Limd1 MGI Mouse Gene Detail - MGI:1352502

Symbol

Limd1
Name

LIM domains containing 1
Synonyms

D9Ertd192e

Feature Type

protein coding gene
IDs

MGI:1352502
NCBI Gene: 29806
Alliance

gene page
Transcription Start Sites

12 TSS

Sequence Map

Chr9:123307771-123350617 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 9, 74.00 cM, cytoband F
Mapping Data

8 experiments

SNPs within 2kb

1244 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1352502	protein coding gene	Chr9:123306790-123350617 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0035477	protein coding gene	Chr9:126528576-126576280 (+)
A/J	MGP_AJ_G0035458	protein coding gene	Chr9:121686104-121728944 (+)
AKR/J	MGP_AKRJ_G0035391	protein coding gene	Chr9:124942921-124987677 (+)
BALB/cJ	MGP_BALBcJ_G0035454	protein coding gene	Chr9:121619286-121663432 (+)
C3H/HeJ	MGP_C3HHeJ_G0035161	protein coding gene	Chr9:125393111-125436862 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0035977	protein coding gene	Chr9:130025352-130073365 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032859	protein coding gene	Chr9:118809791-118850404 (+)
CAST/EiJ	MGP_CASTEiJ_G0034466	protein coding gene	Chr9:125432816-125476829 (+)
CBA/J	MGP_CBAJ_G0035129	protein coding gene	Chr9:134759900-134808385 (+)
DBA/2J	MGP_DBA2J_G0035288	protein coding gene	Chr9:121131278-121174573 (+)
FVB/NJ	MGP_FVBNJ_G0035235	protein coding gene	Chr9:120036952-120075818 (+)
LP/J	MGP_LPJ_G0035367	protein coding gene	Chr9:126864796-126911255 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0035276	protein coding gene	Chr9:135570520-135615224 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0035996	protein coding gene	Chr9:125406995-125456633 (+)
PWK/PhJ	MGP_PWKPhJ_G0034170	protein coding gene	Chr9:121581674-121626807 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0034007	protein coding gene	Chr9:125527066-125572928 (+)
WSB/EiJ	MGP_WSBEiJ_G0034586	protein coding gene	Chr9:125252437-125295164 (+)

Human Ortholog

LIMD1, LIM domain containing 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LIMD1, LIM domain containing 1
Links

HGNC:6612

NCBI Gene ID: 8994

UniProt: Q9UGP4
Chr Location

3p21.31; chr3:45555394-45686341 (+) GRCh38

MGI Vertebrate Homology

Limd1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: LIMD1
Gene Tree

Limd1

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Phenotype Summary

10 phenotypes from 2 alleles in 2 genetic backgrounds
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

7
Endonuclease-mediated

4
Gene trapped

2
Targeted

1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

28 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit normal basal bone osteoclast numbers and bone density but are resistant to physiological and pathologic osteoclastogenic stimuli.

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All GO Annotations

76
GO References

12

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

777
Tissues

68
cDNA Data

193
Literature Summary

13

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA LIMD1

Xenbase limd1

ZFIN limd1b

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All Sequences

91
RefSeq

8
UniProt

2
CCDS

CCDS23660.1

Ensembl

ENSMUSG00000025239 (Evidence)
NCBI Gene

29806

			Length	Strain/Species	Flank
genomic	ENSMUSG00000025239	Ensembl Gene Model \| MGI Sequence Detail	42847	C57BL/6J	± kb
transcript	ENSMUST00000026269	Ensembl \| MGI Sequence Detail	4848	Not Applicable
polypeptide	ENSMUSP00000026269	Ensembl \| MGI Sequence Detail	668	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000029595 LIM domain-containing protein 1

(term hierarchy)
InterPro Domains

IPR047172 Ajuba-like

IPR047245 Ajuba-like, LIM domain 1

IPR047247 Ajuba-like, LIM domain 2

IPR047248 Ajuba-like, LIM domain 3

IPR001781 Zinc finger, LIM-type
GlyGen

Q9QXD8 8 sites, 1 O-linked glycan (6 sites)

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All nucleic 198

Genomic 1

cDNA 193

Primer pair 3

Other 1

Microarray probesets 4

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MGI:1098702, MGI:2143352

Summaries

All 59

Developmental Gene Expression 13

Gene Ontology 12

Phenotypes 10
Earliest

J:59385 Kiss H, et al., A novel gene containing LIM domains (LIMD1) is located within the common eliminated region 1 (C3CER1) in 3p21.3. Hum Genet. 1999 Dec;105(6):552-9
Latest

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

TSS for Limd1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr87914	Chr9:123307722-123307746 (+)	-37 bp
Tssr87915	Chr9:123307758-123307798 (+)	7 bp
Tssr87916	Chr9:123307803-123307847 (+)	54 bp
Tssr87917	Chr9:123338232-123338243 (+)	30,467 bp
Tssr87918	Chr9:123338245-123338270 (+)	30,487 bp
Tssr87919	Chr9:123338287-123338301 (+)	30,523 bp
Tssr87920	Chr9:123338325-123338352 (+)	30,568 bp
Tssr87921	Chr9:123339114-123339134 (+)	31,353 bp
Tssr3058	Chr9:123339550-123339581 (+)	31,795 bp
Tssr87922	Chr9:123339589-123339601 (+)	31,824 bp
Tssr87923	Chr9:123344568-123344582 (+)	36,804 bp
Tssr87924	Chr9:123349655-123349676 (+)	41,895 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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