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Aliases for CLTA Gene

Aliases for CLTA Gene

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

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 Congenital Amaurosis. Among its related pathways are Metabolism and HIV Life Cycle. 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 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).

Additional gene information for CLTA Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLTA Gene

Genomics for CLTA Gene

Regulatory Elements for CLTA Gene

Enhancers for CLTA 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
GH09H035913 1.5 Ensembl ENCODE dbSUPER 11.8 -273.6 -273615 7.7 HDGF ATF1 ARNT ARID4B YBX1 ZBTB7B YY1 TCF12 ZNF766 ELK1 PIGO ARHGEF39 RGP1 TLN1 GBA2 SPAAR CLTA RECK NDUFA5P4 OR13J1
GH09H036138 1.5 FANTOM5 ENCODE dbSUPER 11.2 -48.6 -48583 7.5 TBP PKNOX1 FOXA2 PTBP1 YBX1 RAD21 TCF12 GATA2 ZNF366 RUNX3 GLIPR2 CCIN CLTA HMGB3P24
GH09H036147 1.3 Ensembl ENCODE dbSUPER 11.3 -42.2 -42240 2.5 TBL1XR1 NFIB JUN BATF FOSL1 LCORL POLR2A EED PATZ1 FOS CCIN CLTA ZCCHC7 RECK GLIPR2 GNE
GH09H036256 1.1 ENCODE 10.5 +67.3 67284 2.6 HDGF PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 SLC30A9 TPM2 GNE CCDC107 TLN1 ZCCHC7 RGP1 CLTA ARHGEF39 LOC102724322 RNU4-53P
GH09H036456 1.1 Ensembl ENCODE 10.4 +267.1 267124 3 FOXA2 BMI1 BATF ZNF207 ATF7 ETV6 RUNX3 IKZF2 CREM SMARCA5 RNF38 CLTA GNE MRPS21P4
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLTA on UCSC Golden Path with GeneCards custom track

Promoters for CLTA Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000234754 344 2001 HDGF PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 FOS

Genomic Locations for CLTA Gene

Genomic Locations for CLTA Gene
chr9:36,190,856-36,304,781
(GRCh38/hg38)
Size:
113,926 bases
Orientation:
Plus strand
chr9:36,190,853-36,304,778
(GRCh37/hg19)

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.

    Alternative splice isoforms for CLTA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLTA Gene

Post-translational modifications for CLTA Gene

  • Ubiquitination at Lys141
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for CLTA Gene

Domains & Families for CLTA Gene

Gene Families for CLTA Gene

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

Protein Domains for CLTA Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for CLTA Gene

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

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
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).

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 IBA --
GO:0005515 protein binding IPI 16595675
GO:0032050 clathrin heavy chain binding IPI 4066749
GO:0032403 protein complex binding IEA --
genes like me logo Genes that share ontologies with CLTA: view
genes like me logo Genes that share phenotypes with CLTA: view

Animal Model Products

Clone Products

  • 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
lysosome 4
golgi apparatus 4
endosome 4
cytoskeleton 3

Subcellular locations from the

Human Protein Atlas (HPA)
  • Endosomes (3)
  • Lysosomes (3)
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

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:0007018 microtubule-based movement TAS --
GO:0007049 cell cycle IEA --
GO:0016192 vesicle-mediated transport IEA --
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

Unigene Clusters for CLTA Gene

Clathrin, light chain A:
Representative Sequences:

Clone Products

  • 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
ECgene alternative splicing isoforms for
CLTA

Expression for CLTA Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for CLTA Gene



Protein tissue co-expression partners for CLTA Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLTA Gene:

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(4.4)
  • Skin(3.9)
  • Pancreas(2.9)
  • Eye(2.6)
  • Intestine(2.3)
  • Spleen(2.1)
  • Blood(2)
  • Kidney(2)
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 33 34
  • 99.33 (n)
dog
(Canis familiaris)
Mammalia CLTA 33 34
  • 95.7 (n)
cow
(Bos Taurus)
Mammalia CLTA 33 34
  • 94.1 (n)
mouse
(Mus musculus)
Mammalia Clta 33 16 34
  • 92.61 (n)
rat
(Rattus norvegicus)
Mammalia Clta 33
  • 91.67 (n)
oppossum
(Monodelphis domestica)
Mammalia CLTA 34
  • 89 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLTA 34
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLTA 33 34
  • 77.22 (n)
lizard
(Anolis carolinensis)
Reptilia CLTA 34
  • 81 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clta 33
  • 71.05 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.5904 33
zebrafish
(Danio rerio)
Actinopterygii clta 33 34
  • 73.45 (n)
Dr.28835 33
fruit fly
(Drosophila melanogaster)
Insecta Clc 33 34
  • 53.23 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010608 33
  • 51.97 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.79 34
  • 39 (a)
ManyToMany
-- 34
  • 25 (a)
ManyToMany
Species where no ortholog for CLTA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)

Paralogs for CLTA Gene

Variants for CLTA Gene

Sequence variations from dbSNP and Humsavar for CLTA Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000031030 -- 36,208,424(+) CTGGT(A/G)TAAAA intron-variant
rs1000058249 -- 36,207,910(+) CTCCC(A/T)CTCAT intron-variant
rs1000084519 -- 36,201,165(+) GAGAA(C/G)TACAA intron-variant
rs1000087794 -- 36,209,752(+) CAGCA(A/G)CACCT intron-variant
rs1000188470 -- 36,191,463(+) CAGCA(C/T)GTTTG intron-variant

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

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

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)

Relevant External Links for CLTA Gene

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

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: DISEASES

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

Relevant External Links for CLTA

Genetic Association Database (GAD)
CLTA
Human Genome Epidemiology (HuGE) Navigator
CLTA
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLTA
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 22 60
  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 60
  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 45 60
  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 60
  5. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4 60

Products for CLTA Gene

  • Addgene plasmids for CLTA

Sources for CLTA Gene

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