Human Gene SMARCE1 (ENST00000348513.12_8) from GENCODE V47lift37
  Description: SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 (from RefSeq NM_003079.5)
Gencode Transcript: ENST00000348513.12_8
Gencode Gene: ENSG00000073584.20_16
Transcript (Including UTRs)
   Position: hg19 chr17:38,781,214-38,804,070 Size: 22,857 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr17:38,785,037-38,802,054 Size: 17,018 Coding Exon Count: 10 

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Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:38,781,214-38,804,070)mRNA (may differ from genome)Protein (411 aa)
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-  Comments and Description Text from UniProtKB
  ID: SMCE1_HUMAN
DESCRIPTION: RecName: Full=SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1; AltName: Full=BRG1-associated factor 57; Short=BAF57;
FUNCTION: Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and the neuron-specific chromatin remodeling complex (nBAF complex). During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity). Required for the coactivation of estrogen responsive promoters by Swi/Snf complexes and the SRC/p160 family of histone acetyltransferases (HATs). Also specifically interacts with the CoREST corepressor resulting in repression of neuronal specific gene promoters in non-neuronal cells. Also involved in vitamin D-coupled transcription regulation via its association with the WINAC complex, a chromatin-remodeling complex recruited by vitamin D receptor (VDR), which is required for the ligand-bound VDR-mediated transrepression of the CYP27B1 gene.
SUBUNIT: Component of 6 multiprotein chromatin-remodeling complexes: Swi/Snf-A (BAF), Swi/Snf-B (PBAF), Brm, Brg1(I), WINAC and Brg1(II). Each of the five complexes contains a catalytic subunit (either SMARCA4/BRG1/BAF190A or SMARCA2/BRM/BAF190B), and at least SMARCE1, ACTL6A/BAF53, SMARCC1/BAF155, SMARCC2/BAF170, and SMARCB1 (SNF5/INI1). Other subunits specific to each of the complexes may also be present. Component of the BAF complex, which includes at least actin (ACTB), ARID1A, ARID1B/BAF250, SMARCA2, SMARCA4/BRG1/BAF190A, ACTL6A/BAF53, ACTL6B/BAF53B, SMARCE1/BAF57, SMARCC1/BAF155, SMARCC2/BAF170, SMARCB1/SNF5/INI1, and one or more of SMARCD1/BAF60A, SMARCD2/BAF60B, or SMARCD3/BAF60C. In muscle cells, the BAF complex also contains DPF3. Also binds to the SRC/p160 family of histone acetyltransferases (HATs) composed of NCOA1, NCOA2, and NCOA3. Component of the WINAC complex, at least composed of SMARCA2, SMARCA4, SMARCB1, SMARCC1, SMARCC2, SMARCD1, SMARCE1, ACTL6A, BAZ1B/WSTF, ARID1A, SUPT16H, CHAF1A and TOP2B. Interacts with RCOR1/CoREST, NR3C1 and ZMIM2/ZIMP7. Component of neural progenitors-specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Component of neuron-specific chromatin remodeling complex (nBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B and actin. Interacts with BRDT (By similarity).
INTERACTION: Q68CP9:ARID2; NbExp=4; IntAct=EBI-455078, EBI-637818; Q9HCU9:BRMS1; NbExp=2; IntAct=EBI-455078, EBI-714781; Q9UKL0:RCOR1; NbExp=4; IntAct=EBI-455096, EBI-926563;
SUBCELLULAR LOCATION: Nucleus.
DOMAIN: The HMG domain is essential for CD4 silencing and CD8 activation; mutation of this domain blocks thymus development (By similarity).
PTM: Ubiquitinated by TRIP12, leading to its degradation by the proteasome. Ubiquitination is prevented upon interaction between TRIP12 and SMARCC1.
DISEASE: Note=Defects in SMARCE1 may be a cause of Coffin-Siris syndrome, a highly variable disease characterized by mental retardation associated with a broad spectrum of different clinical features.
SIMILARITY: Contains 1 HMG box DNA-binding domain.

