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SCRT1 Gene

protein-coding   GIFtS: 49
GCID: GC08M145554

Scratch Family Zinc Finger 1

(Previous names: scratch (drosophila homolog) 1, zinc finger protein, scratch...)
  See SCRT1-related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Scratch Family Zinc Finger 11 2     Scratch Homolog 1, Zinc Finger Protein2
SCRT2 3     Transcriptional Repressor Scratch 12
Scratch (Drosophila Homolog) 1, Zinc Finger Protein1     hScrt3
Scratch Homolog 1, Zinc Finger Protein (Drosophila)1     Scratch 13
ZNF8982     Scratch Homolog 1 Zinc Finger Protein3

External Ids:    HGNC: 159501   Entrez Gene: 834822   Ensembl: ENSG000001706167   OMIM: 6058585   UniProtKB: Q9BWW73   

Export aliases for SCRT1 gene to outside databases

Previous GC identifers: GC08U990134 GC08M145160 GC08M145560 GC08M145526 GC08M140668


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SCRT1 Gene:
This gene encodes a C2H2-type zinc finger transcriptional repressor that binds to E-box motifs. The encoded
protein may promote neural differention and may be involved in cancers with neuroendocrine features. (provided by
RefSeq, Jul 2013)

GeneCards Summary for SCRT1 Gene:
SCRT1 (scratch family zinc finger 1) is a protein-coding gene. Diseases associated with SCRT1 include pineal region meningioma, and cerebellar astrocytoma. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity. An important paralog of this gene is SNAI1.

UniProtKB/Swiss-Prot: SCRT1_HUMAN, Q9BWW7
Function: Transcriptional repressor that binds E-box motif CAGGTG. Can modulate the action of basic
helix-loop-helix (bHLH) transcription factors, critical for neuronal differentiation




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000008.10  NC_018919.2  NT_008046.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the SCRT1 gene promoter:
         E2F-3a   E2F-4   CREB   deltaCREB   E2F-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSCRT1 promoter sequence
   Search Chromatin IP Primers for SCRT1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SCRT1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 8q24.3   Ensembl cytogenetic band:  8q24.3   HGNC cytogenetic band: 8q24.3

SCRT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SCRT1 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M145554:  view genomic region     (about GC identifiers)

Start:
145,554,228 bp from pter      End:
145,559,943 bp from pter
Size:
5,716 bases      Orientation:
minus strand

1 alternative location:
Chr8-,NW_003315924 100,050-105,540     

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SCRT1_HUMAN, Q9BWW7 (See protein sequence)
Recommended Name: Transcriptional repressor scratch 1  
Size: 348 amino acids; 35570 Da
Subunit: Interacts (via SNAG domain) with LIMD1 (via LIM domains), WTIP (via LIM domains) and AJUBA (via LIM
domains) (By similarity)
Secondary accessions: A8MX66 Q96C52

Explore the universe of human proteins at neXtProt for SCRT1: NX_Q9BWW7

Explore proteomics data for SCRT1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See SCRT1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_112599.2  
    ENSEMBL proteins: 
     ENSP00000331692  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ZNF: Zinc fingers, C2H2-type

    3 InterPro protein domains:
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q9BWW7

    ProtoNet protein and cluster: Q9BWW7

    UniProtKB/Swiss-Prot: SCRT1_HUMAN, Q9BWW7
    Domain: The N-terminal non zinc-finger region mediates the repressor activity
    Similarity: Belongs to the snail C2H2-type zinc-finger protein family
    Similarity: Contains 5 C2H2-type zinc fingers


    Find genes that share domains with SCRT1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SCRT1_HUMAN, Q9BWW7
    Function: Transcriptional repressor that binds E-box motif CAGGTG. Can modulate the action of basic
    helix-loop-helix (bHLH) transcription factors, critical for neuronal differentiation

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0003700sequence-specific DNA binding transcription factor activity NAS11274425
    GO:0005515protein binding ----
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with SCRT1           About GenesLikeMe


    Phenotypes:
         3 GenomeRNAi human phenotypes for SCRT1:
     High actin ratio cells  Increased HPV18 LCR reporter a  Increased gamma-H2AX phosphory 

    Animal Models:
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    hsa-miR-301a hsa-miR-218 hsa-miR-296-5p hsa-miR-130b hsa-miR-301b hsa-miR-1237 hsa-miR-566 hsa-miR-191*
    SwitchGear 3'UTR luciferase reporter plasmidSCRT1 3' UTR sequence
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SCRT1_HUMAN, Q9BWW7: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    Find genes that share ontologies with SCRT1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SCRT1
    Interactions:

        GeneGlobe Interaction Network for SCRT1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for SCRT1 (ENSP000003316924) via UniProtKB, MINT, STRING, and/or I2D (see all 28)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GOPCENSP000003574844STRING: ENSP00000357484
    SGTAENSP000002215664STRING: ENSP00000221566
    SGTBENSP000003703954STRING: ENSP00000370395
    BMPERENSP000002971614STRING: ENSP00000297161
    CRIM1ENSP000002805274STRING: ENSP00000280527
    About this table

    Gene Ontology (GO): 2 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0006355regulation of transcription, DNA-templated TAS11274425

    Find genes that share ontologies with SCRT1           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SCRT1



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SCRT1 gene: 
    NM_031309.5  

    Unigene Cluster for SCRT1:

    Scratch homolog 1, zinc finger protein (Drosophila)
    Hs.31746  [show with all ESTs]
    Unigene Representative Sequence: NM_031309
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000332135(uc003zbw.1)
    miRNA
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    hsa-miR-301a hsa-miR-218 hsa-miR-296-5p hsa-miR-130b hsa-miR-301b hsa-miR-1237 hsa-miR-566 hsa-miR-191*
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    Inhib. RNA
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      QuantiFast Probe-based Assays in human, mouse, rat SCRT1

