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Aliases for SCX Gene

Aliases for SCX Gene

  • Scleraxis BHLH Transcription Factor 2 3 5
  • Scleraxis Basic Helix-Loop-Helix Transcription Factor 2 3
  • Class A Basic Helix-Loop-Helix Protein 41 3 4
  • Class A Basic Helix-Loop-Helix Protein 48 3 4
  • BHLHa48 3 4
  • SCXA 3 4
  • SCXB 3 4
  • Basic Helix-Loop-Helix Transcription Factor Scleraxis 3
  • Class II BHLH Protein Scleraxis 3
  • Scleraxis Homolog A (Mouse) 2
  • Scleraxis Homolog B (Mouse) 2
  • Scleraxis Homolog (Mouse) 2
  • Scleraxis Homolog A 3
  • Scleraxis Homolog B 3
  • BHLHA41 4

External Ids for SCX Gene

Previous HGNC Symbols for SCX Gene

  • SCXA
  • SCXB

Previous GeneCards Identifiers for SCX Gene

  • GC08U900014

Summaries for SCX Gene

GeneCards Summary for SCX Gene

SCX (Scleraxis BHLH Transcription Factor) is a Protein Coding gene. Diseases associated with SCX include Retinitis Pigmentosa 18 and Acrocallosal Syndrome. GO annotations related to this gene include sequence-specific DNA binding and protein dimerization activity. An important paralog of this gene is TCF15.

UniProtKB/Swiss-Prot for SCX Gene

  • Plays an early essential role in mesoderm formation, as well as a later role in formation of somite-derived chondrogenic lineages.

Gene Wiki entry for SCX Gene

Additional gene information for SCX Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCX Gene

Genomics for SCX Gene

Regulatory Elements for SCX Gene

Enhancers for SCX Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08H144290 1.3 ENCODE dbSUPER 11.3 +28.3 28343 6 PKNOX1 ATF1 ARNT ARID4B SIN3A YY1 GATA2 ELK1 ZNF143 ATF7 DGAT1 ENSG00000254690 BOP1 TONSL-AS1 SCX PARP10 SPATC1 HSF1 GC08P144309 PIR35534
GH08H144298 0.2 dbSUPER 11.3 +33.9 33890 0.6 BOP1 SCX GC08P144309 HSF1 PIR35534
GH08H144296 0.2 dbSUPER 10.8 +32.5 32519 1.7 SCX HSF1 GC08P144309 PIR35534
GH08H144264 1 Ensembl dbSUPER 0.4 +6.1 6074 14.2 SMARCA5 CTCF NRF1 ZNF223 ZMYM3 REST RAD21 SKIL CBX1 EGR1 BOP1 C8orf82 SCX GC08M144285
GH08H144263 0.2 dbSUPER 0.7 -1.6 -1597 0.6 SCX MIR7112
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SCX on UCSC Golden Path with GeneCards custom track

Genomic Locations for SCX Gene

Genomic Locations for SCX Gene
3,424 bases
Plus strand

Genomic View for SCX Gene

Genes around SCX on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for SCX Gene

Proteins for SCX Gene

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

    Protein Symbol:
    Recommended name:
    Basic helix-loop-helix transcription factor scleraxis
    Protein Accession:

    Protein attributes for SCX Gene

    201 amino acids
    Molecular mass:
    21596 Da
    Quaternary structure:
    • Efficient DNA binding requires dimerization with another bHLH protein. Dimerizes and binds the E-box consensus sequence with E12 (By similarity).

neXtProt entry for SCX Gene

Post-translational modifications for SCX Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SCX Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SCX Gene

Domains & Families for SCX Gene

Gene Families for SCX Gene

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

Protein Domains for SCX Gene

Suggested Antigen Peptide Sequences for SCX Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with SCX: view

No data available for UniProtKB/Swiss-Prot for SCX Gene

Function for SCX Gene

Molecular function for SCX Gene

UniProtKB/Swiss-Prot Function:
Plays an early essential role in mesoderm formation, as well as a later role in formation of somite-derived chondrogenic lineages.

Gene Ontology (GO) - Molecular Function for SCX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding IEA --
GO:0001205 transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding IEA --
GO:0003677 DNA binding ISS --
GO:0043425 bHLH transcription factor binding IPI,IEA 10775504
GO:0043565 sequence-specific DNA binding ISS,IEA --
genes like me logo Genes that share ontologies with SCX: view
genes like me logo Genes that share phenotypes with SCX: view

Animal Models for SCX Gene

MGI Knock Outs for SCX:

Animal Model Products

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for SCX Gene

Localization for SCX Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCX Gene


Subcellular locations from

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 SCX gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 1

Gene Ontology (GO) - Cellular Components for SCX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 10775504
GO:0005667 transcription factor complex IDA,IEA 10775504
genes like me logo Genes that share ontologies with SCX: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for SCX Gene

