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Aliases for CCAT1 Gene

Subcategory (RNA class) for CCAT1 Gene

non-coding RNA

Quality Score for this RNA gene is


Aliases for CCAT1 Gene

  • Colon Cancer Associated Transcript 1 2 3
  • Colon Cancer Associated Transcript 1 (Non-Protein Coding) 2 3
  • Onco-LncRNA-40 3
  • CARLo-5 3
  • CARLO5 3

External Ids for CCAT1 Gene

Previous GeneCards Identifiers for CCAT1 Gene

  • GC08M128221

Summaries for CCAT1 Gene

Entrez Gene Summary for CCAT1 Gene

  • This gene produces a long non-coding RNA that promotes tumor formation and is upregulated in colon cancer and other cancer cell types. This transcript may regulate long range chromosomal interactions, including at the Myc oncoprotein locus. This RNA may also function as a molecular sponge for microRNAs. [provided by RefSeq, Dec 2017]

GeneCards Summary for CCAT1 Gene

CCAT1 (Colon Cancer Associated Transcript 1) is an RNA Gene, and is affiliated with the non-coding RNA class. Diseases associated with CCAT1 include Intrahepatic Cholangiocarcinoma and Retinoblastoma.

Additional gene information for CCAT1 Gene

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CCAT1 Gene

Genomics for CCAT1 Gene

GeneHancer (GH) Regulatory Elements for CCAT1 Gene

Promoters and enhancers for CCAT1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH08J126318 Enhancer 0.8 Ensembl 4.7 +900.4 900367 0.2 GTF2F1 LEF1 TAF9B NFRKB CEBPG ZBTB40 E2F1 CTBP1 MTA3 POLR2A CCAT1 LOC101927657 RFPL4AP5
GH08J127204 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 0.7 +2.6 2612 24.9 HDGF PKNOX1 FOXA2 SMAD1 MLX ARID4B SIN3A DMAP1 YBX1 IRF4 CCAT1 PCAT2 CASC19 GC08P127149 PCAT1
GH08J127195 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 0.3 +22.2 22235 3.5 HDGF SMAD1 RB1 BATF KLF5 IRF4 ZNF143 ATF7 ETV6 RCOR1 CCAT1 CASC19 PCAT2 GC08P127149 PCAT1
GH08J127183 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 0.3 +34.6 34573 1.4 PKNOX1 STAT5A EBF1 BATF IRF4 RELA NFATC1 ATF7 ETV6 BCLAF1 CCAT1 GC08P127149 CASC19 PCAT2 PCAT1
GH08J127178 Enhancer 1 ENCODE dbSUPER 0.3 +39.3 39312 2.8 HDGF PKNOX1 ATF1 SMAD1 RB1 STAT5A YBX1 BATF IRF4 RAD21 GC08P127149 CCAT1 PCAT2 CASC19 PCAT1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCAT1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for CCAT1 Gene

Genomic Locations for CCAT1 Gene
11,887 bases
Minus strand
11,705 bases
Minus strand

Genomic View for CCAT1 Gene

Genes around CCAT1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCAT1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCAT1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CCAT1 Gene

Proteins for CCAT1 Gene

Post-translational modifications for CCAT1 Gene

No Post-translational modifications

No data available for DME Specific Peptides for CCAT1 Gene

Domains & Families for CCAT1 Gene

Gene Families for CCAT1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with CCAT1: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences and UniProtKB/Swiss-Prot for CCAT1 Gene

Function for CCAT1 Gene

Phenotypes From GWAS Catalog for CCAT1 Gene

Animal Model Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for CCAT1 Gene

Localization for CCAT1 Gene

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from COMPARTMENTS , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for CCAT1 Gene

Pathways & Interactions for CCAT1 Gene

SuperPathways for CCAT1 Gene

No Data Available

Interacting Proteins for CCAT1 Gene

Gene Ontology (GO) - Biological Process for CCAT1 Gene


No data available for Pathways by source and SIGNOR curated interactions for CCAT1 Gene

