Ldb1 MGI Mouse Gene Detail - MGI:894762

Symbol

Ldb1
Name

LIM domain binding 1
Synonyms

CLIM2

Feature Type

protein coding gene
IDs

MGI:894762
NCBI Gene: 16825
Alliance

gene page
Transcription Start Sites

20 TSS

Sequence Map

Chr19:46020009-46033653 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 19, 38.75 cM
Mapping Data

4 experiments

SNPs within 2kb

343 from dbSNP Build 142
Strain Annotations

18
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_894762	protein coding gene	Chr19:46019963-46036584 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0025197	protein coding gene	Chr19:45689226-45703885 (-)
A/J	MGP_AJ_G0025173	protein coding gene	Chr19:43442953-43457748 (-)
AKR/J	MGP_AKRJ_G0025142	protein coding gene	Chr19:44850150-44862798 (-)
BALB/cJ	MGP_BALBcJ_G0025168	protein coding gene	Chr19:43499714-43513636 (-)
C3H/HeJ	MGP_C3HHeJ_G0024928	protein coding gene	Chr19:45022667-45036348 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0025611	protein coding gene	Chr19:46827735-46841077 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0023025	protein coding gene	Chr19:42681003-42693853 (-)
CAST/EiJ	MGP_CASTEiJ_G0024393	protein coding gene	Chr19:44793667-44806311 (-)
CBA/J	MGP_CBAJ_G0024908	protein coding gene	Chr19:49185241-49198514 (-)
DBA/2J	MGP_DBA2J_G0025040	protein coding gene	Chr19:43262270-43275970 (-)
FVB/NJ	MGP_FVBNJ_G0025001	protein coding gene	Chr19:43038602-43051879 (-)
LP/J	MGP_LPJ_G0025126	protein coding gene	Chr19:45599403-45613361 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0025032	protein coding gene	Chr19:48545324-48560474 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025669	protein coding gene	Chr19:44955528-44970749 (-)
PWK/PhJ	MGP_PWKPhJ_G0024142	protein coding gene	Chr19:43192901-43206759 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0023946	protein coding gene	Chr19:43613533-43626348 (-)
WSB/EiJ	MGP_WSBEiJ_G0024463	protein coding gene	Chr19:45099904-45115910 (-)

Human Ortholog

LDB1, LIM domain binding 1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LDB1, LIM domain binding 1
Synonyms

CLIM-2, CLIM2, LDB-1, NLI
Links

HGNC:6532

NCBI Gene ID: 8861

neXtProt AC: NX_Q86U70

UniProt: Q86U70
Chr Location

10q24.32; chr10:102102088-102121442 (-) GRCh38

MGI Vertebrate Homology

Ldb1 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: LDB1
Gene Tree

Ldb1

Diseases

1 with Ldb1 mouse models

Human Disease

Mouse Models

nail-patella syndrome

IDs

View 1 model

Click on a disease name to see all genes associated with that disease.

Mutations/Alleles

1 with disease annotations

References

1 with disease annotations

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Phenotype Summary

56 phenotypes from 4 alleles in 6 genetic backgrounds
2 phenotypes from multigenic genotypes
32 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

98
Endonuclease-mediated

1
Gene trapped

90
Targeted

7
Genomic Mutations

1 involving Ldb1
Incidental Mutations

APF
Find Mice (IMSR)

35 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for disruptions in this gene die as embryos at E9.5-E10 with impaired primitive erythropoiesis and vascular development.

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All GO Annotations

85
GO References

30

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

971
Tissues

174
cDNA Data

159
Literature Summary

54

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA LDB1

Xenbase ldb1

ZFIN ldb1a, ldb1b

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All Sequences

65
RefSeq

14
UniProt

2
CCDS

CCDS29870.1, CCDS50455.1

Ensembl

ENSMUSG00000025223 (Evidence)
NCBI Gene

16825

			Length	Strain/Species	Flank
genomic	ENSMUSG00000025223	Ensembl Gene Model \| MGI Sequence Detail	13645	C57BL/6J	± kb
transcript	ENSMUST00000185355	Ensembl \| MGI Sequence Detail	2088	Not Applicable
polypeptide	ENSMUSP00000139562	Ensembl \| MGI Sequence Detail	411	Not Applicable

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UniProt

2 Sequences
Protein Ontology

PR:000009736 LIM domain-binding protein 1

(term hierarchy)
PDB

1J2O, 1M3V, 1RUT, 2JTN, 2L6Y, 2L6Z, 2LXD, 4JCJ, 6PTL
InterPro Domains

IPR029005 LIM-domain binding protein/SEUSS

IPR041363 LIM interaction domain
GlyGen

P70662 2 sites, 1 N-linked glycan (1 site), 1 O-linked glycan (1 site)

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All nucleic 173

Genomic 7

cDNA 161

Primer pair 2

Other 3

Microarray probesets 3

Summaries

All 121

Developmental Gene Expression 54

Diseases 1

Gene Ontology 30

Phenotypes 32
Earliest

J:41552 Agulnick AD, et al., Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins. Nature. 1996 21;384(6606):270-2
Latest

J:341393 Cheffer A, et al., DOT1L deletion impairs the development of cortical parvalbumin-expressing interneurons. Cereb Cortex. 2023 Sep 26;33(19):10272-10285

TSS for Ldb1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr159608	Chr19:46033972-46033981 (-)	-324 bp
Tssr159607	Chr19:46033929-46033960 (-)	-292 bp
Tssr159606	Chr19:46033828-46033839 (-)	-181 bp
Tssr159605	Chr19:46033801-46033825 (-)	-160 bp
Tssr159604	Chr19:46033788-46033799 (-)	-141 bp
Tssr159603	Chr19:46033770-46033786 (-)	-125 bp
Tssr159602	Chr19:46033746-46033757 (-)	-99 bp
Tssr159601	Chr19:46033663-46033683 (-)	-20 bp
Tssr159600	Chr19:46033633-46033661 (-)	6 bp
Tssr159599	Chr19:46033571-46033590 (-)	72 bp
Tssr159598	Chr19:46033431-46033566 (-)	154 bp
Tssr159597	Chr19:46033418-46033427 (-)	230 bp
Tssr159596	Chr19:46028804-46028816 (-)	4,843 bp
Tssr159595	Chr19:46028068-46028101 (-)	5,568 bp
Tssr159594	Chr19:46027976-46028040 (-)	5,645 bp
Tssr159593	Chr19:46027881-46027894 (-)	5,765 bp
Tssr159592	Chr19:46027647-46027668 (-)	5,995 bp
Tssr159591	Chr19:46027615-46027628 (-)	6,031 bp
Tssr159590	Chr19:46021641-46021664 (-)	12,000 bp
Tssr159589	Chr19:46020009-46020013 (-)	13,642 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 12/10/2024 MGI 6.24