Lima1 MGI Mouse Gene Detail - MGI:1920992 - LIM domain and actin binding 1

Symbol

Lima1
Name

LIM domain and actin binding 1
Synonyms

1110021C24Rik, 3526402A12Rik, epithelial protein lost in neoplasm, EPLIN

Feature Type

protein coding gene
IDs

MGI:1920992
NCBI Gene: 65970
Gene Overview

MyGene.info: LIMA1
Alliance

gene page
Transcription Start Sites

8 TSS

Sequence Map

Chr15:99778470-99875456 bp, - strand
From Ensembl annotation of GRCm38

View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 15, 56.13 cM
Mapping Data

3 experiments

SNPs within 2kb

690 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1920992	protein coding gene	Chr15:99778468-99875456 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0022344	protein coding gene	Chr15:101662936-101766691 (-)
A/J	MGP_AJ_G0022302	protein coding gene	Chr15:97606533-97708355 (-)
AKR/J	MGP_AKRJ_G0022278	protein coding gene	Chr15:100607502-100708102 (-)
BALB/cJ	MGP_BALBcJ_G0022308	protein coding gene	Chr15:97779871-97879345 (-)
C3H/HeJ	MGP_C3HHeJ_G0022076	protein coding gene	Chr15:100671641-100773924 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0022753	protein coding gene	Chr15:105444253-105556361 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0020279	protein coding gene	Chr15:93488157-93578485 (-)
CAST/EiJ	MGP_CASTEiJ_G0021600	protein coding gene	Chr15:101540398-101642667 (-)
CBA/J	MGP_CBAJ_G0022045	protein coding gene	Chr15:109042027-109154176 (-)
DBA/2J	MGP_DBA2J_G0022172	protein coding gene	Chr15:97035780-97135487 (-)
FVB/NJ	MGP_FVBNJ_G0022152	protein coding gene	Chr15:96031599-96132740 (-)
LP/J	MGP_LPJ_G0022243	protein coding gene	Chr15:101806676-101905908 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0022172	protein coding gene	Chr15:112916191-113021038 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022768	protein coding gene	Chr15:100720091-100823091 (-)
PWK/PhJ	MGP_PWKPhJ_G0021339	protein coding gene	Chr15:97176784-97278797 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0021174	protein coding gene	Chr15:100560348-100665004 (-)
WSB/EiJ	MGP_WSBEiJ_G0021651	protein coding gene	Chr15:101232237-101346016 (-)

Human Ortholog

LIMA1, LIM domain and actin binding 1

Vertebrate Orthologs

10

Human Ortholog

LIMA1, LIM domain and actin binding 1
Orthology source: HomoloGene, HGNC
Synonyms

EPLIN, LDLCQ8, SREBP3
Links

HGNC:24636

NCBI Gene ID: 51474

neXtProt AC: NX_Q9UHB6

UniProt: Q9UHB6
Chr Location

12q13.12; chr12:50175780-50283570 (-) GRCh38.p7

HomoloGene

Vertebrate Homology Class 9484
1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog;1 chicken;1 zebrafish;1 frog, western clawed;1 macaque, rhesus
HCOP

human homology predictions: LIMA1
Gene Tree

Lima1

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References

1 with disease annotations

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Phenotype Summary

10 phenotypes from 3 alleles in 3 genetic backgrounds
35 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	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

262
Chemically induced (other)

1
Gene trapped

255
Radiation induced

2
Targeted

4
Genomic Mutations

3 involving Lima1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

42 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit decreased intestinal cholesterol absorption.

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All GO Annotations

32
GO References

8

External Resources

FuncBase

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 death	cell differentiation	cell proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	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	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	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

69
Tissues

38
cDNA Data

19
Literature Summary

3

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase lima1

ZFIN lima1a

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Lima1 interacts with 282 markers (Mir1b, Mir7-1, Mir7-2, ...) View All

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All Sequences

75
RefSeq

7
UniProt

6
CCDS

CCDS37206.1, CCDS49729.1

Ensembl

ENSMUSG00000023022 (Evidence)
NCBI Gene

65970

			Length	Strain/Species	Flank
genomic	ENSMUSG00000023022	Ensembl Gene Model \| MGI Sequence Detail	96987	C57BL/6J	± kb
transcript	ENSMUST00000073691	Ensembl \| MGI Sequence Detail	4243	Not Applicable
polypeptide	ENSMUSP00000073371	Ensembl \| MGI Sequence Detail	753	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000009814 LIM domain and actin-binding protein 1

(term hierarchy)
InterPro Domains

IPR028740 LIM domain and actin-binding protein 1

IPR001781 Zinc finger, LIM-type

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All nucleic 22

cDNA 19

Primer pair 3

Microarray probesets 9

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MGI:1196235, MGI:2443059

Summaries

All 70

Developmental Gene Expression 3

Diseases 1

Gene Ontology 8

Phenotypes 35
Earliest

J:7688 Lane PW, et al., Association of megacolon with a new dominant spotting gene (Dom) in the mouse. J Hered. 1984 Nov-Dec;75(6):435-9
Latest

J:263730 Zhang YY, et al., A LIMA1 variant promotes low plasma LDL cholesterol and decreases intestinal cholesterol absorption. Science. 2018 Jun 8;360(6393):1087-1092

TSS for Lima1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr136404	Chr15:99875382-99875447 (-)	41 bp
Tssr136401	Chr15:99820072-99820154 (-)	55,343 bp
Tssr136400	Chr15:99820027-99820032 (-)	55,426 bp
Tssr136399	Chr15:99819932-99819939 (-)	55,520 bp
Tssr136398	Chr15:99819819-99819835 (-)	55,629 bp
Tssr136397	Chr15:99819700-99819715 (-)	55,748 bp
Tssr136395	Chr15:99780566-99780585 (-)	94,880 bp
Tssr136394	Chr15:99780372-99780378 (-)	95,081 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
Citing These Resources Funding Information Warranty Disclaimer & Copyright Notice Send questions and comments to User Support.	last database update 11/06/2018 MGI 6.13