Drugs & Compounds for CCAT1 Gene

No Compound Related Data Available

Transcripts for CCAT1 Gene

mRNA/cDNA for CCAT1 Gene

(7) Additional mRNA sequences :
(1) RNA Central transcripts :

Unigene Clusters for CCAT1 Gene

Colon cancer associated transcript 1 (non-protein coding):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CCAT1 Gene

No ASD Table

Relevant External Links for CCAT1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CCAT1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CCAT1 Gene

mRNA differential expression in normal tissues according to GTEx for CCAT1 Gene

This gene is overexpressed in Esophagus - Mucosa (x23.4) and Liver (x18.0).

NURSA nuclear receptor signaling pathways regulating expression of CCAT1 Gene:


SOURCE GeneReport for Unigene cluster for CCAT1 Gene:

genes like me logo Genes that share expression patterns with CCAT1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CCAT1 Gene

Orthologs for CCAT1 Gene

No data available for Orthologs and Evolution for CCAT1 Gene

Paralogs for CCAT1 Gene

No data available for Paralogs for CCAT1 Gene

Variants for CCAT1 Gene

Sequence variations from dbSNP and Humsavar for CCAT1 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000111217 -- 127,215,519(-) T/G intron_variant
rs1000203645 -- 127,207,197(-) C/G downstream_transcript_variant
rs1000575419 -- 127,207,460(-) A/G non_coding_transcript_variant
rs1000694899 -- 127,209,582(-) T/C non_coding_transcript_variant
rs1000962611 -- 127,214,662(-) C/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CCAT1 Gene

Variant ID Type Subtype PubMed ID
nsv499795 OTHER inversion 21111241
nsv7419 OTHER inversion 18451855
nsv831457 CNV gain 17160897

Additional Variant Information for CCAT1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Variation tolerance for CCAT1 Gene

Disorders for CCAT1 Gene

MalaCards: The human disease database

(24) MalaCards diseases for CCAT1 Gene - From: LncRNADisease, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
intrahepatic cholangiocarcinoma
  • intrahepatic bile duct carcinoma
  • rb1
gallbladder cancer
  • gallbladder ca
oral squamous cell carcinoma
  • mouth squamous cell carcinoma
lung squamous cell carcinoma
  • epidermoid cell carcinoma of the lung
- elite association - COSMIC cancer census association via MalaCards
Search CCAT1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CCAT1

genes like me logo Genes that share disorders with CCAT1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CCAT1 Gene

Publications for CCAT1 Gene

  1. Long-range interaction and correlation between MYC enhancer and oncogenic long noncoding RNA CARLo-5. (PMID: 24594601) Kim T … Croce CM (Proceedings of the National Academy of Sciences of the United States of America 2014) 2 3 58
  2. Detection of a long non-coding RNA (CCAT1) in living cells and human adenocarcinoma of colon tissues using FIT-PNA molecular beacons. (PMID: 23416875) Kam Y … Yavin E (Cancer letters 2014) 2 3 58
  3. Long noncoding RNA CCAT1, which could be activated by c-Myc, promotes the progression of gastric carcinoma. (PMID: 23143645) Yang F … Fang G (Journal of cancer research and clinical oncology 2013) 2 3 58
  4. Colon cancer associated transcript-1: a novel RNA expressed in malignant and pre-malignant human tissues. (PMID: 21547902) Nissan A … Gure AO (International journal of cancer 2012) 2 3 58
  5. Long non-coding RNA CCAT1 promotes multiple myeloma progression by acting as a molecular sponge of miR-181a-5p to modulate HOXA1 expression. (PMID: 29228867) Chen L … Gu Y (Cell cycle (Georgetown, Tex.) 2018) 3 58

Products for CCAT1 Gene

Sources for CCAT1 Gene

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