Clta MGI Mouse Gene Detail - MGI:894297

Symbol

Clta
Name

clathrin light chain A

Feature Type

protein coding gene
IDs

MGI:894297
NCBI Gene: 12757
Alliance

gene page
Transcription Start Sites

8 TSS

Sequence Map

Chr4:44004452-44032846 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 23.09 cM, cytoband B1
Mapping Data

2 experiments

SNPs within 2kb

1023 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_894297	protein coding gene	Chr4:44003816-44032846 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0028231	protein coding gene	Chr4:42142142-42173635 (+)
A/J	MGP_AJ_G0028188	protein coding gene	Chr4:40649161-40678872 (+)
AKR/J	MGP_AKRJ_G0028140	protein coding gene	Chr4:41601366-41630688 (+)
BALB/cJ	MGP_BALBcJ_G0028208	protein coding gene	Chr4:40745498-40774763 (+)
C3H/HeJ	MGP_C3HHeJ_G0027930	protein coding gene	Chr4:42213554-42243842 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0028649	protein coding gene	Chr4:43751725-43779934 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025959	protein coding gene	Chr4:38076574-38106281 (+)
CAST/EiJ	MGP_CASTEiJ_G0027369	protein coding gene	Chr4:41735456-41763361 (+)
CBA/J	MGP_CBAJ_G0027896	protein coding gene	Chr4:45099173-45129806 (+)
DBA/2J	MGP_DBA2J_G0028045	protein coding gene	Chr4:40557937-40586499 (+)
FVB/NJ	MGP_FVBNJ_G0028012	protein coding gene	Chr4:39788945-39818214 (+)
LP/J	MGP_LPJ_G0028144	protein coding gene	Chr4:42222018-42250074 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0028036	protein coding gene	Chr4:48300135-48330066 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028685	protein coding gene	Chr4:41816461-41844083 (+)
PWK/PhJ	MGP_PWKPhJ_G0027093	protein coding gene	Chr4:40608290-40636479 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0026922	protein coding gene	Chr4:41337897-41373249 (+)
WSB/EiJ	MGP_WSBEiJ_G0027447	protein coding gene	Chr4:41690272-41718659 (+)

Human Ortholog

CLTA, clathrin light chain A

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CLTA, clathrin light chain A
Synonyms

LCA
Links

HGNC:2090

NCBI Gene ID: 1211

neXtProt AC: NX_P09496

UniProt: P09496
Chr Location

9p13.3; chr9:36190856-36304781 (+) GRCh38

MGI Vertebrate Homology

Clta stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CLTA
Gene Tree

Clta

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Phenotype Summary

12 phenotypes from 1 allele in 1 genetic background
10 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

18
Chemically and radiation induced

1
Endonuclease-mediated

2
Gene trapped

11
Targeted

4
Genomic Mutations

1 involving Clta
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

11 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous null mice exhibit an enhanced isotype switch to IgA production, abnormal synaptic vesicle recycling, a reduced synaptic vesicle pool, impaired neurotransmission, and deficits in motor coordination. About 50% die within a week of birth.

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All GO Annotations

29
GO References

8

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

706
cDNA Data

283
Literature Summary

5

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase clta

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All Sequences

97
RefSeq

28
UniProt

7
CCDS

CCDS38746.1, CCDS38747.1, CCDS38748.1, CCDS38749.1, CCDS71377.1

Ensembl

ENSMUSG00000028478 (Evidence)
NCBI Gene

12757

			Length	Strain/Species	Flank
genomic	ENSMUSG00000028478	Ensembl Gene Model \| MGI Sequence Detail	28395	C57BL/6J	± kb
transcript	ENSMUST00000107851	Ensembl \| MGI Sequence Detail	1135	Not Applicable
polypeptide	ENSMUSP00000103483	Ensembl \| MGI Sequence Detail	248	Not Applicable

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UniProt

7 Sequences
Protein Ontology

PR:000005612 clathrin light chain A

(term hierarchy)
InterPro Domains

IPR000996 Clathrin light chain
GlyGen

O08585 1 site, 1 O-linked glycan (1 site)

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All nucleic 284

cDNA 284

Microarray probesets 5

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MGI:2140516

Summaries

All 47

Developmental Gene Expression 5

Gene Ontology 8

Phenotypes 10
Earliest

J:35784 Scott LM, et al., E3, a hematopoietic-specific transcript directly regulated by the retinoic acid receptor alpha. Blood. 1996 Oct 1;88(7):2517-30
Latest

J:352092 Wang L, et al., Membrane remodeling by FAM92A1 during brain development regulates neuronal morphology, synaptic function, and cognition. Nat Commun. 2024 Jul 23;15(1):6209

TSS for Clta:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr37012	Chr4:44004438-44004455 (+)	-5 bp
Tssr37013	Chr4:44012657-44012660 (+)	8,207 bp
Tssr37014	Chr4:44012661-44012694 (+)	8,226 bp
Tssr37015	Chr4:44012954-44012983 (+)	8,517 bp
Tssr37016	Chr4:44018796-44018816 (+)	14,354 bp
Tssr37017	Chr4:44019864-44019891 (+)	15,426 bp
Tssr37018	Chr4:44019930-44019946 (+)	15,486 bp
Tssr37019	Chr4:44032360-44032373 (+)	27,915 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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