-  Primer design for this transcript
 

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-  MalaCards Disease Associations
  MalaCards Gene Search: SMARCE1
Diseases sorted by gene-association score: meningioma, familial* (1331), coffin-siris syndrome 5* (1230), coffin-siris syndrome 1* (331), smarce1-related coffin-siris syndrome* (100), meningioma, familial susceptibility* (71), clear cell meningioma (25), meningothelial meningioma (15), hypertrichosis (9), spinal canal and spinal cord meningioma (8), spinal meningioma (6), schwannomatosis (6), borjeson-forssman-lehmann syndrome (5), spinal cancer (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.10 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 183.15 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -31.2091-0.343 Picture PostScript Text
3' UTR -1026.503823-0.269 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR009071 - HMG_superfamily

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on Q969G3
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003713 transcription coactivator activity
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0008080 N-acetyltransferase activity
GO:0016922 ligand-dependent nuclear receptor binding
GO:0047485 protein N-terminus binding
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0031492 nucleosomal DNA binding

Biological Process:
GO:0006325 chromatin organization
GO:0006337 nucleosome disassembly
GO:0006338 chromatin remodeling
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0007399 nervous system development
GO:0022008 neurogenesis
GO:0043044 ATP-dependent chromatin remodeling
GO:0045892 negative regulation of transcription, DNA-templated

Cellular Component:
GO:0000228 nuclear chromosome
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0016514 SWI/SNF complex
GO:0017053 transcriptional repressor complex
GO:0032991 macromolecular complex
GO:0071564 npBAF complex
GO:0071565 nBAF complex


-  Descriptions from all associated GenBank mRNAs
  BC063700 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, mRNA (cDNA clone MGC:74664 IMAGE:4540040), complete cds.
BC069196 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, mRNA (cDNA clone IMAGE:6277521).
AK095047 - Homo sapiens cDNA FLJ37728 fis, clone BRHIP2020182, highly similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1.
AK294218 - Homo sapiens cDNA FLJ55512 complete cds, highly similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1.
AK294666 - Homo sapiens cDNA FLJ55202 complete cds, highly similar to SWI/SNF-related matrix-associatedactin-dependent regulator of chromatin subfamily E member 1.
BC007082 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, mRNA (cDNA clone MGC:14622 IMAGE:4076036), complete cds.
BC011017 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, mRNA (cDNA clone MGC:13498 IMAGE:4287132), complete cds.
AK001532 - Homo sapiens cDNA FLJ10670 fis, clone NT2RP2006312, highly similar to SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily Emember 1.
EU327017 - Homo sapiens Smarce1 variant 3 mRNA, complete cds, alternatively spliced.
EU327018 - Homo sapiens Smarce1 variant 4 mRNA, complete cds, alternatively spliced.
EU327019 - Homo sapiens Smarce1 variant 5 mRNA, complete cds, alternatively spliced.
EU327020 - Homo sapiens Smarce1 variant 6 mRNA, complete cds, alternatively spliced.
BT007176 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 mRNA, complete cds.
DQ890712 - Synthetic construct clone IMAGE:100003342; FLH165378.01X; RZPDo839B07160D SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 (SMARCE1) gene, encodes complete protein.
DQ893481 - Synthetic construct clone IMAGE:100006111; FLH193818.01X; RZPDo839C0579D SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 (SMARCE1) gene, encodes complete protein.
KJ897582 - Synthetic construct Homo sapiens clone ccsbBroadEn_06976 SMARCE1 gene, encodes complete protein.
DQ893894 - Synthetic construct Homo sapiens clone IMAGE:100008354; FLH165374.01L; RZPDo839B07159D SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 (SMARCE1) gene, encodes complete protein.
DQ896382 - Synthetic construct Homo sapiens clone IMAGE:100010842; FLH193814.01L; RZPDo839C0569D SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1 (SMARCE1) gene, encodes complete protein.
KJ905926 - Synthetic construct Homo sapiens clone ccsbBroadEn_15596 SMARCE1 gene, encodes complete protein.
AB529184 - Synthetic construct DNA, clone: pF1KB7690, Homo sapiens SMARCE1 gene for SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, without stop codon, in Flexi system.
AK092967 - Homo sapiens cDNA FLJ35648 fis, clone SPLEN2013195, highly similar to Homo sapiens BAF57 (BAF57) gene.
CU687810 - Synthetic construct Homo sapiens gateway clone IMAGE:100021779 5' read SMARCE1 mRNA.
EU327021 - Homo sapiens Smarce1 variant 10 mRNA, partial cds, alternatively spliced.
BC047731 - Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily e, member 1, mRNA (cDNA clone IMAGE:6471369).
AK023653 - Homo sapiens cDNA FLJ13591 fis, clone PLACE1009410.
AK095738 - Homo sapiens cDNA FLJ38419 fis, clone FEBRA2009846.
JD148026 - Sequence 129050 from Patent EP1572962.
JD529066 - Sequence 510090 from Patent EP1572962.
JD515039 - Sequence 496063 from Patent EP1572962.
JD282904 - Sequence 263928 from Patent EP1572962.
JD443847 - Sequence 424871 from Patent EP1572962.
JD503797 - Sequence 484821 from Patent EP1572962.
JD265525 - Sequence 246549 from Patent EP1572962.
JD559468 - Sequence 540492 from Patent EP1572962.
JD053800 - Sequence 34824 from Patent EP1572962.
JD123060 - Sequence 104084 from Patent EP1572962.
JD168132 - Sequence 149156 from Patent EP1572962.
JD539950 - Sequence 520974 from Patent EP1572962.
JD344908 - Sequence 325932 from Patent EP1572962.
JD322048 - Sequence 303072 from Patent EP1572962.
JD261716 - Sequence 242740 from Patent EP1572962.
JD071218 - Sequence 52242 from Patent EP1572962.
JD074319 - Sequence 55343 from Patent EP1572962.
JD552299 - Sequence 533323 from Patent EP1572962.
JD359683 - Sequence 340707 from Patent EP1572962.
JD426826 - Sequence 407850 from Patent EP1572962.
JD464824 - Sequence 445848 from Patent EP1572962.
JD338159 - Sequence 319183 from Patent EP1572962.
JD052336 - Sequence 33360 from Patent EP1572962.
JD247532 - Sequence 228556 from Patent EP1572962.
JD463028 - Sequence 444052 from Patent EP1572962.
JD212909 - Sequence 193933 from Patent EP1572962.
JD407514 - Sequence 388538 from Patent EP1572962.
JD152195 - Sequence 133219 from Patent EP1572962.
JD526253 - Sequence 507277 from Patent EP1572962.
JD293419 - Sequence 274443 from Patent EP1572962.
JD428380 - Sequence 409404 from Patent EP1572962.
JD493781 - Sequence 474805 from Patent EP1572962.
JD308684 - Sequence 289708 from Patent EP1572962.
JD440933 - Sequence 421957 from Patent EP1572962.
DQ573717 - Homo sapiens piRNA piR-41829, complete sequence.
JD341824 - Sequence 322848 from Patent EP1572962.
JD341686 - Sequence 322710 from Patent EP1572962.
JD134025 - Sequence 115049 from Patent EP1572962.
JD146047 - Sequence 127071 from Patent EP1572962.
JD565399 - Sequence 546423 from Patent EP1572962.
JD385680 - Sequence 366704 from Patent EP1572962.
DQ584735 - Homo sapiens piRNA piR-51847, complete sequence.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_hSWI-SNFpathway - Chromatin Remodeling by hSWI/SNF ATP-dependent Complexes
h_vdrPathway - Control of Gene Expression by Vitamin D Receptor

