Human Gene CLTA (uc003zzc.3) Description and Page Index
  Description: Homo sapiens clathrin, light chain A (CLTA), transcript variant 2, mRNA.
RefSeq Summary (NM_007096): 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].
Transcript (Including UTRs)
   Position: hg19 chr9:36,190,853-36,212,059 Size: 21,207 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr9:36,191,054-36,211,771 Size: 20,718 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr9:36,190,853-36,212,059)mRNA (may differ from genome)Protein (248 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Clathrin light chain A; Short=Lca;
FUNCTION: Clathrin is the major protein of the polyhedral coat of coated pits and vesicles.
SUBUNIT: 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.
SUBCELLULAR LOCATION: Cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Membrane, coated pit; Peripheral membrane protein; Cytoplasmic side. Note=Cytoplasmic face of coated pits and vesicles.
SIMILARITY: Belongs to the clathrin light chain family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CLTA
CDC HuGE Published Literature: CLTA
Positive Disease Associations: smoking cessation
Related Studies:
  1. smoking cessation
    Uhl ,et al. Pharmacogenomics 2010, Genome-wide association for smoking cessation success: participants in the Patch in Practice trial of nicotine replacement , Pharmacogenomics 2010 11- 3 : 357-67. [PubMed 20235792]

-  MalaCards Disease Associations
  MalaCards Gene Search: CLTA
Diseases sorted by gene-association score: leber congenital amaurosis (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 65.45 RPKM in Ovary
Total median expression: 2365.24 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -76.71201-0.382 Picture PostScript Text
3' UTR -78.50288-0.273 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000996 - Clathrin_L-chain

Pfam Domains:
PF01086 - Clathrin light chain

ModBase Predicted Comparative 3D Structure on P09496
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein SequenceProtein Sequence   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003674 molecular_function
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0032050 clathrin heavy chain binding
GO:0042277 peptide binding
GO:0044877 macromolecular complex binding
GO:0051020 GTPase binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0006897 endocytosis
GO:0007049 cell cycle
GO:0016192 vesicle-mediated transport
GO:0019886 antigen processing and presentation of exogenous peptide antigen via MHC class II
GO:0032802 low-density lipoprotein particle receptor catabolic process
GO:0034383 low-density lipoprotein particle clearance
GO:0048268 clathrin coat assembly
GO:0051301 cell division
GO:0061024 membrane organization
GO:0072583 clathrin-dependent endocytosis

Cellular Component:
GO:0005737 cytoplasm
GO:0005819 spindle
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005886 plasma membrane
GO:0005905 clathrin-coated pit
GO:0016020 membrane
GO:0030118 clathrin coat
GO:0030125 clathrin vesicle coat
GO:0030130 clathrin coat of trans-Golgi network vesicle
GO:0030132 clathrin coat of coated pit
GO:0030136 clathrin-coated vesicle
GO:0030659 cytoplasmic vesicle membrane
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0032588 trans-Golgi network membrane
GO:0036020 endolysosome membrane
GO:0045334 clathrin-coated endocytic vesicle
GO:0071439 clathrin complex

