Cltc clathrin heavy chain [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cltcprovided by RGD
Official Full Name: clathrin heavy chainprovided by RGD
Primary source: RGD:2364
See related: Ensembl:ENSRNOG00000004291 AllianceGenome:RGD:2364
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables several functions, including ankyrin binding activity; heat shock protein binding activity; and protein C-terminus binding activity. Involved in Golgi organization; endocytosis; and mitotic cell cycle. Located in T-tubule and spindle. Part of clathrin coat. Is extrinsic component of synaptic vesicle membrane. Human ortholog(s) of this gene implicated in autosomal dominant mental retardation 56. Orthologous to human CLTC (clathrin heavy chain). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Kidney (RPKM 1547.0), Brain (RPKM 1139.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q26

Exon count:: 33

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (72014984..72073308, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (71517661..71574591, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (74014560..74070578, complement)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

SP-A transiently enhances the basal protein expression of CHC and alpha-adaptin.
Title: Surfactant Protein A Enhances Constitutive Immune Functions of Clathrin Heavy Chain and Clathrin Adaptor Protein 2.
findings reveal a novel role for neuronal clathrin-independent endocytosis controlled by actin dynamics.
Title: Clathrin-independent trafficking of AMPA receptors.
Cellular uptake of PC12 cell-derived exosomes was imaged by high-throughput microscopy and statistically analyzed. It was found that the uptake was through clathrin-mediated endocytosis and macropinocytosis.
Title: Exosome uptake through clathrin-mediated endocytosis and macropinocytosis and mediating miR-21 delivery.
Clathrin levels are a dynamic property of presynaptic terminals that can influence short-term plasticity.
Title: Presynaptic clathrin levels are a limiting factor for synaptic transmission.
Data indicate that dynamin-2, clathrin, and lipid rafts mediate Na/K/2Cl cotransporter NKCC2 endocytosis and maintain steady-state apical surface NKCC2 in the renal thick ascending limb (THAL).
Title: Dynamin2, clathrin, and lipid rafts mediate endocytosis of the apical Na/K/2Cl cotransporter NKCC2 in thick ascending limbs.
Single-particle fluorescence imaging tracks the dynamics of Hsc70 and its clathrin substrate in real time.
Title: Single-molecule analysis of a molecular disassemblase reveals the mechanism of Hsc70-driven clathrin uncoating.
Lipid rafts and clathrin cooperate in the internalization of PrP in epithelial FRT cells
Title: Lipid rafts and clathrin cooperate in the internalization of PrP in epithelial FRT cells.
Ca(2+) signaling pathway via a sphingosine kinase (SK) is dependent on clathrin.
Title: Cross-linking of FcepsilonRI causes Ca2+ mobilization via a sphingosine kinase pathway in a clathrin-dependent manner.
Coats assembled from recombinant clathrin are good substrates for ATP- and auxilin-dependent, Hsc70-catalyzed uncoating.
Title: A motif in the clathrin heavy chain required for the Hsc70/auxilin uncoating reaction.
clathrin-FKBP36-Hsp72 complexes resulting from both identified interactions are bound to the matrices of clathrin-coated vesicles in spermatocytes, which indicates a possible role of FKBP36 and Hsp72 in the disassembly of clathrin coats
Title: FKBP36 forms complexes with clathrin and Hsp72 in spermatocytes.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH11769 (e-PCR)
- UniSTS:65808

