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

    Gene ID: 29995, updated on 9-Dec-2024

    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; AllianceGenome:HGNC:6633
    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
    NEW
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    Genomic context

    See LMCD1 in Genome Data Viewer
    Location:
    3p25.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (8501823..8574668)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (8492967..8566009)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (8543509..8616354)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101927394 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:8061875-8062376 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:8082288-8083487 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:8155298-8155871 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:8270919-8271420 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:8271421-8271920 Neighboring gene LMCD1 antisense RNA 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:8361398-8362597 Neighboring gene uncharacterized LOC107986010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8413440-8413972 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8413973-8414503 Neighboring gene RNA, U4atac small nuclear 17, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:8453270-8453770 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:8482473-8482990 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:8497791-8498357 Neighboring gene Sharpr-MPRA regulatory region 2381 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:8540163-8541096 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:8541097-8542030 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr3:8577298-8578266 Neighboring gene uncharacterized LOC107986009 Neighboring gene long intergenic non-protein coding RNA 312 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8652364-8653245 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:8653246-8654126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:8664536-8665156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19390 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19391 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19392 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19393 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14028 Neighboring gene ssu-2 homolog Neighboring gene olfactory receptor family 7 subfamily E member 122 pseudogene

    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

    Clone Names

    • FLJ23868

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transcription corepressor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transcription corepressor activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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/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/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
      B4DG80, 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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      8492967..8566009
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)