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PDLIM4 PDZ and LIM domain 4 [ Homo sapiens (human) ]

Gene ID: 8572, updated on 27-Dec-2018

Summary

Official Symbol
PDLIM4provided by HGNC
Official Full Name
PDZ and LIM domain 4provided by HGNC
Primary source
HGNC:HGNC:16501
See related
Ensembl:ENSG00000131435 MIM:603422
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RIL
Summary
This gene encodes a protein which may be involved in bone development. Mutations in this gene are associated with susceptibility to osteoporosis. [provided by RefSeq, Nov 2009]
Expression
Ubiquitous expression in endometrium (RPKM 8.6), prostate (RPKM 6.1) and 21 other tissues See more
Orthologs

Genomic context

See PDLIM4 in Genome Data Viewer
Location:
5q31.1
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (132257658..132273454)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (131593351..131609147)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene P4HA2 antisense RNA 1 Neighboring gene prolyl 4-hydroxylase subunit alpha 2 Neighboring gene microRNA 6830 Neighboring gene VISTA enhancer hs1449 Neighboring gene CAGE-defined mid-level expression enhancer upstream of SLC22A4 Neighboring gene solute carrier family 22 member 4 Neighboring gene MIR3936 host gene

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Postmenopausal osteoporosis
MedGen: C0029458 OMIM: 166710 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
NHGRI GWA Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
alpha-actinin binding IPI
Inferred from Physical Interaction
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IDA
Inferred from Direct Assay
more info
PubMed 
protein phosphatase binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
actin cytoskeleton reorganization IDA
Inferred from Direct Assay
more info
PubMed 
excitatory chemical synaptic transmission ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cell junction IEA
Inferred from Electronic Annotation
more info
 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
dendritic spine ISS
Inferred from Sequence or Structural Similarity
more info
 
early endosome lumen ISS
Inferred from Sequence or Structural Similarity
more info
 
early endosome membrane IEA
Inferred from Electronic Annotation
more info
 
filamentous actin IDA
Inferred from Direct Assay
more info
PubMed 
lamellipodium IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
postsynaptic membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
recycling endosome lumen ISS
Inferred from Sequence or Structural Similarity
more info
 
recycling endosome membrane IEA
Inferred from Electronic Annotation
more info
 
stress fiber IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
PDZ and LIM domain protein 4
Names
LIM domain protein
LIM protein RIL
enigma homolog
reversion-induced LIM protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_015836.2 RefSeqGene

    Range
    5001..20797
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001131027.1NP_001124499.1  PDZ and LIM domain protein 4 isoform 2

    See identical proteins and their annotated locations for NP_001124499.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a coding exon in the 3' region, as compared to variant 1. The resulting isoform (2) has a shorter and distinct C-terminus, as compared to isoform 1.
    Source sequence(s)
    AF153882, AW590987, BC003096, BC016765, BF689609, BF690514, DN997097
    Consensus CDS
    CCDS47261.1
    UniProtKB/Swiss-Prot
    P50479
    UniProtKB/TrEMBL
    A0A0S2Z4N4
    Related
    ENSP00000368303.3, ENST00000379018.7
    Conserved Domains (2) summary
    cd00992
    Location:280
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam15936
    Location:148224
    DUF4749; Domain of unknown function (DUF4749)
  2. NM_003687.4NP_003678.2  PDZ and LIM domain protein 4 isoform 1

    See identical proteins and their annotated locations for NP_003678.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AF153882, AW590987, BC016765, BF689609, BF690514, DN997097
    Consensus CDS
    CCDS4152.1
    UniProtKB/Swiss-Prot
    P50479
    Related
    ENSP00000253754.3, ENST00000253754.7
    Conserved Domains (3) summary
    cd09451
    Location:255307
    LIM_RIL; The LIM domain of RIL
    cd00992
    Location:280
    PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    pfam15936
    Location:148220
    DUF4749; Domain of unknown function (DUF4749)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    132257658..132273454
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010002.1XP_016865491.1  PDZ and LIM domain protein 4 isoform X1

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