    Additional mRNA sequence: 

    AL512683.1 AY014996.1 BC014675.1 BC024967.2 BC093806.1 BC112229.1 

    2 DOTS entries:

    DT.91681637  DT.70101489 

    10 AceView cDNA sequences:

    BM672235 BX282754 BC014675 BF346626 BX441587 NM_031309 AY014996 BX423429 
    BX440119 BM700885 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SCRT1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GGCCCCCTCC
    SCRT1 Expression
    About this image


    SCRT1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 3) fully expand
     
     Brain (Nervous System)    fully expand to see all 15 entries
             Cerebral Cortex
             Septum   
     
     Neural Tube (Nervous System)
             Primitive Spinal Cord
     
     Eye (Sensory Organs)
    SCRT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SCRT1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.31746

    UniProtKB/Swiss-Prot: SCRT1_HUMAN, Q9BWW7
    Tissue specificity: Brain specific

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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for SCRT1 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Scrt11 , 5 scratch homolog 1, zinc finger protein (Drosophila)1, 5 89.08(n)1
    93.1(a)1
      15 (36.01 cM)5
    1707291  NM_130893.31  NP_570963.11 
     765162035 
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia scrt11 scratch homolog 1, zinc finger protein (Drosophila) 84.94(n)
    91.85(a)
      100486069  XM_004920023.1  XP_004920080.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.293982 Danio rerio scratch-a transcription factor (scrta) more 76.81(n)    AY147850.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG126053   -- 78(a)
    (best of 3)
      64A1   --
    worm
    (Caenorhabditis elegans)
    Secernentea K02D7.23 zinc finger protein 54(a)   IV(311184-312352)   --


    ENSEMBL Gene Tree for SCRT1 (if available)
    TreeFam Gene Tree for SCRT1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SCRT1 gene
    SNAI12  SNAI22  SNAI32  SCRT22  
    15 SIMAP similar genes for SCRT1 using alignment to 1 protein entry:     SCRT1_HUMAN:
    SNAI1    SNAI2    ZNF78L1    SCRT2    SNAI3    ZNF72
    ZFP41    ZNF844    ZNF323    ZNF589    ZNF697    ZNF833P
    ZNF137P    ZNF702P    ZNF808

    Find genes that share paralogs with SCRT1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SCRT1 (see all 90)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1488521051,2
    C--145554005(+) TCCACC/GTACCC 1 -- ds50010--------
    rs1922458431,2
    --145554009(+) CCTACC/GCCAGG 1 -- ds50010--------
    rs1846336021,2
    --145554015(+) CCAGGA/GGAAAT 1 -- ds50010--------
    rs625303781,2
    C,F--145554076(+) GCCTGT/CCCTCC 1 -- ds50017Minor allele frequency- C:0.20NA WA CSA 133
    rs1429228371,2
    --145554946(+) GACATA/GGCAGA 1 -- ut310--------
    rs1125147371,2
    C,F--145555099(+) AGGAGC/TGTAGG 1 -- ut311Minor allele frequency- T:0.50CSA 2
    rs2006641711,2
    --145555180(+) ACCCC-/TGTCCT 1 -- ut310--------
    rs78202691,2
    C--145555250(+) catagG/Taggtg 1 -- ut310--------
    rs1451781771,2
    --145555344(+) CAGCCA/GCCGGG 1 -- ut310--------
    rs117756561,2
    C,F,H--145555712(+) GTCTCG/AGGGGC 1 -- ut31 ese31Minor allele frequency- A:0.50NA 2

    HapMap Linkage Disequilibrium report for SCRT1 (145554228 - 145559943 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for SCRT1 (see all 24):    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv7962n71CNV Loss21882294
    nsv891841CNV Loss21882294
    dgv7960n71CNV Loss21882294
    nsv891846CNV Loss21882294
    dgv7955n71CNV Loss21882294
    nsv891817CNV Loss21882294
    dgv7957n71CNV Loss21882294
    nsv891807CNV Loss21882294
    dgv7958n71CNV Loss21882294
    dgv7940n71CNV Loss21882294

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 605858    OMIM disorders: --

    5 diseases for SCRT1:    
    About MalaCards
    pineal region meningioma    cerebellar astrocytoma    optic nerve sheath meningioma    skull base meningioma
    meningioma

    4 diseases from the University of Copenhagen DISEASES database for SCRT1:
    Pineal region meningioma     Optic nerve sheath meningioma     Skull base meningioma     Cerebellar astrocytoma

    Find genes that share disorders with SCRT1           About GenesLikeMe


    Export disorders for SCRT1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SCRT1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with SCRT1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mammalian scratch: a neural-specific snail family transcriptional repressor. (PubMed id 11274425)1, 2, 3 Nakakura E.K.... Ball D.W. (Proc. Natl. Acad. Sci. U.S.A. 2001)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. The SNAIL family member SCRATCH1 is not expressed in human tumors. (PubMed id 20043117)1 Bastid J....Ansieau S. (Oncol. Rep. 2010)
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    5. Mammalian Scratch participates in neuronal differentiation in P19 embryonal carcinoma cells. (PubMed id 11687288)1 Nakakura E.K....Ball D.W. (Brain Res. Mol. Brain Res. 2001)
    6. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 83482 HGNC: 15950 AceView: SCRT1 Ensembl:ENSG00000170616 euGenes: HUgn83482
    ECgene: SCRT1 H-InvDB: SCRT1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SCRT1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SCRT1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SCRT1 gene:
    Search GeneIP for patents involving SCRT1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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