2000006)
    Fold Change: -0.0467
    Cell Significance Index: -5.5000
  • Cell Name: placental villous trophoblast (CL2000060)
    Fold Change: -0.0506
    Cell Significance Index: -1.3500
  • Cell Name: dopaminergic neuron (CL0000700)
    Fold Change: -0.0654
    Cell Significance Index: -18.8100
  • Cell Name: lung endothelial cell (CL1001567)
    Fold Change: -0.0703
    Cell Significance Index: -3.6600
  • Cell Name: pancreatic acinar cell (CL0002064)
    Fold Change: -0.0731
    Cell Significance Index: -12.4900
  • Cell Name: abnormal cell (CL0001061)
    Fold Change: -0.0821
    Cell Significance Index: -8.3900
  • Cell Name: epithelial cell of stomach (CL0002178)
    Fold Change: -0.0844
    Cell Significance Index: -9.8400
  • Cell Name: cerebellar granule cell (CL0001031)
    Fold Change: -0.0928
    Cell Significance Index: -1.5900
  • Cell Name: lactocyte (CL0002325)
    Fold Change: -0.1184
    Cell Significance Index: -15.3000
  • Cell Name: pancreatic D cell (CL0000173)
    Fold Change: -0.1221
    Cell Significance Index: -25.7200
  • Cell Name: transit amplifying cell of small intestine (CL0009012)
    Fold Change: -0.1547
    Cell Significance Index: -3.2100
  • Cell Name: pancreatic ductal cell (CL0002079)
    Fold Change: -0.1580
    Cell Significance Index: -18.1000
  • Cell Name: sebum secreting cell (CL0000317)
    Fold Change: -0.1828
    Cell Significance Index: -12.9300
  • Cell Name: luminal adaptive secretory precursor cell of mammary gland (CL4033057)
    Fold Change: -0.1904
    Cell Significance Index: -8.9500
  • Cell Name: smooth muscle cell of sphincter of pupil (CL0002243)
    Fold Change: -0.1917
    Cell Significance Index: -19.9600
  • Cell Name: transit amplifying cell of colon (CL0009011)
    Fold Change: -0.2058
    Cell Significance Index: -6.5900
  • Cell Name: pro-T cell (CL0000827)
    Fold Change: -0.2294
    Cell Significance Index: -5.8600
  • Cell Name: intestinal tuft cell (CL0019032)
    Fold Change: -0.2424
    Cell Significance Index: -14.8600
  • Cell Name: progenitor cell of mammary luminal epithelium (CL0009116)
    Fold Change: -0.2467
    Cell Significance Index: -18.3900
  • Cell Name: mesenchymal cell (CL0008019)
    Fold Change: -0.2539
    Cell Significance Index: -4.2500
  • Cell Name: kidney loop of Henle descending limb epithelial cell (CL1001021)
    Fold Change: -0.2592
    Cell Significance Index: -20.5300
  • Cell Name: leptomeningeal cell (CL0000708)
    Fold Change: -0.2608
    Cell Significance Index: -5.5800
  • Cell Name: intestinal crypt stem cell of small intestine (CL0009017)
    Fold Change: -0.2662
    Cell Significance Index: -5.6700
  • Cell Name: fibro/adipogenic progenitor cell (CL0009099)
    Fold Change: -0.2791
    Cell Significance Index: -14.1000
  • Cell Name: medial ganglionic eminence derived interneuron (CL4023063)
    Fold Change: -0.3184
    Cell Significance Index: -4.5600
  • Cell Name: pvalb GABAergic cortical interneuron (CL4023018)
    Fold Change: -0.3265
    Cell Significance Index: -6.9300
  • Cell Name: glycinergic neuron (CL1001509)
    Fold Change: -0.3335
    Cell Significance Index: -17.5100
  • Cell Name: mesonephric nephron tubule epithelial cell (CL1000022)
    Fold Change: -0.3407
    Cell Significance Index: -11.8400
  • Cell Name: hippocampal pyramidal neuron (CL1001571)
    Fold Change: -0.3739
    Cell Significance Index: -10.6700
  • Cell Name: sst GABAergic cortical interneuron (CL4023017)
    Fold Change: -0.4071
    Cell Significance Index: -8.0500
  • Cell Name: fibroblast of dermis (CL0002551)
    Fold Change: -0.4113
    Cell Significance Index: -8.6100
  • Cell Name: corticothalamic-projecting glutamatergic cortical neuron (CL4023013)
    Fold Change: -0.4141
    Cell Significance Index: -13.1900
  • Cell Name: granulosa cell (CL0000501)
    Fold Change: -0.4229
    Cell Significance Index: -11.1200
  • Cell Name: OFF midget ganglion cell (CL4033047)
    Fold Change: -0.4242
    Cell Significance Index: -5.2900
  • Cell Name: L6b glutamatergic cortical neuron (CL4023038)
    Fold Change: -0.4299
    Cell Significance Index: -14.0800
  • Cell Name: basal cell of prostate epithelium (CL0002341)
    Fold Change: -0.4467
    Cell Significance Index: -12.1600
  • Cell Name: VIP GABAergic cortical interneuron (CL4023016)
    Fold Change: -0.4493
    Cell Significance Index: -9.0200
  • Cell Name: CD4-positive, alpha-beta memory T cell, CD45RO-positive (CL0001204)
    Fold Change: -0.4495
    Cell Significance Index: -13.2000
  • Cell Name: fibroblast of cardiac tissue (CL0002548)
    Fold Change: -0.4547
    Cell Significance Index: -6.5300

