Format

Send to:

Choose Destination

LMCD1 LIM and cysteine rich domains 1 [ Homo sapiens (human) ]

Gene ID: 29995, updated on 20-Sep-2020

Summary

Official Symbol
LMCD1provided by HGNC
Official Full Name
LIM and cysteine rich domains 1provided by HGNC
Primary source
HGNC:HGNC:6633
See related
Ensembl:ENSG00000071282 MIM:604859
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
Summary
This gene encodes a member of the LIM-domain family of zinc finger proteins. The encoded protein contains an N-terminal cysteine-rich domain and two C-terminal LIM domains. The presence of LIM domains suggests involvement in protein-protein interactions. The protein may act as a co-regulator of transcription along with other transcription factors. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]
Expression
Broad expression in lung (RPKM 21.9), fat (RPKM 21.1) and 24 other tissues See more
Orthologs

Genomic context

See LMCD1 in Genome Data Viewer
Location:
3p25.3
Exon count:
7
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (8501823..8574668)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (8543493..8609811)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927394 Neighboring gene LMCD1 antisense RNA 1 Neighboring gene uncharacterized LOC107986010 Neighboring gene RNA, U4atac small nuclear 17, pseudogene Neighboring gene uncharacterized LOC107986009 Neighboring gene long intergenic non-protein coding RNA 312 Neighboring gene ssu-2 homolog Neighboring gene olfactory receptor family 7 subfamily E member 122 pseudogene Neighboring gene caveolin 3

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 Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ23868

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
transcription corepressor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transcription corepressor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
cellular protein metabolic process TAS
Traceable Author Statement
more info
 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
positive regulation of calcineurin-NFAT signaling cascade IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cardiac muscle hypertrophy IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
LIM and cysteine-rich domains protein 1
Names
dyxin

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.

mRNA and Protein(s)

  1. NM_001278233.2NP_001265162.1  LIM and cysteine-rich domains protein 1 isoform 2

    See identical proteins and their annotated locations for NP_001265162.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region and uses a downstream start codon compared to variant 1. The encoded isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC087859, AK294455, BC000646, BU619403, CN388104
    Consensus CDS
    CCDS63534.1
    UniProtKB/Swiss-Prot
    Q9NZU5
    Related
    ENSP00000396515.1, ENST00000454244.4
    Conserved Domains (3) summary
    cd09340
    Location:170227
    LIM1_Testin_like; The first LIM domain of Testin-like family
    cd09829
    Location:43130
    PET_testin; The PET domain of Testin
    cl02475
    Location:233286
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  2. NM_001278234.2NP_001265163.1  LIM and cysteine-rich domains protein 1 isoform 3

    See identical proteins and their annotated locations for NP_001265163.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC087859, AK293849, BC000646, BU619403, CN388104
    Consensus CDS
    CCDS63533.1
    UniProtKB/Swiss-Prot
    Q9NZU5
    UniProtKB/TrEMBL
    B4DEY6
    Related
    ENSP00000380542.3, ENST00000397386.7
    Conserved Domains (3) summary
    cd09340
    Location:131188
    LIM1_Testin_like; The first LIM domain of Testin-like family
    cd09829
    Location:1891
    PET_testin; The PET domain of Testin
    cl02475
    Location:194247
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers
  3. NM_001278235.2NP_001265164.1  LIM and cysteine-rich domains protein 1 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate 3' terminal exon which results in an early stop codon, compared to variant 1. It encodes isoform 4, which has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AI693011, AI951010, AK300803, BC000646, BX114807, N95437, W47274
    Consensus CDS
    CCDS63532.1
    UniProtKB/Swiss-Prot
    Q9NZU5
    UniProtKB/TrEMBL
    B7Z6R5, H7C3D2
    Related
    ENSP00000411222.2, ENST00000426878.2
    Conserved Domains (1) summary
    cd09829
    Location:116203
    PET_testin; The PET domain of Testin
  4. NM_014583.4NP_055398.1  LIM and cysteine-rich domains protein 1 isoform 1

    See identical proteins and their annotated locations for NP_055398.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC087859, AF169284, BU619403, CN388104
    Consensus CDS
    CCDS33688.1
    UniProtKB/Swiss-Prot
    Q9NZU5
    Related
    ENSP00000157600.3, ENST00000157600.8
    Conserved Domains (3) summary
    cd09340
    Location:243300
    LIM1_Testin_like; The first LIM domain of Testin-like family
    cd09829
    Location:116203
    PET_testin; The PET domain of Testin
    cl02475
    Location:306359
    LIM; LIM is a small protein-protein interaction domain, containing two zinc fingers

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    8501823..8574668
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center