Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alterna... See more...

Aliases for CLTA Gene

Aliases for CLTA Gene

  • Clathrin Light Chain A 2 3 4 5
  • Clathrin, Light Polypeptide (Lca) 2 3
  • Lca 2 4
  • Clathrin, Light Chain A 2
  • CLTA 5
  • LCA 3

External Ids for CLTA Gene

Previous GeneCards Identifiers for CLTA Gene

  • GC09P036503
  • GC09P036360

Summaries for CLTA Gene

Entrez Gene Summary for CLTA Gene

  • Clathrin is a large, soluble protein composed of heavy and light chains. It functions as the main structural component of the lattice-type cytoplasmic face of coated pits and vesicles which entrap specific macromolecules during receptor-mediated endocytosis. This gene encodes one of two clathrin light chain proteins which are believed to function as regulatory elements. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 8 and 12. [provided by RefSeq, May 2010]

GeneCards Summary for CLTA Gene

CLTA (Clathrin Light Chain A) is a Protein Coding gene. Diseases associated with CLTA include Leber Plus Disease. Among its related pathways are Signaling by GPCR and L1CAM interactions. Gene Ontology (GO) annotations related to this gene include structural molecule activity and clathrin heavy chain binding. An important paralog of this gene is CLTB.

UniProtKB/Swiss-Prot Summary for CLTA Gene

  • Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Acts as component of the TACC3/ch-TOG/clathrin complex proposed to contribute to stabilization of kinetochore fibers of the mitotic spindle by acting as inter-microtubule bridge (PubMed:15858577, PubMed:21297582).

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

Genomics for CLTA Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for CLTA 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
GH09J036189 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 256.2 +1.1 1146 4.8 TBP ZBTB10 MXD4 SP1 MNT SMAD5 ETS1 MBD2 ZNF217 POLR2A CLTA lnc-GNE-3 TPM2 GNE CCDC107 ZCCHC7 TLN1 GLIPR2 HMGB3P24 ARHGEF39
GH09J036135 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 11.3 -49.8 -49754 11 TBP CEBPA IRF2 CTCF BHLHE40 ZIC2 SIN3A REST NFATC3 FOXA2 GLIPR2 HSALNG0070980 TPM2 CCDC107 TLN1 CCIN CLTA ARHGEF39 HMGB3P24 TMEM8B
GH09J036256 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 10.5 +67.3 67267 2.6 TBP ZBTB10 MXD4 SP1 FEZF1 MNT BRCA1 SMAD5 IRF2 MBD2 GNE LOC102724322 MN298678-096 TPM2 CCDC107 TLN1 TMEM8B NPR2 CLTA ARHGEF39
GH09J035914 Promoter/Enhancer 1.5 Ensembl ENCODE dbSUPER 11.8 -273.5 -273514 7.5 TBP PLRG1 IKZF1 MBD2 ZBTB7B NONO MCM3 ARNT RAD51 REST HSALNG0070967 lnc-HRCT1-6 PIGO TLN1 GBA2 SPAAR ARHGEF39 CLTA RECK FANCG
GH09J035515 Enhancer 1.5 FANTOM5 ENCODE CraniofacialAtlas dbSUPER 11.2 -671.7 -671730 8 MXD4 ZNF217 BRCA1 ELF1 CTCF HOMEZ THAP11 CEBPB SIN3A MBD2 FAM166B TMEM8B CLTA RUSC2 OR13J1 CCDC107 ARHGEF39 CREB3 VCP STOML2
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

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

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

Top Transcription factor binding sites by QIAGEN in the CLTA gene promoter:
  • c-Myb
  • C/EBPalpha
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • E2F-4
  • E2F-5
  • GATA-1
  • Pax-5

Genomic Locations for CLTA Gene

Latest Assembly
chr9:36,190,855-36,304,781
(GRCh38/hg38)
Size:
113,927 bases
Orientation:
Plus strand

Previous Assembly
chr9:36,190,918-36,212,056
(GRCh37/hg19 by Entrez Gene)
Size:
21,139 bases
Orientation:
Plus strand

chr9:36,190,853-36,304,778
(GRCh37/hg19 by Ensembl)
Size:
113,926 bases
Orientation:
Plus strand

Genomic View for CLTA Gene

Genes around CLTA on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for CLTA Gene

Proteins for CLTA Gene

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

    Protein Symbol:
    P09496-CLCA_HUMAN
    Recommended name:
    Clathrin light chain A
    Protein Accession:
    P09496
    Secondary Accessions:
    • A8K4W3
    • B4DIN1
    • F5H6N3
    • Q2XPN5
    • Q53XZ1

    Protein attributes for CLTA Gene

    Size:
    248 amino acids
    Molecular mass:
    27077 Da
    Quaternary structure:
    • Clathrin coats are formed from molecules containing 3 heavy chains and 3 light chains. Interacts with CALY; the interaction stimulates clathrin self-assembly and clathrin-mediated endocytosis. Interacts with CKAP5 and TACC3 forming the TACC3/ch-TOG/clathrin complex located at spindle inter-microtubules bridges; the complex implicates clathrin triskelions.