Reactome (by CSHL, EBI, and GO)

Protein Q969G3 (Reactome details) participates in the following event(s):

R-HSA-3215448 SWI/SNF chromatin remodelling complex enhances MEP50:PRMT5 methyltransferase activity
R-HSA-8938217 RUNX1 binds the SWI/SNF complex
R-HSA-3214858 RMTs methylate histone arginines
R-HSA-8939243 RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-8878171 Transcriptional regulation by RUNX1
R-HSA-4839726 Chromatin organization
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B3KMC1, B4DFR4, BAF57, C0IMW4, C0IMW5, C0IMW7, ENST00000348513.1, ENST00000348513.10, ENST00000348513.11, ENST00000348513.2, ENST00000348513.3, ENST00000348513.4, ENST00000348513.5, ENST00000348513.6, ENST00000348513.7, ENST00000348513.8, ENST00000348513.9, H7C3F6, NM_003079, O43539, Q969G3, SMCE1_HUMAN, uc317xrq.1, uc317xrq.2
UCSC ID: ENST00000348513.12_8
RefSeq Accession: NM_003079.5
Protein: Q969G3 (aka SMCE1_HUMAN or SME1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SMARCE1:
cdh-ov (Congenital Diaphragmatic Hernia Overview)
coffin-siris (Coffin-Siris Syndrome)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.