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] See more...

Aliases for SCRT1 Gene

Aliases for SCRT1 Gene

  • Scratch Family Transcriptional Repressor 1 2 3 5
  • Transcriptional Repressor Scratch 1 3 4
  • ZNF898 2 3
  • SCRT 3 4
  • Scratch (Drosophila Homolog) 1, Zinc Finger Protein 2
  • Scratch Homolog 1, Zinc Finger Protein (Drosophila) 2
  • Scratch Homolog 1, Zinc Finger Protein 3
  • Scratch Homolog 1 Zinc Finger Protein 4
  • Scratch Family Zinc Finger 1 3
  • DKFZp547F072 2
  • Scratch 1 4
  • SCRT1 5
  • HScrt 4

External Ids for SCRT1 Gene

Previous GeneCards Identifiers for SCRT1 Gene

  • GC08U990134
  • GC08M145160
  • GC08M145560
  • GC08M145526
  • GC08M140668
  • GC08M145554

Summaries for SCRT1 Gene

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 Transcriptional Repressor 1) is a Protein Coding gene. Diseases associated with SCRT1 include Pineal Region Meningioma and Extrahepatic Bile Duct Adenocarcinoma. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity. An important paralog of this gene is SCRT2.

UniProtKB/Swiss-Prot Summary for SCRT1 Gene

  • Transcriptional repressor that binds E-box motif CAGGTG. Can modulate the action of basic helix-loop-helix (bHLH) transcription factors, critical for neuronal differentiation.

Additional gene information for SCRT1 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SCRT1 Gene

Genomics for SCRT1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SCRT1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J144336 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 -0.8 -789 3.3 CREB1 HNRNPL ATF7 TEAD4 PRDM10 REST ZNF629 TFE3 IKZF1 NFKBIZ SCRT1 CPSF1 SLC52A2
GH08J144334 Enhancer 0.8 FANTOM5 611.4 +1.2 1243 0.6 ZBTB33 PRDM10 ZSCAN4 POLR2A REST EZH2 SCRT2 MNT ZNF524 USF1 SCRT1 KIFC2 LRRC24 ZNF252P ZNF34 ZNF517 CYHR1 DGAT1
GH08J144683 Promoter/Enhancer 1.6 FANTOM5 ENCODE CraniofacialAtlas 4.2 -349.5 -349451 4.5 SP1 HNRNPL GATAD2A CTCF PRDM10 ZNF629 SIX5 NFKBIZ KDM1A ZNF692 ZNF34 RECQL4 ADCK5 ZNF252P RPL8 SCRT1 ARHGAP39 KIFC2 LRRC24 ZNF517
GH08J144620 Enhancer 0.7 FANTOM5 Ensembl ENCODE 2 -285.9 -285932 3.6 ZIC2 ZNF34 SLC39A4 TMEM249 SCRT1 ARHGAP39 KIFC2 ENSG00000255456 piR-36588-446 C8orf82
GH08J144331 Enhancer 0.8 ENCODE dbSUPER 0.7 +4.5 4539 0.2 CREB1 ATF7 ZNF629 JUND PATZ1 EZH2 KLF9 SP2 ATF1 ATF2 SCRT1 DGAT1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SCRT1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SCRT1

Top Transcription factor binding sites by QIAGEN in the SCRT1 gene promoter:
  • CREB
  • deltaCREB
  • E2F-2
  • E2F-3a
  • E2F-4

Genomic Locations for SCRT1 Gene

Genomic Locations for SCRT1 Gene
chr8:144,330,565-144,336,482
(GRCh38/hg38)
Size:
5,918 bases
Orientation:
Minus strand
chr8:145,554,228-145,559,943
(GRCh37/hg19)
Size:
5,716 bases
Orientation:
Minus strand

Genomic View for SCRT1 Gene

Genes around SCRT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCRT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCRT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCRT1 Gene

Proteins for SCRT1 Gene

  • Protein details for SCRT1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BWW7-SCRT1_HUMAN
    Recommended name:
    Transcriptional repressor scratch 1
    Protein Accession:
    Q9BWW7
    Secondary Accessions:
    • A8MX66
    • Q96C52

    Protein attributes for SCRT1 Gene

    Size:
    348 amino acids
    Molecular mass:
    35570 Da
    Quaternary structure:
    • Interacts (via SNAG domain) with LIMD1 (via LIM domains), WTIP (via LIM domains) and AJUBA (via LIM domains).

neXtProt entry for SCRT1 Gene

Post-translational modifications for SCRT1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SCRT1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SCRT1 Gene

Domains & Families for SCRT1 Gene

Gene Families for SCRT1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins
  • Transcription factors

Protein Domains for SCRT1 Gene

Suggested Antigen Peptide Sequences for SCRT1 Gene

GenScript: Design optimal peptide antigens:
  • Scratch homolog 1 zinc finger protein (SCRT1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BWW7

UniProtKB/Swiss-Prot:

SCRT1_HUMAN :
  • The N-terminal non zinc-finger region mediates the repressor activity.
  • Belongs to the snail C2H2-type zinc-finger protein family.
Domain:
  • The N-terminal non zinc-finger region mediates the repressor activity.
Family:
  • Belongs to the snail C2H2-type zinc-finger protein family.
genes like me logo Genes that share domains with SCRT1: view

Function for SCRT1 Gene

Molecular function for SCRT1 Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for SCRT1 Gene

Gene Ontology (GO) - Molecular Function for SCRT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IDA 11274425
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific IDA 11274425
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding IBA 21873635
GO:0003700 DNA-binding transcription factor activity IBA,NAS 11274425
genes like me logo Genes that share ontologies with SCRT1: view
genes like me logo Genes that share phenotypes with SCRT1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCRT1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SCRT1 Gene

