Human Gene CLTB (ENST00000310418.9) from GENCODE V44
  Description: Homo sapiens clathrin light chain B (CLTB), transcript variant 6, non-coding RNA. (from RefSeq NR_157088)
RefSeq Summary (NM_007097): 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. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000310418.9
Gencode Gene: ENSG00000175416.16
Transcript (Including UTRs)
   Position: hg38 chr5:176,392,501-176,416,539 Size: 24,039 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg38 chr5:176,392,774-176,416,363 Size: 23,590 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:176,392,501-176,416,539)mRNA (may differ from genome)Protein (229 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLCB_HUMAN
DESCRIPTION: RecName: Full=Clathrin light chain B; Short=Lcb;
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 (via N-terminus) with HIP1. Interacts with HIP1R.
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.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CLTB
Diseases sorted by gene-association score: leber congenital amaurosis 6 (3), leber congenital amaurosis (1)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 180.13 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 2789.92 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 -95.90176-0.545 Picture PostScript Text
3' UTR -110.80273-0.406 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 P09497
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-  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
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005198 structural molecule activity
GO:0005515 protein binding
GO:0032050 clathrin heavy chain binding
GO:0042277 peptide binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0016192 vesicle-mediated transport
GO:0061024 membrane organization
GO:0072583 clathrin-dependent endocytosis

Cellular Component:
GO:0005802 trans-Golgi network
GO:0005829 cytosol
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:0030659 cytoplasmic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0043231 intracellular membrane-bounded organelle
GO:0045334 clathrin-coated endocytic vesicle
GO:0060170 ciliary membrane


-  Descriptions from all associated GenBank mRNAs
  LF209797 - JP 2014500723-A/17300: Polycomb-Associated Non-Coding RNAs.
MA445374 - JP 2018138019-A/17300: Polycomb-Associated Non-Coding RNAs.
X81637 - H.sapiens clathrin light chain b gene.
BC006332 - Homo sapiens clathrin, light chain (Lcb), mRNA (cDNA clone MGC:12930 IMAGE:4299637), complete cds.
BC006457 - Homo sapiens clathrin, light chain (Lcb), mRNA (cDNA clone MGC:1776 IMAGE:3538261), complete cds.
M20470 - Human lymphocyte clathrin light-chain B mRNA, complete cds.
M20469 - Human brain-type clathrin light-chain b mRNA, complete cds.
JD383496 - Sequence 364520 from Patent EP1572962.
LF331716 - JP 2014500723-A/139219: Polycomb-Associated Non-Coding RNAs.
MA567293 - JP 2018138019-A/139219: Polycomb-Associated Non-Coding RNAs.
JD517125 - Sequence 498149 from Patent EP1572962.
JD523560 - Sequence 504584 from Patent EP1572962.
JD385762 - Sequence 366786 from Patent EP1572962.
JD210764 - Sequence 191788 from Patent EP1572962.
JD288922 - Sequence 269946 from Patent EP1572962.
AK300200 - Homo sapiens cDNA FLJ60885 complete cds, moderately similar to Clathrin light chain B.
JD174245 - Sequence 155269 from Patent EP1572962.
JD204815 - Sequence 185839 from Patent EP1572962.
JD317945 - Sequence 298969 from Patent EP1572962.
JD466448 - Sequence 447472 from Patent EP1572962.
JD103906 - Sequence 84930 from Patent EP1572962.
JD275832 - Sequence 256856 from Patent EP1572962.
JD064933 - Sequence 45957 from Patent EP1572962.
JD547241 - Sequence 528265 from Patent EP1572962.
JD161302 - Sequence 142326 from Patent EP1572962.
JD381732 - Sequence 362756 from Patent EP1572962.
JD405313 - Sequence 386337 from Patent EP1572962.
BT007028 - Homo sapiens clathrin, light polypeptide (Lcb) mRNA, complete cds.
CR536577 - Homo sapiens full open reading frame cDNA clone RZPDo834B0322D for gene CLTB, clathrin, light polypeptide (Lcb); complete cds, incl. stopcodon.
CU675411 - Synthetic construct Homo sapiens gateway clone IMAGE:100018586 5' read CLTB mRNA.
AB528704 - Synthetic construct DNA, clone: pF1KB6942, Homo sapiens CLTB gene for clathrin, light chain, without stop codon, in Flexi system.
LF331720 - JP 2014500723-A/139223: Polycomb-Associated Non-Coding RNAs.
MA567297 - JP 2018138019-A/139223: Polycomb-Associated Non-Coding RNAs.
JD483138 - Sequence 464162 from Patent EP1572962.
JD407007 - Sequence 388031 from Patent EP1572962.
JD520415 - Sequence 501439 from Patent EP1572962.

-  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

BioCarta from NCI Cancer Genome Anatomy Project
h_arapPathway - ADP-Ribosylation Factor

Reactome (by CSHL, EBI, and GO)

Protein P09497 (Reactome details) participates in the following event(s):

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-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-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-3928665 EPH-ephrin mediated repulsion of cells
R-HSA-8856828 Clathrin-mediated endocytosis
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-190873 Gap junction degradation
R-HSA-422475 Axon guidance
R-HSA-4086400 PCP/CE pathway
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-5653656 Vesicle-mediated transport
R-HSA-190828 Gap junction trafficking
R-HSA-1266738 Developmental Biology
R-HSA-3858494 Beta-catenin independent WNT signaling
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-157858 Gap junction trafficking and regulation
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: CLCB_HUMAN, ENST00000310418.1, ENST00000310418.2, ENST00000310418.3, ENST00000310418.4, ENST00000310418.5, ENST00000310418.6, ENST00000310418.7, ENST00000310418.8, NR_157088, P09497, Q53Y37, Q6FHW1, uc003meh.1, uc003meh.2, uc003meh.3, uc003meh.4, uc003meh.5
UCSC ID: ENST00000310418.9
RefSeq Accession: NM_007097
Protein: P09497 (aka CLCB_HUMAN)
CCDS: CCDS4403.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.