Pathways & Interactions for SCX Gene

No Data Available

Interacting Proteins for SCX Gene

Selected Interacting proteins: Q7RTU7-SCX_HUMAN for SCX Gene via IID

Symbol External ID(s) Details

Gene Ontology (GO) - Biological Process for SCX Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001707 mesoderm formation IEA,ISS --
GO:0001894 tissue homeostasis IEA,ISS --
GO:0001958 endochondral ossification IEA,ISS --
GO:0002062 chondrocyte differentiation ISS,IEA --
GO:0003179 heart valve morphogenesis IEA,ISS --
genes like me logo Genes that share ontologies with SCX: view

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

Drugs & Compounds for SCX Gene

No Compound Related Data Available

Transcripts for SCX Gene

mRNA/cDNA for SCX Gene

(3) REFSEQ mRNAs :
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Inhibitory RNA Products

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

No ASD Table

Relevant External Links for SCX Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SCX Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SCX Gene

This gene is overexpressed in Urine (64.6).

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

Protein tissue co-expression partners for SCX Gene

NURSA nuclear receptor signaling pathways regulating expression of SCX Gene:


Evidence on tissue expression from TISSUES for SCX Gene

  • Urine(2.1)
  • Liver(2)
genes like me logo Genes that share expression patterns with SCX: view

Primer Products

No data available for mRNA expression in normal human tissues , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SCX Gene

Orthologs for SCX Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCX Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia SCXA 33
  • 90.17 (n)
(Bos Taurus)
Mammalia LOC615157 33
  • 89.22 (n)
(Mus musculus)
Mammalia Scx 33 16
  • 87.56 (n)
(Rattus norvegicus)
Mammalia Scx 33
  • 87.4 (n)
(Gallus gallus)
Aves SCXB 33
  • 78.97 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100490170 33
  • 72.68 (n)
(Danio rerio)
Actinopterygii scxa 33
  • 67.03 (n)
Species where no ortholog for SCX was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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 squirt (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)
  • worm (Caenorhabditis elegans)

Evolution for SCX Gene

Gene Tree for SCX (if available)
Gene Tree for SCX (if available)

Paralogs for SCX Gene

Paralogs for SCX Gene

genes like me logo Genes that share paralogs with SCX: view

Variants for SCX Gene

Sequence variations from dbSNP and Humsavar for SCX Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs1000043853 -- 144,263,436(+) AGCAC(A/G)GTGCC intron-variant, upstream-variant-2KB
rs1000166670 -- 144,267,636(+) TGTCC(A/G)TCCCC intron-variant
rs1000211146 -- 144,264,802(+) GGTCC(C/T)GCCCT upstream-variant-2KB, reference, missense
rs1000321051 -- 144,264,977(+) GCAGG(A/G)GCTTG upstream-variant-2KB, reference, missense
rs1001939112 -- 144,265,661(+) TTCCT(C/G)CAACA intron-variant, upstream-variant-2KB, utr-variant-5-prime

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

Variant ID Type Subtype PubMed ID
nsv515809 CNV gain+loss 19592680
nsv470249 CNV loss 18288195
nsv428208 CNV gain 18775914
nsv1025071 CNV gain 25217958

Relevant External Links for SCX Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for SCX Gene

Disorders for SCX Gene

MalaCards: The human disease database

(4) MalaCards diseases for SCX Gene - From: DISEASES

Disorder Aliases PubMed IDs
retinitis pigmentosa 18
  • rp18
acrocallosal syndrome
  • joubert syndrome 12
wilson-turner syndrome
  • mental retardation, x-linked, syndromic 6
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search SCX in MalaCards View complete list of genes associated with diseases

Relevant External Links for SCX

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SCX: view

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

Publications for SCX Gene

  1. The basic helix-loop-helix transcription factor scleraxis regulates fibroblast collagen synthesis. (PMID: 19362560) Espira L … Czubryt MP (Journal of molecular and cellular cardiology 2009) 2 3 60
  2. DNA sequence and analysis of human chromosome 8. (PMID: 16421571) Nusbaum C … Lander ES (Nature 2006) 3 4 60
  3. Exhaustive identification of human class II basic helix-loop-helix proteins by virtual library screening. (PMID: 12617822) McLellan AS … Kealey T (Gene expression patterns : GEP 2002) 3 4 60
  4. Pharmacological Regulation of In Situ Tissue Stem Cells Differentiation for Soft Tissue Calcification Treatment. (PMID: 26851078) Hu JJ … Ouyang HW (Stem cells (Dayton, Ohio) 2016) 3 60
  5. Tgfβ-Smad and MAPK signaling mediate scleraxis and proteoglycan expression in heart valves. (PMID: 24157418) Barnette DN … Lincoln J (Journal of molecular and cellular cardiology 2013) 3 60

Products for SCX Gene

Sources for SCX Gene

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