-  Descriptions from all associated GenBank mRNAs
  LF383863 - JP 2014500723-A/191366: Polycomb-Associated Non-Coding RNAs.
AK291078 - Homo sapiens cDNA FLJ77116 complete cds, highly similar to Homo sapiens clathrin, light polypeptide (Lca) (CLTA), transcript variant nonbrain, mRNA.
AK295692 - Homo sapiens cDNA FLJ60566 complete cds, highly similar to Clathrin light chain A.
BC009201 - Homo sapiens clathrin, light chain (Lca), mRNA (cDNA clone MGC:15367 IMAGE:3944942), complete cds.
LF354392 - JP 2014500723-A/161895: Polycomb-Associated Non-Coding RNAs.
AK225153 - Homo sapiens mRNA for clathrin, light polypeptide A isoform b variant, clone: CBL08872.
BC019287 - Homo sapiens clathrin, light chain (Lca), mRNA (cDNA clone MGC:4014 IMAGE:2823495), complete cds.
M20472 - Human lymphocyte clathrin light-chain A mRNA, complete cds.
M20471 - Human brain-type clathrin light-chain a mRNA, complete cds.
AB463527 - Synthetic construct DNA, clone: pF1KB8221, Homo sapiens CLTA gene for clathrin, light chain, without stop codon, in Flexi system.
CU676418 - Synthetic construct Homo sapiens gateway clone IMAGE:100016795 5' read CLTA mRNA.
KJ890935 - Synthetic construct Homo sapiens clone ccsbBroadEn_00329 CLTA gene, encodes complete protein.
BT007170 - Homo sapiens clathrin, light polypeptide (Lca) mRNA, complete cds.
DQ270158 - Homo sapiens brain-specific clathrin light polypeptide mRNA, complete cds, alternatively spliced.
LF354393 - JP 2014500723-A/161896: Polycomb-Associated Non-Coding RNAs.
LF354409 - JP 2014500723-A/161912: Polycomb-Associated Non-Coding RNAs.
LF354411 - JP 2014500723-A/161914: Polycomb-Associated Non-Coding RNAs.
X81636 - H.sapiens clathrin light chain a gene.
LF354414 - JP 2014500723-A/161917: Polycomb-Associated Non-Coding RNAs.
JD020190 - Sequence 1214 from Patent EP1572962.
JD032080 - Sequence 13104 from Patent EP1572962.
LF354415 - JP 2014500723-A/161918: Polycomb-Associated Non-Coding RNAs.
JD511757 - Sequence 492781 from Patent EP1572962.
JD191271 - Sequence 172295 from Patent EP1572962.
LF354416 - JP 2014500723-A/161919: Polycomb-Associated Non-Coding RNAs.
JD112985 - Sequence 94009 from Patent EP1572962.
JD113263 - Sequence 94287 from Patent EP1572962.
JD065637 - Sequence 46661 from Patent EP1572962.
JD340301 - Sequence 321325 from Patent EP1572962.
JD215681 - Sequence 196705 from Patent EP1572962.
JD073721 - Sequence 54745 from Patent EP1572962.
JD200828 - Sequence 181852 from Patent EP1572962.
MA619440 - JP 2018138019-A/191366: Polycomb-Associated Non-Coding RNAs.
MA589969 - JP 2018138019-A/161895: Polycomb-Associated Non-Coding RNAs.
MA589970 - JP 2018138019-A/161896: Polycomb-Associated Non-Coding RNAs.
MA589986 - JP 2018138019-A/161912: Polycomb-Associated Non-Coding RNAs.
MA589988 - JP 2018138019-A/161914: Polycomb-Associated Non-Coding RNAs.
MA589991 - JP 2018138019-A/161917: Polycomb-Associated Non-Coding RNAs.
MA589992 - JP 2018138019-A/161918: Polycomb-Associated Non-Coding RNAs.
MA589993 - JP 2018138019-A/161919: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04142 - Lysosome
hsa04144 - Endocytosis
hsa05016 - Huntington's disease
hsa05100 - Bacterial invasion of epithelial cells

Reactome (by CSHL, EBI, and GO)

Protein P09496 (Reactome details) participates in the following event(s):