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics** SMARCAL1 is classified as an ATP-dependent chromatin remodeler, possessing helicase and hydrolase activities that facilitate the exchange of nucleosomes and chromatin remodeling. Its structure and function are closely related to the SWI/SNF complex, which is a multi-subunit complex that regulates chromatin structure and transcriptional activity. SMARCAL1 is also involved in DNA damage response, DNA repair, and replication fork processing, indicating its role in maintaining genome integrity. Additionally, its expression in various cell types highlights its potential involvement in tissue-specific functions and cellular differentiation. **Pathways and Functions** SMARCAL1 is involved in several key pathways, including: 1. **Atp-dependent chromatin remodeler activity**: SMARCAL1 participates in chromatin remodeling by interacting with other subunits of the SWI/SNF complex to facilitate the exchange of nucleosomes. 2. **Atp-dependent DNA/DNA annealing activity**: SMARCAL1 possesses helicase activity, which is necessary for unwinding DNA and facilitating the annealing of DNA strands. 3. **DNA damage response**: SMARCAL1 is involved in the response to DNA damage, including double-strand break repair via nonhomologous end joining. 4. **DNA repair**: SMARCAL1 participates in the repair of DNA lesions, including base excision repair and nucleotide excision repair. 5. **DNA replication factor A complex**: SMARCAL1 interacts with the DNA replication factor A complex to regulate DNA replication and replication fork processing. 6. **Regulation of transcription by RNA polymerase II**: SMARCAL1 influences transcriptional activity by modulating the interaction between RNA polymerase II and chromatin. **Clinical Significance** SMARCAL1 mutations have been associated with several genetic disorders, including: 1. **Mucopolysaccharidosis type VI**: SMARCAL1 mutations have been identified as a cause of mucopolysaccharidosis type VI, a lysosomal storage disorder characterized by progressive neurological and skeletal degeneration. 2. **Progeria**: SMARCAL1 mutations have also been linked to progeria, a rare genetic disorder characterized by premature aging. 3. **Neurodegenerative disorders**: SMARCAL1 has been implicated in the pathogenesis of neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease. In conclusion, SMARCAL1 plays a critical role in regulating chromatin structure and function, influencing various cellular processes and maintaining genome stability. Its involvement in genetic disorders highlights the importance of understanding the function and regulation of this gene in the context of human disease.

Genular Protein ID: 951040853

Symbol: SMAL1_HUMAN

Name: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

UniProtKB Accession Codes:

Database IDs:

Citations:

PubMed ID: 10857751

Title: Cloning and characterization of HARP/SMARCAL1: a prokaryotic HepA-related SNF2 helicase protein from human and mouse.

PubMed ID: 10857751

DOI: 10.1006/geno.2000.6174

PubMed ID: 11799392

Title: Mutant chromatin remodeling protein SMARCAL1 causes Schimke immuno-osseous dysplasia.

PubMed ID: 11799392

DOI: 10.1038/ng821

PubMed ID: 15815621

Title: Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

PubMed ID: 15815621

DOI: 10.1038/nature03466

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 18669648

Title: A quantitative atlas of mitotic phosphorylation.

