Pdlim1 MGI Mouse Gene Detail - MGI:1860611 - PDZ and LIM domain 1 (elfin)

Symbol

Pdlim1
Name

PDZ and LIM domain 1 (elfin)
Synonyms

CLP36, mClim1

Feature Type

protein coding gene
IDs

MGI:1860611
NCBI Gene: 54132
Alliance

gene page
Transcription Start Sites

7 TSS

Sequence Map

Chr19:40210683-40260060 bp, - strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 19, 34.24 cM, cytoband D1
Mapping Data

3 experiments

SNPs within 2kb

1782 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1860611	protein coding gene	Chr19:40209617-40260286 (-)
129S1/SvImJ	MGP_129S1SvImJ_G0025110	protein coding gene	Chr19:39419721-39473747 (-)
A/J	MGP_AJ_G0025087	protein coding gene	Chr19:37486347-37545932 (-)
AKR/J	MGP_AKRJ_G0025055	protein coding gene	Chr19:38779044-38829664 (-)
BALB/cJ	MGP_BALBcJ_G0025081	protein coding gene	Chr19:37583983-37635442 (-)
C3H/HeJ	MGP_C3HHeJ_G0024841	protein coding gene	Chr19:38907105-38970816 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0025525	protein coding gene	Chr19:40488954-40552330 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022938	protein coding gene	Chr19:36904395-36954882 (-)
CAST/EiJ	MGP_CASTEiJ_G0024306	protein coding gene	Chr19:38536035-38598339 (-)
CBA/J	MGP_CBAJ_G0024821	protein coding gene	Chr19:42469885-42526333 (-)
DBA/2J	MGP_DBA2J_G0024953	protein coding gene	Chr19:37390110-37442325 (-)
FVB/NJ	MGP_FVBNJ_G0024914	protein coding gene	Chr19:37144246-37195447 (-)
LP/J	MGP_LPJ_G0025039	protein coding gene	Chr19:39458235-39512085 (-)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024945	protein coding gene	Chr19:42193527-42246678 (-)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025582	protein coding gene	Chr19:38795758-38851054 (-)
PWK/PhJ	MGP_PWKPhJ_G0024056	protein coding gene	Chr19:37235190-37289005 (-)
SPRET/EiJ	MGP_SPRETEiJ_G0023859	protein coding gene	Chr19:37545136-37593370 (-)
WSB/EiJ	MGP_WSBEiJ_G0024376	protein coding gene	Chr19:38952273-39013397 (-)

Human Ortholog

PDLIM1, PDZ and LIM domain 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

PDLIM1, PDZ and LIM domain 1
Synonyms

CLIM1, CLP-36, CLP36, hCLIM1, HEL-S-112
Links

HGNC:2067

NCBI Gene ID: 9124

neXtProt AC: NX_O00151

UniProt: O00151
Chr Location

10q23.33; chr10:95237572-95291012 (-) GRCh38

MGI Vertebrate Homology

Pdlim1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: PDLIM1
Gene Tree

Pdlim1

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Phenotype Summary

6 phenotypes from 2 alleles in 2 genetic backgrounds
11 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

17
Endonuclease-mediated

5
Gene trapped

12
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

32 strains or lines available

Mice homozygous for a gene trap allele exhibit enhanced platelet response to GPVI agonists and thrombosis.

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All GO Annotations

38
GO References

8

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

929
Tissues

98
cDNA Data

15
Literature Summary

13

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA PDLIM1

Xenbase pdlim1

ZFIN pdlim1

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All Sequences

47
RefSeq

2
UniProt

3
CCDS

CCDS37977.1

Ensembl

ENSMUSG00000055044 (Evidence)
NCBI Gene

54132

			Length	Strain/Species	Flank
genomic	54132	NCBI Gene Model \| MGI Sequence Detail	49378	C57BL/6J	± kb
transcript	NM_016861	RefSeq \| MGI Sequence Detail	1524	C57BL/6
polypeptide	O70400	UniProt \| EBI \| MGI Sequence Detail	327	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000012508 PDZ and LIM domain protein 1

(term hierarchy)
InterPro Domains

IPR050604 PDZ and LIM domain-containing

IPR031847 PDZ and LIM domain protein 1-4/Zasp-like, middle domain

IPR028537 PDZ and LIM domain protein 1, LIM domain

IPR001478 PDZ domain

IPR036034 PDZ superfamily

IPR006643 Zasp-like motif

IPR001781 Zinc finger, LIM-type
GlyGen

O70400 6 sites, 1 N-linked glycan (1 site), 1 O-linked glycan (5 sites)

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All nucleic 18

cDNA 15

Primer pair 3

Microarray probesets 4

Summaries

All 55

Developmental Gene Expression 13

Gene Ontology 8

Phenotypes 11
Earliest

J:74188 Kotaka M, et al., Elfin is expressed during early heart development. J Cell Biochem. 2001 Aug 21-Sep 5;83(3):463-72
Latest

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

TSS for Pdlim1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr159163	Chr19:40260318-40260332 (-)	-265 bp
Tssr159162	Chr19:40260288-40260309 (-)	-239 bp
Tssr159161	Chr19:40260257-40260266 (-)	-202 bp
Tssr159160	Chr19:40260216-40260238 (-)	-167 bp
Tssr159159	Chr19:40260080-40260142 (-)	-51 bp
Tssr159158	Chr19:40259950-40260021 (-)	74 bp
Tssr159157	Chr19:40219639-40219655 (-)	40,413 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 11/19/2024 MGI 6.24