R-HSA-421831 trans-Golgi Network Coat Assembly
R-HSA-432706 trans-Golgi Network Lysosome Vesicle Destined Membrane Coat Assembly
R-HSA-421836 trans-Golgi Network Derived Vesicle Uncoating
R-HSA-432688 trans-Golgi Network Derived Lysosomal Vesicle Uncoating
R-HSA-2213236 TGN-lysosome vesicle uncoating and release of nonameric complex to lysosome
R-HSA-421835 trans-Golgi Network Vesicle Scission
R-HSA-432707 trans-Golgi Network Lysosomal Vesicle Scission
R-HSA-8951498 Dissociation of Arf1:GDP, AP-1 Clathrin coated nonameric complex
R-HSA-2130641 Translocation of TGN-lysosome vesicle to lysosome
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-432720 Lysosome Vesicle Biogenesis
R-HSA-2132295 MHC class II antigen presentation
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-1280218 Adaptive Immune System
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-168256 Immune System
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport
R-HSA-177491 Formation of clathrin-coated vesicle
R-HSA-392748 L1 binds to AP-2 Clathrin complex
R-HSA-2130640 Recruitment of clathrin coated vesicle by Ii
R-HSA-6784735 PCSK9:LDLR bind to Clathrin
R-HSA-8855131 VLDLR:PCSK9 binds Clathrin-coated vesicles
R-HSA-445071 Reinsertion of L1 into the plasma membrane
R-HSA-8856808 Recruitment of AP-2 complex and clathrin
R-HSA-8871196 Initial binding of AP-2 and clathrin to PI(4,5)P2
R-HSA-2130486 Uncoating of clathrin-coated vesicles and fusion with endosomes
R-HSA-177479 Axonal transport of NGF:Trk complexes
R-HSA-177501 Endocytosis (internalization) of clathrin-coated vesicle
R-HSA-374696 Phosphorylation of L1 by p90rsk
R-HSA-392749 Transport of L1 into endosomes
R-HSA-555065 Formation of clathrin coated vesicle
R-HSA-445077 Transport of L1 from C-domain to P-domain
R-HSA-445079 Phosphorylation of L1 by ERK
R-HSA-6784729 PCSK9:LDLR:Clathrin-coated vesicle transport from plasma membrane to endolysosome
R-HSA-196026 Dab2 is recruited to the junctional plaques
R-HSA-5138433 p-DVL2 recruits AP-2 and beta-arrestin 2 to promote clathrin-mediated endocytosis
R-HSA-5333658 CLAT:AP1:CLVS bind PI(3,5)P2
R-HSA-8866283 ARBB recruits GPCRs into clathrin-coated pits
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8856813 AAK1 phosphorylates AP-2 mu subunit at T156
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8862280 FCHo proteins bind nascent clathrin-coated pit
R-HSA-8866279 Epsin family proteins bind ubiquitinated cargo
R-HSA-196017 Dynamin is recruited to the gap junction plaque
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-190519 Internalization of gap junction plaques
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-177504 Retrograde neurotrophin signalling
R-HSA-437239 Recycling pathway of L1
R-HSA-2132295 MHC class II antigen presentation
R-HSA-8964038 LDL clearance
R-HSA-8866427 VLDLR internalisation and degradation
R-HSA-3928665 EPH-ephrin mediated repulsion of cells
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-187037 Signaling by NTRK1 (TRKA)
R-HSA-373760 L1CAM interactions
R-HSA-1280218 Adaptive Immune System
R-HSA-8964043 Plasma lipoprotein clearance
R-HSA-196025 Formation of annular gap junctions
R-HSA-2682334 EPH-Ephrin signaling
R-HSA-5099900 WNT5A-dependent internalization of FZD4
R-HSA-432720 Lysosome Vesicle Biogenesis
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-199991 Membrane Trafficking
R-HSA-166520 Signaling by NTRKs
R-HSA-422475 Axon guidance
R-HSA-168256 Immune System
R-HSA-174824 Plasma lipoprotein assembly, remodeling, and clearance
R-HSA-190873 Gap junction degradation
R-HSA-4086400 PCP/CE pathway
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-5653656 Vesicle-mediated transport
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-1266738 Developmental Biology
R-HSA-382551 Transport of small molecules
R-HSA-190828 Gap junction trafficking
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-162582 Signal Transduction
R-HSA-157858 Gap junction trafficking and regulation
R-HSA-195721 Signaling by WNT

-  Other Names for This Gene
  Alternate Gene Symbols: A8K4W3, B4DIN1, CLCA_HUMAN, NM_007096, NP_009027, P09496, Q2XPN5, Q53XZ1
UCSC ID: uc003zzc.3
RefSeq Accession: NM_007096
Protein: P09496 (aka CLCA_HUMAN)
CCDS: CCDS6601.1, CCDS43802.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_007096.3
exon count: 7CDS single in 3' UTR: no RNA size: 1246
ORF size: 747CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1656.00frame shift in genome: no % Coverage: 99.20
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.