Limch1 MGI Mouse Gene Detail - MGI:1924819 - LIM and calponin homology domains 1

Symbol

Limch1
Name

LIM and calponin homology domains 1
Synonyms

3732412D22Rik, mKIAA1102

Feature Type

protein coding gene
IDs

MGI:1924819
NCBI Gene: 77569
Alliance

gene page
Transcription Start Sites

19 TSS

Sequence Map

Chr5:66903232-67214502 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 5, 35.95 cM
Mapping Data

2 experiments

SNPs within 2kb

9265 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1924819	protein coding gene	Chr5:66903170-67214502 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0029591	protein coding gene	Chr5:66492877-66823348 (+)
A/J	MGP_AJ_G0029559	protein coding gene	Chr5:63997192-64314226 (+)
AKR/J	MGP_AKRJ_G0029507	protein coding gene	Chr5:66050159-66362990 (+)
BALB/cJ	MGP_BALBcJ_G0029568	protein coding gene	Chr5:64691081-65001289 (+)
C3H/HeJ	MGP_C3HHeJ_G0029291	protein coding gene	Chr5:66374665-66693356 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0030022	protein coding gene	Chr5:69243552-69582379 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0027262	protein coding gene	Chr5:60065999-60377168 (+)
CAST/EiJ	MGP_CASTEiJ_G0028699	protein coding gene	Chr5:65550136-65871213 (+)
CBA/J	MGP_CBAJ_G0029260	protein coding gene	Chr5:71469715-71815929 (+)
DBA/2J	MGP_DBA2J_G0029406	protein coding gene	Chr5:64021730-64336895 (+)
FVB/NJ	MGP_FVBNJ_G0029366	protein coding gene	Chr5:63205377-63513683 (+)
LP/J	MGP_LPJ_G0029491	protein coding gene	Chr5:66990997-67321900 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0029394	protein coding gene	Chr5:74283798-74601353 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0030055	protein coding gene	Chr5:65724809-66041917 (+)
PWK/PhJ	MGP_PWKPhJ_G0028423	protein coding gene	Chr5:63042572-63364546 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0028257	protein coding gene	Chr5:65068292-65393253 (+)
WSB/EiJ	MGP_WSBEiJ_G0028779	protein coding gene	Chr5:65948428-66279177 (+)

Human Ortholog

LIMCH1, LIM and calponin homology domains 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LIMCH1, LIM and calponin homology domains 1
Synonyms

LIMCH1A, LMO7B
Links

HGNC:29191

NCBI Gene ID: 22998

neXtProt AC: NX_Q9UPQ0

UniProt: Q9UPQ0
Chr Location

4p13; chr4:41359607-41700044 (+) GRCh38

MGI Vertebrate Homology

Limch1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: LIMCH1
Gene Tree

Limch1

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Phenotype Summary

10 phenotypes from 2 alleles in 2 genetic backgrounds
26 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

11
Chemically induced (other)

2
Endonuclease-mediated

2
Gene trapped

2
Radiation induced

1
Spontaneous

1
Targeted

3
Genomic Mutations

4 involving Limch1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

60 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a deletion of the six exons encoding the muscle-specific isoform, exclusively express the fetal predominant isoform in adult skeletal muscle and show decreased grip strength, muscle weakness, deficits in skeletal muscle force generation, and defects in calcium-handling during myofiber stimulation.

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All GO Annotations

23
GO References

5

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

794
Tissues

56
cDNA Data

79
Literature Summary

9

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase limch1

ZFIN limch1a

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All Sequences

140
RefSeq

59
UniProt

12
CCDS

CCDS39102.1, CCDS57347.1, CCDS89925.1

Ensembl

ENSMUSG00000037736 (Evidence)
NCBI Gene

77569

			Length	Strain/Species	Flank
genomic	77569	NCBI Gene Model \| MGI Sequence Detail	311271	C57BL/6J	± kb
transcript	NM_001401420	RefSeq \| MGI Sequence Detail	7606	C57BL/6
polypeptide	Q3UH68	UniProt \| EBI \| MGI Sequence Detail	1057	Not Applicable

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UniProt

12 Sequences
Protein Ontology

PR:000030693 LIM and calponin homology domains-containing protein 1

(term hierarchy)
InterPro Domains

IPR001715 Calponin homology domain

IPR001997 Calponin/LIMCH1

IPR036872 CH domain superfamily

IPR031865 Domain of unknown function DUF4757

IPR001781 Zinc finger, LIM-type
GlyGen

Q3UH68 3 sites, 1 O-linked glycan (3 sites)

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All nucleic 81

cDNA 79

Primer pair 1

Other 1

Microarray probesets 5

Summaries

All 61

Developmental Gene Expression 9

Gene Ontology 5

Phenotypes 26
Earliest

J:5021 Batchelor AL, et al., A comparison of the mutagenic effectiveness of chronic neutron- and gamma-irradiation of mouse spermatogonia. Mutat Res. 1966 Jun;3(3):218-29
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Limch1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr46539	Chr5:66902739-66902750 (+)	-487 bp
Tssr46540	Chr5:66902765-66902783 (+)	-458 bp
Tssr46541	Chr5:66902839-66902853 (+)	-386 bp
Tssr46542	Chr5:66903175-66903180 (+)	-54 bp
Tssr46543	Chr5:66903199-66903239 (+)	-13 bp
Tssr46544	Chr5:66928278-66928285 (+)	25,050 bp
Tssr46545	Chr5:67010747-67010775 (+)	107,529 bp
Tssr46546	Chr5:67014800-67014818 (+)	111,577 bp
Tssr46547	Chr5:67015075-67015099 (+)	111,855 bp
Tssr46550	Chr5:67055753-67055806 (+)	152,548 bp
Tssr46551	Chr5:67055820-67055837 (+)	152,597 bp
Tssr46552	Chr5:67115942-67115947 (+)	212,713 bp
Tssr1500	Chr5:67120022-67120048 (+)	216,803 bp
Tssr46557	Chr5:67134355-67134380 (+)	231,136 bp
Tssr46558	Chr5:67154374-67154411 (+)	251,161 bp
Tssr46559	Chr5:67154429-67154478 (+)	251,222 bp
Tssr46561	Chr5:67186142-67186164 (+)	282,921 bp
Tssr46562	Chr5:67211805-67211812 (+)	308,577 bp
Tssr46563	Chr5:67212108-67212118 (+)	308,881 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)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/12/2024 MGI 6.24