    Three dimensional structures from OCA and Proteopedia for CLTA Gene

    Alternative splice isoforms for CLTA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLTA Gene

Post-translational modifications for CLTA Gene

  • Ubiquitination at Lys141 and Lys242
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CLTA Gene

Domains & Families for CLTA Gene

Gene Families for CLTA Gene

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

Protein Domains for CLTA Gene

InterPro:
Blocks:
  • Clathrin light chain
ProtoNet:

Suggested Antigen Peptide Sequences for CLTA Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ60566, highly similar to Clathrin light chain A (B4DIN1_HUMAN)
  • Clathrin light chain A (CLCA_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P09496

UniProtKB/Swiss-Prot:

CLCA_HUMAN :
  • Belongs to the clathrin light chain family.
Family:
  • Belongs to the clathrin light chain family.
genes like me logo Genes that share domains with CLTA: view

Function for CLTA Gene

Molecular function for CLTA Gene

UniProtKB/Swiss-Prot Function:
Clathrin is the major protein of the polyhedral coat of coated pits and vesicles. Acts as component of the TACC3/ch-TOG/clathrin complex proposed to contribute to stabilization of kinetochore fibers of the mitotic spindle by acting as inter-microtubule bridge (PubMed:15858577, PubMed:21297582).
GENATLAS Biochemistry:
clathrin,light chain A (Lca),component of coated vesicles and coated pits,translocated to plasma membrane through AP2 binding,also expressed in synaptic vesicles

Phenotypes From GWAS Catalog for CLTA Gene

Gene Ontology (GO) - Molecular Function for CLTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005198 structural molecule activity IEA --
GO:0005515 protein binding IPI 16595675
GO:0032050 clathrin heavy chain binding IPI 4066749
GO:0042277 peptide binding IEA --
genes like me logo Genes that share ontologies with CLTA: view
genes like me logo Genes that share phenotypes with CLTA: view

Inhibitory RNAs for research

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

Clone products for research

  • Addgene plasmids for CLTA

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

Localization for CLTA Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLTA Gene

Cytoplasmic vesicle membrane. Peripheral membrane protein. Cytoplasmic side. Membrane, coated pit. Peripheral membrane protein. Cytoplasmic side. Cytoplasm, cytoskeleton, spindle. Note=Cytoplasmic face of coated pits and vesicles. In complex with TACC3 and CKAP5 (forming the TACC3/ch-TOG/clathrin complex) localized to inter-microtubule bridges in mitotic spindles. {ECO:0000305}.

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 CLTA gene
Compartment Confidence
cytosol 5
plasma membrane 4
cytoskeleton 4
endosome 4
lysosome 4
golgi apparatus 4
extracellular 2
mitochondrion 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endosomes (4)
  • Lysosomes (4)
  • Vesicles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005819 spindle IEA --
GO:0005829 cytosol TAS --
GO:0005856 cytoskeleton IEA --
GO:0005886 plasma membrane TAS --
genes like me logo Genes that share ontologies with CLTA: view

Pathways & Interactions for CLTA Gene

genes like me logo Genes that share pathways with CLTA: view

Pathways by source for CLTA Gene

5 GeneGo (Thomson Reuters) pathways for CLTA Gene
  • Cholesterol and Sphingolipids transport / Influx to the early endosome in lung (normal and CF)
  • Development Angiotensin signaling via beta-Arrestin
  • Transport Clathrin-coated vesicle cycle
  • wtCFTR and delta508 traffic / Clathrin coated vesicles formation (norm and CF)
  • wtCFTR and delta508-CFTR traffic / Generic schema (norm and CF)
3 Qiagen pathways for CLTA Gene
  • CTLA4 Signaling
  • Endocytic Trafficking of EGFR
  • Remodeling of Adherens Junctions

Gene Ontology (GO) - Biological Process for CLTA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IEA --
GO:0006897 endocytosis IEA --
GO:0007049 cell cycle IEA --
GO:0016192 vesicle-mediated transport IEA --
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II TAS --
genes like me logo Genes that share ontologies with CLTA: view

No data available for SIGNOR curated interactions for CLTA Gene

Drugs & Compounds for CLTA Gene

No Compound Related Data Available

Transcripts for CLTA Gene

mRNA/cDNA for CLTA Gene

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

Inhibitory RNAs for research

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

Clone products for research

  • Addgene plasmids for CLTA

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

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c · 7d
SP1:
SP2: -
SP3: - -
SP4: -
SP5: - -
SP6: - -
SP7: - - - -
SP8: -
SP9: - - -

Relevant External Links for CLTA Gene

GeneLoc Exon Structure for
CLTA

Expression for CLTA Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for CLTA Gene

This gene is overexpressed in Brain (23.0) and Bone (8.2).

