Lims1 MGI Mouse Gene Detail - MGI:1195263 - LIM and senescent cell antigen-like domains 1

Symbol

Lims1
Name

LIM and senescent cell antigen-like domains 1
Synonyms

2310016J22Rik, 4921524A02Rik, C430041B13Rik, Lims1l, PINCH1

Feature Type

protein coding gene
IDs

MGI:1195263
NCBI Gene: 110829
Alliance

gene page
Transcription Start Sites

22 TSS

Sequence Map

Chr10:58159288-58260513 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 10, 29.31 cM
Mapping Data

6 experiments

SNPs within 2kb

2260 from dbSNP Build 142
Strain Annotations

18
PCR

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1195263	protein coding gene	Chr10:58159164-58260513 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0017246	protein coding gene	Chr10:57414919-57523463 (+)
A/J	MGP_AJ_G0017223	protein coding gene	Chr10:55759614-55862325 (+)
AKR/J	MGP_AKRJ_G0017182	protein coding gene	Chr10:57211551-57317489 (+)
BALB/cJ	MGP_BALBcJ_G0017184	protein coding gene	Chr10:55840409-55951412 (+)
C3H/HeJ	MGP_C3HHeJ_G0017007	protein coding gene	Chr10:57126520-57232662 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0017642	protein coding gene	Chr10:59512378-59621827 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0015333	protein coding gene	Chr10:52878078-52981921 (+)
CAST/EiJ	MGP_CASTEiJ_G0016578	protein coding gene	Chr10:57037473-57144082 (+)
CBA/J	MGP_CBAJ_G0016979	protein coding gene	Chr10:61643371-61752530 (+)
DBA/2J	MGP_DBA2J_G0017084	protein coding gene	Chr10:55086065-55190129 (+)
FVB/NJ	MGP_FVBNJ_G0017078	protein coding gene	Chr10:54323033-54430329 (+)
LP/J	MGP_LPJ_G0017159	protein coding gene	Chr10:57806410-57916344 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0017106	protein coding gene	Chr10:64209865-64318836 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0017679	protein coding gene	Chr10:57012922-57127284 (+)
PWK/PhJ	MGP_PWKPhJ_G0016361	protein coding gene	Chr10:54864762-54968160 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0016146	protein coding gene	Chr10:56387618-56496733 (+)
WSB/EiJ	MGP_WSBEiJ_G0016642	protein coding gene	Chr10:56923236-57026401 (+)

Human Ortholog

LIMS1, LIM zinc finger domain containing 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LIMS1, LIM zinc finger domain containing 1
Synonyms

PINCH, PINCH-1, PINCH1
Links

HGNC:6616

NCBI Gene ID: 3987

neXtProt AC: NX_P48059

UniProt: P48059
Chr Location

2q12.3; chr2:108533671-108687246 (+) GRCh38

MGI Vertebrate Homology

Lims1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: LIMS1
Protein SuperFamily

PINCH
Gene Tree

Lims1

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Phenotype Summary

13 phenotypes from 5 alleles in 3 genetic backgrounds
23 phenotypes from multigenic genotypes
28 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

55
Chemically induced (other)

1
Endonuclease-mediated

2
Gene trapped

44
Radiation induced

1
Targeted

7
Genomic Mutations

2 involving Lims1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

53 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Homozygous null mice die shortly after implantation and have a disorganized egg cylinder by E5.5, which is degenerated by E6.5. E5.5 null embryos exhibit decreased cell proliferation and excessive cell death.

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All GO Annotations

47
GO References

13

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

1087
Tissues

146
cDNA Data

32
Literature Summary

16

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lims1

ZFIN lims1

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All Sequences

97
RefSeq

26
UniProt

8
CCDS

CCDS23860.1, CCDS56703.1, CCDS83697.1, CCDS88008.1

Ensembl

ENSMUSG00000019920 (Evidence)
NCBI Gene

110829

			Length	Strain/Species	Flank
genomic	ENSMUSG00000019920	Ensembl Gene Model \| MGI Sequence Detail	101226	C57BL/6J	± kb
transcript	ENSMUST00000020077	Ensembl \| MGI Sequence Detail	1565	Not Applicable
polypeptide	ENSMUSP00000020077	Ensembl \| MGI Sequence Detail	396	Not Applicable

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UniProt

8 Sequences
Protein Ontology

PR:000009818 LIM and senescent cell antigen-like-containing domain protein 1

(term hierarchy)
InterPro Domains

IPR047946 LIM and senescent cell antigen-like-containing domain protein 1/2-like

IPR047944 LIMS1/2-like, LIM domain 1

IPR001781 Zinc finger, LIM-type
GlyGen

Q99JW4 1 site, 1 N-linked glycan (1 site)

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All nucleic 36

cDNA 33

Primer pair 3

Microarray probesets 8

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MGI:1914678, MGI:1919149, MGI:2143635, MGI:2143741, MGI:2143862, MGI:2445157

Summaries

All 81

Developmental Gene Expression 16

Gene Ontology 13

Phenotypes 28
Earliest

J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
Latest

J:335157 Wu X, et al., Brief research report: Effects of Pinch deficiency on cartilage homeostasis in adult mice. Front Cell Dev Biol. 2023;11:1116128

TSS for Lims1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr93423	Chr10:58159301-58159321 (+)	23 bp
Tssr93424	Chr10:58159348-58159355 (+)	64 bp
Tssr93425	Chr10:58159362-58159429 (+)	108 bp
Tssr93426	Chr10:58160507-58160510 (+)	1,221 bp
Tssr93429	Chr10:58187714-58187765 (+)	28,452 bp
Tssr93430	Chr10:58187766-58187793 (+)	28,492 bp
Tssr93431	Chr10:58187809-58187812 (+)	28,523 bp
Tssr93432	Chr10:58187924-58187942 (+)	28,645 bp
Tssr93433	Chr10:58195702-58195707 (+)	36,417 bp
Tssr93434	Chr10:58207231-58207321 (+)	47,988 bp
Tssr3206	Chr10:58207327-58207358 (+)	48,055 bp
Tssr93435	Chr10:58207415-58207426 (+)	48,133 bp
Tssr93436	Chr10:58207432-58207449 (+)	48,153 bp
Tssr93437	Chr10:58210968-58210987 (+)	51,690 bp
Tssr93438	Chr10:58227289-58227324 (+)	68,019 bp
Tssr93439	Chr10:58230183-58230202 (+)	70,905 bp
Tssr93440	Chr10:58230203-58230217 (+)	70,922 bp
Tssr93441	Chr10:58236331-58236337 (+)	77,046 bp
Tssr93442	Chr10:58243495-58243530 (+)	84,225 bp
Tssr93443	Chr10:58254242-58254269 (+)	94,968 bp
Tssr93444	Chr10:58257463-58257490 (+)	98,189 bp
Tssr93445	Chr10:58258434-58258447 (+)	99,153 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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