Localization for SCRT1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCRT1 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCRT1 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCRT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0016604 nuclear body IDA --
genes like me logo Genes that share ontologies with SCRT1: view

Pathways & Interactions for SCRT1 Gene

PathCards logo

SuperPathways for SCRT1 Gene

No Data Available

Interacting Proteins for SCRT1 Gene

Gene Ontology (GO) - Biological Process for SCRT1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA,IDA 11274425
GO:0006355 regulation of transcription, DNA-templated TAS 11274425
GO:2001222 regulation of neuron migration IEA --
genes like me logo Genes that share ontologies with SCRT1: view

No data available for Pathways by source and SIGNOR curated interactions for SCRT1 Gene

Drugs & Compounds for SCRT1 Gene

No Compound Related Data Available

Transcripts for SCRT1 Gene

mRNA/cDNA for SCRT1 Gene

1 REFSEQ mRNAs :
6 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCRT1

Alternative Splicing Database (ASD) splice patterns (SP) for SCRT1 Gene

No ASD Table

Relevant External Links for SCRT1 Gene

GeneLoc Exon Structure for
SCRT1

Expression for SCRT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SCRT1 Gene

mRNA differential expression in normal tissues according to GTEx for SCRT1 Gene

This gene is overexpressed in Brain - Cerebellum (x8.6), Brain - Cortex (x7.2), Brain - Cerebellar Hemisphere (x7.1), and Brain - Frontal Cortex (BA9) (x5.9).

Protein differential expression in normal tissues from HIPED for SCRT1 Gene

This gene is overexpressed in Brain (25.4), Liver, secretome (22.0), and Bone (19.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SCRT1 Gene



Protein tissue co-expression partners for SCRT1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SCRT1

SOURCE GeneReport for Unigene cluster for SCRT1 Gene:

Hs.31746

mRNA Expression by UniProt/SwissProt for SCRT1 Gene:

Q9BWW7-SCRT1_HUMAN
Tissue specificity: Brain specific.

Evidence on tissue expression from TISSUES for SCRT1 Gene

  • Nervous system(4.6)
genes like me logo Genes that share expression patterns with SCRT1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for SCRT1 Gene

Orthologs for SCRT1 Gene

This gene was present in the common ancestor of animals.

Orthologs for SCRT1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SCRT1 30
  • 99.25 (n)
Dog
(Canis familiaris)
Mammalia SCRT1 30
  • 90.06 (n)
Cow
(Bos Taurus)
Mammalia SCRT1 30
  • 89.18 (n)
Mouse
(Mus musculus)
Mammalia Scrt1 30 17
  • 89.08 (n)
Rat
(Rattus norvegicus)
Mammalia Scrt1 30
  • 88.98 (n)
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia scrt1 30
  • 84.94 (n)
Zebrafish
(Danio rerio)
Actinopterygii scrt1a 30
  • 84.69 (n)
Dr.29398 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG12605 32
  • 78 (a)
CG17181 32
  • 64 (a)
scrt 32
  • 56 (a)
Worm
(Caenorhabditis elegans)
Secernentea K02D7.2 32
  • 54 (a)
Species where no ortholog for SCRT1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SCRT1 Gene

ENSEMBL:
Gene Tree for SCRT1 (if available)
TreeFam:
Gene Tree for SCRT1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCRT1: view image

Paralogs for SCRT1 Gene

(15) SIMAP similar genes for SCRT1 Gene using alignment to 1 proteins:

  • SCRT1_HUMAN
genes like me logo Genes that share paralogs with SCRT1: view

Variants for SCRT1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SCRT1 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs7013127 - p.Ser133Ala

Additional dbSNP identifiers (rs#s) for SCRT1 Gene

Structural Variations from Database of Genomic Variants (DGV) for SCRT1 Gene

Variant ID Type Subtype PubMed ID
dgv12434n54 CNV loss 21841781
esv2759652 CNV gain+loss 17122850
nsv1126868 CNV deletion 24896259
nsv428208 CNV gain 18775914
nsv470249 CNV loss 18288195
nsv515809 CNV gain+loss 19592680
nsv612919 CNV gain 21841781
nsv612920 CNV loss 21841781
nsv824804 CNV gain 20364138

Variation tolerance for SCRT1 Gene

Residual Variation Intolerance Score: 44.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.38; 8.32% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCRT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCRT1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCRT1 Gene

Disorders for SCRT1 Gene

MalaCards: The human disease database

(12) MalaCards diseases for SCRT1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
pineal region meningioma
  • pineal meningioma
extrahepatic bile duct adenocarcinoma
  • adenocarcinoma of extrahepatic bile duct
optic nerve sheath meningioma
  • meningioma of optic nerve sheath
spermatocele
nasal cavity lymphoma
  • lymphoma of nasal cavity
- elite association - COSMIC cancer census association via MalaCards
Search SCRT1 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with SCRT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SCRT1 Gene

Publications for SCRT1 Gene

  1. Mammalian Scratch: a neural-specific Snail family transcriptional repressor. (PMID: 11274425) Nakakura EK … Ball DW (Proceedings of the National Academy of Sciences of the United States of America 2001) 2 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. (PMID: 25201988) Rietveld CA … Koellinger PD (Proceedings of the National Academy of Sciences of the United States of America 2014) 3
  4. DNA-binding specificities of human transcription factors. (PMID: 23332764) Jolma A … Taipale J (Cell 2013) 3
  5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. (PMID: 21873635) Gaudet P … Thomas PD (Briefings in bioinformatics 2011) 3

Products for SCRT1 Gene

Sources for SCRT1 Gene