PubMed ID: 18669648

DOI: 10.1073/pnas.0805139105

PubMed ID: 19793863

Title: The annealing helicase HARP is recruited to DNA repair sites via an interaction with RPA.

PubMed ID: 19793863

DOI: 10.1101/gad.1831509

PubMed ID: 19793861

Title: The annealing helicase SMARCAL1 maintains genome integrity at stalled replication forks.

PubMed ID: 19793861

DOI: 10.1101/gad.1839909

PubMed ID: 19793862

Title: The SIOD disorder protein SMARCAL1 is an RPA-interacting protein involved in replication fork restart.

PubMed ID: 19793862

DOI: 10.1101/gad.1832309

PubMed ID: 20068231

Title: Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.

PubMed ID: 20068231

DOI: 10.1126/scisignal.2000475

PubMed ID: 21269460

Title: Initial characterization of the human central proteome.

PubMed ID: 21269460

DOI: 10.1186/1752-0509-5-17

PubMed ID: 22814378

Title: N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB.

PubMed ID: 22814378

DOI: 10.1073/pnas.1210303109

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

DOI: 10.1021/pr300630k

PubMed ID: 24275569

Title: An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.

PubMed ID: 24275569

DOI: 10.1016/j.jprot.2013.11.014

PubMed ID: 16959974

Title: The consensus coding sequences of human breast and colorectal cancers.

PubMed ID: 16959974

DOI: 10.1126/science.1133427

PubMed ID: 18974355

Title: HARP is an ATP-driven annealing helicase.

PubMed ID: 18974355

DOI: 10.1126/science.1161233

Sequence Information:

  • Length: 954
  • Mass: 105938
  • Checksum: C5C762C24A2FDD3A
  • Sequence:
  • MSLPLTEEQR KKIEENRQKA LARRAEKLLA EQHQRTSSGT SIAGNPFQAK QGPSQNFPRE 
    SCKPVSHGVI FKQQNLSSSS NADQRPHDSH SFQAKGIWKK PEEMPTACPG HSPRSQMALT 
    GISPPLAQSP PEVPKQQLLS YELGQGHAQA SPEIRFTPFA NPTHKPLAKP KSSQETPAHS 
    SGQPPRDAKL EAKTAKASPS GQNISYIHSS SESVTPRTEG RLQQKSGSSV QKGVNSQKGK 
    CVRNGDRFQV LIGYNAELIA VFKTLPSKNY DPDTKTWNFS MNDYSALMKA AQSLPTVNLQ 
    PLEWAYGSSE SPSTSSEGQA GLPSAPSLSF VKGRCMLISR AYFEADISYS QDLIALFKQM 
    DSRRYDVKTR KWSFLLEEHS KLIAKVRCLP QVQLDPLPTT LTLAFASQLK KTSLSLTPDV 
    PEADLSEVDP KLVSNLMPFQ RAGVNFAIAK GGRLLLADDM GLGKTIQAIC IAAFYRKEWP 
    LLVVVPSSVR FTWEQAFLRW LPSLSPDCIN VVVTGKDRLT AGLINIVSFD LLSKLEKQLK 
    TPFKVVIIDE SHFLKNSRTA RCRAAMPVLK VAKRVILLSG TPAMSRPAEL YTQIIAVKPT 
    FFPQFHAFGL RYCDAKRMPW GWDYSGSSNL GELKLLLEEA VMLRRLKSDV LSQLPAKQRK 
    IVVIAPGRIN ARTRAALDAA AKEMTTKDKT KQQQKDALIL FFNRTAEAKI PSVIEYILDL 
    LESGREKFLV FAHHKVVLDA ITQELERKHV QHIRIDGSTS SAEREDLCQQ FQLSERHAVA 
    VLSITAANMG LTFSSADLVV FAELFWNPGV LIQAEDRVHR IGQTSSVGIH YLVAKGTADD 
    YLWPLIQEKI KVLAEAGLSE TNFSEMTEST DYLYKDPKQQ KIYDLFQKSF EKEGSDMELL 
    EAAESFDPGS ASGTSGSSSQ NMGDTLDESS LTASPQKKRR FEFFDNWDSF TSPL

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.