RH129507 (e-PCR)
- UniSTS:212810

RH125101 (e-PCR)
- UniSTS:161923

RH25272 (e-PCR)
- UniSTS:72661

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ankyrin binding	IDA Inferred from Direct Assay more info	PubMed
enables clathrin light chain binding	IBA Inferred from Biological aspect of Ancestor more info
enables clathrin light chain binding	IEA Inferred from Electronic Annotation more info
enables clathrin light chain binding	ISO Inferred from Sequence Orthology more info
enables disordered domain specific binding	IEA Inferred from Electronic Annotation more info
enables disordered domain specific binding	ISO Inferred from Sequence Orthology more info
enables double-stranded RNA binding	IEA Inferred from Electronic Annotation more info
enables double-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables heat shock protein binding	IDA Inferred from Direct Assay more info	PubMed
enables low-density lipoprotein particle receptor binding	IEA Inferred from Electronic Annotation more info
enables low-density lipoprotein particle receptor binding	ISO Inferred from Sequence Orthology more info
enables peptide binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein serine/threonine kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin-specific protease binding	IEA Inferred from Electronic Annotation more info
enables ubiquitin-specific protease binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in Golgi organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in amyloid-beta clearance by transcytosis	IEA Inferred from Electronic Annotation more info
involved_in amyloid-beta clearance by transcytosis	ISO Inferred from Sequence Orthology more info
involved_in autophagy	IEA Inferred from Electronic Annotation more info
involved_in clathrin coat assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in clathrin coat assembly	IEA Inferred from Electronic Annotation more info
involved_in clathrin coat assembly	ISO Inferred from Sequence Orthology more info
involved_in clathrin coat disassembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in clathrin-dependent endocytosis	IEA Inferred from Electronic Annotation more info
involved_in clathrin-dependent endocytosis	ISO Inferred from Sequence Orthology more info
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
involved_in mitotic cell cycle	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in mitotic cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitotic cell cycle	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within mitotic spindle assembly	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of hyaluronan biosynthetic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of hyaluronan biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of hyaluronan biosynthetic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of protein localization to plasma membrane	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein localization to plasma membrane	ISO Inferred from Sequence Orthology more info
involved_in receptor internalization	IEA Inferred from Electronic Annotation more info
involved_in receptor internalization	ISO Inferred from Sequence Orthology more info
involved_in receptor-mediated endocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in receptor-mediated endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in receptor-mediated endocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitotic spindle organization	IEA Inferred from Electronic Annotation more info
involved_in regulation of mitotic spindle organization	ISO Inferred from Sequence Orthology more info
involved_in retrograde transport, endosome to Golgi	IEA Inferred from Electronic Annotation more info
involved_in retrograde transport, endosome to Golgi	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle endocytosis	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic vesicle endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transferrin transport	IEA Inferred from Electronic Annotation more info
involved_in transferrin transport	ISO Inferred from Sequence Orthology more info
involved_in vesicle-mediated transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Myb complex	ISO Inferred from Sequence Orthology more info
located_in T-tubule	IDA Inferred from Direct Assay more info	PubMed
part_of clathrin coat	IDA Inferred from Direct Assay more info	PubMed
part_of clathrin coat	ISO Inferred from Sequence Orthology more info
part_of clathrin coat	TAS Traceable Author Statement more info	PubMed
part_of clathrin coat of coated pit	IEA Inferred from Electronic Annotation more info
part_of clathrin coat of trans-Golgi network vesicle	IEA Inferred from Electronic Annotation more info
part_of clathrin complex	IBA Inferred from Biological aspect of Ancestor more info
part_of clathrin complex	IEA Inferred from Electronic Annotation more info
part_of clathrin complex	ISO Inferred from Sequence Orthology more info
is_active_in clathrin-coated endocytic vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in clathrin-coated endocytic vesicle membrane	TAS Traceable Author Statement more info
located_in clathrin-coated pit	ISO Inferred from Sequence Orthology more info
located_in clathrin-coated vesicle	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in endosome	IEA Inferred from Electronic Annotation more info
located_in endosome	ISO Inferred from Sequence Orthology more info
is_active_in extrinsic component of synaptic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
located_in lysosome	ISO Inferred from Sequence Orthology more info
located_in melanosome	IEA Inferred from Electronic Annotation more info
located_in membrane	ISO Inferred from Sequence Orthology more info
part_of membrane coat	ISO Inferred from Sequence Orthology more info
located_in mitotic spindle	ISO Inferred from Sequence Orthology more info
located_in mitotic spindle microtubule	IEA Inferred from Electronic Annotation more info
located_in mitotic spindle microtubule	ISO Inferred from Sequence Orthology more info
is_active_in photoreceptor ribbon synapse	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic endocytic zone	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic endocytic zone membrane	ISO Inferred from Sequence Orthology more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
located_in sarcolemma	IDA Inferred from Direct Assay more info	PubMed
is_active_in spindle	IBA Inferred from Biological aspect of Ancestor more info
located_in spindle	IDA Inferred from Direct Assay more info	PubMed
located_in spindle	ISO Inferred from Sequence Orthology more info
located_in terminal bouton	HDA more info	PubMed

General protein information

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Preferred Names: clathrin heavy chain 1

Names: clathrin, heavy chain (Hc); clathrin, heavy polypeptide (Hc)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_019299.2 → NP_062172.2 clathrin heavy chain 1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

P11442

Related

ENSRNOP00000005987.3, ENSRNOT00000005987.4

Conserved Domains (6) summary

smart00299
Location:1274 → 1416

CLH; Clathrin heavy chain repeat homology

sd00006
Location:1105 → 1131

TPR; TPR repeat [structural motif]

pfam00637
Location:979 → 1119

Clathrin; Region in Clathrin and VPS

pfam01394
Location:198 → 234

Clathrin_propel; Clathrin propeller repeat

pfam09268
Location:331 → 354

Clathrin-link; Clathrin, heavy-chain linker

pfam13838
Location:356 → 421

Clathrin_H_link; Clathrin-H-link

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

72014984..72073308 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006247108.5 → XP_006247170.1 clathrin heavy chain 1 isoform X1

UniProtKB/Swiss-Prot

P11442

Conserved Domains (6) summary

smart00299
Location:1274 → 1416

CLH; Clathrin heavy chain repeat homology

sd00006
Location:1105 → 1131

TPR; TPR repeat [structural motif]

pfam00637
Location:979 → 1119

Clathrin; Region in Clathrin and VPS

pfam01394
Location:198 → 234

Clathrin_propel; Clathrin propeller repeat

pfam09268
Location:331 → 354

Clathrin-link; Clathrin, heavy-chain linker

pfam13838
Location:356 → 421

Clathrin_H_link; Clathrin-H-link
XM_063269684.1 → XP_063125754.1 clathrin heavy chain 1 isoform X3
XM_063269683.1 → XP_063125753.1 clathrin heavy chain 1 isoform X2

UniProtKB/TrEMBL

A0A8I6AGZ0