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



Protein tissue co-expression partners for CLTA Gene

- Elite partner

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

SOURCE GeneReport for Unigene cluster for CLTA Gene:

Hs.522114

Evidence on tissue expression from TISSUES for CLTA Gene

  • Nervous system(4.9)
  • Lung(4.8)
  • Liver(4.5)
  • Skin(4.2)
  • Pancreas(3.3)
  • Eye(3)
  • Intestine(2.9)
  • Kidney(2.8)
  • Lymph node(2.7)
  • Spleen(2.6)
  • Blood(2.5)
  • Thyroid gland(2.4)
  • Stomach(2.4)
  • Adrenal gland(2.3)
  • Heart(2.2)
  • Bone marrow(2.1)
genes like me logo Genes that share expression patterns with CLTA: view

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

Orthologs for CLTA Gene

This gene was present in the common ancestor of animals.

Orthologs for CLTA Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia CLTA 30 31
  • 99.33 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia CLTA 30 31
  • 95.7 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia CLTA 30 31
  • 94.1 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Clta 30 17 31
  • 92.61 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Clta 30
  • 91.67 (n)
Oppossum
(Monodelphis domestica)
Mammalia CLTA 31
  • 89 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia CLTA 31
  • 79 (a)
OneToOne
Chicken
(Gallus gallus)
Aves CLTA 30 31
  • 77.22 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia CLTA 31
  • 81 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia clta 30
  • 71.05 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.5904 30
Zebrafish
(Danio rerio)
Actinopterygii clta 30 31
  • 73.45 (n)
OneToOne
Dr.28835 30
Fruit Fly
(Drosophila melanogaster)
Insecta Clc 30 31
  • 53.23 (n)
OneToMany
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010608 30
  • 51.97 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea CSA.79 31
  • 39 (a)
ManyToMany
-- 31
  • 25 (a)
ManyToMany
Species where no ortholog for CLTA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • 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 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 CLTA Gene

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

Paralogs for CLTA Gene

Paralogs for CLTA Gene

Pseudogenes.org Pseudogenes for CLTA Gene

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

Variants for CLTA Gene

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

SNP ID Clinical significance and condition Chr 09 pos Variation AA Info Type
rs149517035 Benign: not provided 36,204,081(+) G/A
NM_001833.4(CLTA):c.387G>A (p.Arg129=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs79205619 Benign: not provided 36,198,973(+) G/A
NM_001833.4(CLTA):c.256-6G>A
INTRON

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CLTA Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
esv34080 CNV loss 18971310
nsv1017711 CNV gain 25217958
nsv1115174 CNV deletion 24896259
nsv1125318 OTHER inversion 24896259

Variation tolerance for CLTA Gene

Residual Variation Intolerance Score: 35.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.25; 24.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLTA Gene

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

SNP Genotyping and Copy Number Assays for research

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

Disorders for CLTA Gene

MalaCards: The human disease database

(1) MalaCards diseases for CLTA Gene - From: COP

Disorder Aliases PubMed IDs
leber plus disease
  • lhon plus disease
- elite association - COSMIC cancer census association via MalaCards
Search CLTA in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLTA

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CLTA: view

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

Publications for CLTA Gene

  1. Chromosomal location and some structural features of human clathrin light-chain genes (CLTA and CLTB). (PMID: 7713494) Ponnambalam S … Parham P (Genomics 1994) 2 3 23
  2. A TACC3/ch-TOG/clathrin complex stabilises kinetochore fibres by inter-microtubule bridging. (PMID: 21297582) Booth DG … Royle SJ (The EMBO journal 2011) 3 4
  3. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 41
  4. Calcyon, a novel partner of clathrin light chain, stimulates clathrin-mediated endocytosis. (PMID: 16595675) Xiao J … Bergson C (The Journal of biological chemistry 2006) 3 4
  5. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4

Products for CLTA Gene

Sources for CLTA Gene