CCDC140 Gene (RNA Gene)

CCDC140 LncRNA

GC02P222298
GIFtS:
31
This gene encodes a protein that appears to be restricted to select higher primate species. This protein contains a C-terminal coiled-coil domain, which is a versatile structural motif consisting of multiple amphipathic alpha-helices that twist around each other to form a supercoil. [provided by RefSeq, Aug 2011] See more...

Aliases for CCDC140 Gene

Subcategory (RNA class) for CCDC140 Gene

lncRNA

Number of RNA Genes sources:

1 / 14

Aliases for CCDC140 Gene

  • CCDC140 LncRNA 2 3
  • Coiled-Coil Domain Containing 140 2 3 5
  • Coiled-Coil Domain-Containing Protein 140 3 4
  • HSALNG0022520 167
  • CCDC140 2

External Ids for CCDC140 Gene

Previous GeneCards Identifiers for CCDC140 Gene

  • GC02P222872
  • GC02P223162
  • GC02P215016

Summaries for CCDC140 Gene

Entrez Gene Summary for CCDC140 Gene

  • This gene encodes a protein that appears to be restricted to select higher primate species. This protein contains a C-terminal coiled-coil domain, which is a versatile structural motif consisting of multiple amphipathic alpha-helices that twist around each other to form a supercoil. [provided by RefSeq, Aug 2011]

GeneCards Summary for CCDC140 Gene

CCDC140 (CCDC140 LncRNA) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with CCDC140 include Craniofacial-Deafness-Hand Syndrome and Waardenburg's Syndrome.

Additional gene information for CCDC140 Gene

No data available for CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CCDC140 Gene

Genomics for CCDC140 Gene

GeneHancer (GH) Regulatory Elements for CCDC140 Gene

Promoters and enhancers for CCDC140 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
GH02J222293 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 500.7 -1.2 -1201 5.9 ZBTB10 ZBTB26 TRIM28 EZH2 POLR2A SP2 ZNF263 GABPA ZNF76 ZBTB11 CCDC140 PAX3 RF02543-032
GH02J222289 Enhancer 0.9 FANTOM5 ENCODE 4.2 -7.1 -7121 3.4 USF1 HDAC2 OSR2 TCF7L2 YY1 TCF12 CBX8 ZNF189 TAF15 CTCF PAX3 CCDC140 RF02543-032
GH02J222795 Enhancer 1.4 FANTOM5 Ensembl ENCODE 1.2 +498.9 498854 4.4 EP300 FOXK2 CTCF TCF12 POLR2G NCOR1 ZIC2 KDM6A TCF7 FOXA1 SGPP2 CCDC140 piR-52438-066 LOC105373903
GH02J222302 Enhancer 0.5 Ensembl 0.7 +4.4 4354 0.6 CBX8 SUZ12 RNF2 CTBP2 EZH2 CTCF FARSB CCDC140 CT75 PAX3
GH02J222301 Enhancer 0.4 ENCODE 0.7 +2.9 2930 0.2 EZH2 CBX8 RNF2 CHD1 SUZ12 FARSB CCDC140 CT75 PAX3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCDC140 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CCDC140

Top Transcription factor binding sites by QIAGEN in the CCDC140 gene promoter:
  • AP-2alpha
  • AP-2alpha isoform 2
  • AP-2alpha isoform 3
  • AP-2alphaA

Genomic Locations for CCDC140 Gene

Genomic Locations for CCDC140 Gene
chr2:222,298,147-222,305,217
(GRCh38/hg38)
Size:
7,071 bases
Orientation:
Plus strand
chr2:223,162,866-223,169,936
(GRCh37/hg19)
Size:
7,071 bases
Orientation:
Plus strand

Genomic View for CCDC140 Gene

Genes around CCDC140 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCDC140 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCDC140 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CCDC140 Gene

Proteins for CCDC140 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for CCDC140 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96MF4-CC140_HUMAN
    Recommended name:
    Coiled-coil domain-containing protein 140
    Protein Accession:
    Q96MF4

    Protein attributes for CCDC140 Gene

    Size:
    163 amino acids
    Molecular mass:
    18252 Da
    Quaternary structure:
    No Data Available

neXtProt entry for CCDC140 Gene

Protein Expression for CCDC140 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CCDC140 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for CCDC140 Gene

ENSEMBL proteins:

No data available for DME Specific Peptides for CCDC140 Gene

Domains & Families for CCDC140 Gene

Gene Families for CCDC140 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for CCDC140 Gene

ProtoNet:

Suggested Antigen Peptide Sequences for CCDC140 Gene

GenScript: Design optimal peptide antigens:
  • Coiled-coil domain-containing protein 140 (CC140_HUMAN)
genes like me logo Genes that share domains with CCDC140: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for CCDC140 Gene

Function for CCDC140 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Phenotypes From GWAS Catalog for CCDC140 Gene

genes like me logo Genes that share phenotypes with CCDC140: view

Animal Model Products

CRISPR Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CCDC140 Gene

Localization for CCDC140 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 CCDC140 gene
Compartment Confidence
nucleus 3

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for CCDC140 Gene

Pathways & Interactions for CCDC140 Gene

PathCards logo

SuperPathways for CCDC140 Gene

No Data Available

Interacting Proteins for CCDC140 Gene

STRING Interaction Network Preview (showing top 2 STRING interactants - click image to see details)
STRING Interaction Network
Selected Interacting proteins: ENSP00000295226 Q96MF4-CC140_HUMAN for CCDC140 Gene via STRING IID

;

Gene Ontology (GO) - Biological Process for CCDC140 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for CCDC140 Gene

Drugs & Compounds for CCDC140 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for CCDC140 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for CCDC140 Gene

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

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CCDC140 Gene

No ASD Table

Relevant External Links for CCDC140 Gene

GeneLoc Exon Structure for
CCDC140

Expression for CCDC140 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CCDC140 Gene

mRNA expression in normal human tissues for CCDC140 Gene
mRNA expression by GTEx for CCDC140 Gene

mRNA differential expression in normal tissues according to GTEx for CCDC140 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x8.4), Minor Salivary Gland (x7.4), Muscle - Skeletal (x6.8), and Brain - Cerebellum (x5.6).

Protein differential expression in normal tissues from HIPED for CCDC140 Gene

This gene is overexpressed in Platelet (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for CCDC140 Gene



Protein tissue co-expression partners for CCDC140 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CCDC140

SOURCE GeneReport for Unigene cluster for CCDC140 Gene:

Hs.350729
genes like me logo Genes that share expression patterns with CCDC140: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for CCDC140 Gene

Orthologs for CCDC140 Gene

This gene was present in the common ancestor of human and chimp.

Orthologs for CCDC140 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia CCDC140 31 30
  • 99.59 (n)
 OneToOne
Species where no ortholog for CCDC140 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)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • dog (Canis familiaris)
  • 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)
  • mouse (Mus musculus)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • 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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for CCDC140 Gene

ENSEMBL:
Gene Tree for CCDC140 (if available)
TreeFam:
Gene Tree for CCDC140 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCDC140: view image

Paralogs for CCDC140 Gene

No data available for Paralogs for CCDC140 Gene

Variants for CCDC140 Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CCDC140 Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs1553594554 Likely Pathogenic: not provided 222,298,528(+) T/TA SPLICE_DONOR_VARIANT
rs1553594600 Pathogenic: not provided 222,298,576(+) GC/G FRAMESHIFT_VARIANT
rs377366463 Likely Benign: not specified 222,298,607(+) C/T SYNONYMOUS_VARIANT
rs45501095 Likely Benign: Craniofacial deafness hand syndrome; Waardenburg syndrome 222,298,974(+) C/A FIVE_PRIME_UTR_VARIANT
rs565554258 Likely Benign: Craniofacial deafness hand syndrome; Waardenburg syndrome 222,298,820(+) G/A FIVE_PRIME_UTR_VARIANT

Additional dbSNP identifiers (rs#s) for CCDC140 Gene

Structural Variations from Database of Genomic Variants (DGV) for CCDC140 Gene

Variant ID Type Subtype PubMed ID
nsv834550 CNV gain 17160897

Variation tolerance for CCDC140 Gene

Residual Variation Intolerance Score: 55.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.20; 24.08% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCDC140 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCDC140

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCDC140 Gene

Disorders for CCDC140 Gene

MalaCards: The human disease database

(2) MalaCards diseases for CCDC140 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
craniofacial-deafness-hand syndrome
  • cdhs
waardenburg's syndrome
  • waardenburg syndrome, type 4a
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for CCDC140

Genetic Association Database
(GAD)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with CCDC140: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CCDC140 Gene

Publications for CCDC140 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 54
  2. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 54
  3. Early de novo DNA methylation and prolonged demethylation in the muscle lineage. (PMID: 23417056) Tsumagari K … Ehrlich M (Epigenetics 2013) 3 54
  4. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PMID: 15815621) Hillier LW … Wilson RK (Nature 2005) 4 54
  5. 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) 4 54

ExternalLinks

View latest publications for CCDC140 gene in Mastermind

Products for CCDC140 Gene

Sources for CCDC140 Gene