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    LRRC39 leucine rich repeat containing 39 [ Homo sapiens (human) ]

    Gene ID: 127495, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LRRC39provided by HGNC
    Official Full Name
    leucine rich repeat containing 39provided by HGNC
    Primary source
    HGNC:HGNC:28228
    See related
    Ensembl:ENSG00000122477 AllianceGenome:HGNC:28228
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to be involved in signal transduction. Predicted to be located in M band. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in heart (RPKM 35.2), prostate (RPKM 6.5) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRRC39 in Genome Data Viewer
    Location:
    1p21.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (100148448..100179667, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (99996563..100027756, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (100614004..100643812, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:100503123-100503725 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1366 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1367 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:100514024-100514739 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1370 Neighboring gene major facilitator superfamily domain containing 14A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1371 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1372 Neighboring gene SAS-6 centriolar assembly protein Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100578889-100579078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1373 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100598108-100598271 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:100598267-100598869 Neighboring gene Sharpr-MPRA regulatory region 13340 Neighboring gene tRNA methyltransferase 13 homolog Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:100665653-100666490 Neighboring gene ribosomal protein L23a pseudogene 90 Neighboring gene dihydrolipoamide branched chain transacylase E2 Neighboring gene brain protein I3 pseudogene 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Myomasp/LRRC39, a heart- and muscle-specific protein, is a novel component of the sarcomeric M-band and is involved in stretch sensing. Will RD, et al. Circ Res, 2010 Nov 12. PMID 20847312
    2. The LIFEdb database in 2006. Mehrle A, et al. Nucleic Acids Res, 2006 Jan 1. PMID 16381901, Free PMC Article
    3. From ORFeome to biology: a functional genomics pipeline. Wiemann S, et al. Genome Res, 2004 Oct. PMID 15489336, Free PMC Article
    4. DNA cloning using in vitro site-specific recombination. Hartley JL, et al. Genome Res, 2000 Nov. PMID 11076863, Free PMC Article
    5. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Reveal myomasp/LRRC39 as a previously unrecognized component of an M-band-associated signaling pathway that regulates cardiomyocyte gene expression in response to biomechanical stress.
      Title: Myomasp/LRRC39, a heart- and muscle-specific protein, is a novel component of the sarcomeric M-band and is involved in stretch sensing.
    2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC14816, DKFZp313O1122

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in intracellular signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in M band IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat-containing protein 39
    Names
    densin hlg
    myomasp
    myosin-interacting M-band-associated stress-responsive protein

    NCBI Reference Sequences (RefSeq)

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    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_001256385.2 → NP_001243314.1  leucine-rich repeat-containing protein 39 isoform 1

      See identical proteins and their annotated locations for NP_001243314.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and it encodes the longest protein (isoform 1).
      Source sequence(s)
      AL711357, AL833417, BC009613, BX645870, DB449006, N70864
      Consensus CDS
      CCDS58014.1
      UniProtKB/Swiss-Prot
      Q96DD0
      Related
      ENSP00000359157.1, ENST00000370138.1
      Conserved Domains (3) summary
      cd00116
      Location:79 → 263
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00033
      Location:85 → 107
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:84 → 141
      LRR_8; Leucine rich repeat

    2. NM_001256386.2 → NP_001243315.1  leucine-rich repeat-containing protein 39 isoform 2

      See identical proteins and their annotated locations for NP_001243315.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region which results in the use of a different stop codon, compared to variant 1. The resulting protein (isoform 2) has a distinct and shorter C-terminus compared to isoform 1. Variants 2, 3, and 4 encode the same protein.
      Source sequence(s)
      AL711357, BC009613, BX645870, DB449006, N70864
      Consensus CDS
      CCDS766.1
      UniProtKB/Swiss-Prot
      B3KUD2, D3DT56, Q5VVK7, Q96DD0
      Related
      ENSP00000344470.3, ENST00000342895.8
      Conserved Domains (2) summary
      COG4886
      Location:37 → 282
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:85 → 107
      LRR_RI; leucine-rich repeat [structural motif]

    3. NM_001256387.2 → NP_001243316.1  leucine-rich repeat-containing protein 39 isoform 2

      See identical proteins and their annotated locations for NP_001243316.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) has multiple differences, compared to variant 1. The resulting protein (isoform 2) has a distinct and shorter C-terminus compared to isoform 1. Variants 2, 3, and 4 encode the same protein.
      Source sequence(s)
      AY358131, BC009613, BX645870, DB449006, N70864
      Consensus CDS
      CCDS766.1
      UniProtKB/Swiss-Prot
      B3KUD2, D3DT56, Q5VVK7, Q96DD0
      Conserved Domains (2) summary
      COG4886
      Location:37 → 282
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:85 → 107
      LRR_RI; leucine-rich repeat [structural motif]

    4. NM_144620.4 → NP_653221.1  leucine-rich repeat-containing protein 39 isoform 2

      See identical proteins and their annotated locations for NP_653221.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses a different splice site in the 5' UTR and lacks an alternate exon in the 3' coding region which results in the use of a different stop codon, compared to variant 1. The resulting protein (isoform 2) has a distinct and shorter C-terminus compared to isoform 1. Variants 2, 3, and 4 encode the same protein.
      Source sequence(s)
      AW961910, BC009613, BX645870, DB449006, N70864
      Consensus CDS
      CCDS766.1
      UniProtKB/Swiss-Prot
      B3KUD2, D3DT56, Q5VVK7, Q96DD0
      Related
      ENSP00000359156.1, ENST00000370137.6
      Conserved Domains (2) summary
      COG4886
      Location:37 → 282
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:85 → 107
      LRR_RI; leucine-rich repeat [structural motif]

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      100148448..100179667 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047445522.1 → XP_047301478.1  leucine-rich repeat-containing protein 39 isoform X1

      UniProtKB/Swiss-Prot
      B3KUD2, D3DT56, Q5VVK7, Q96DD0

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      99996563..100027756 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334339.1 → XP_054190314.1  leucine-rich repeat-containing protein 39 isoform X1

      UniProtKB/Swiss-Prot
      B3KUD2, D3DT56, Q5VVK7, Q96DD0
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96DD0.1 GenPept UniProtKB/Swiss-Prot:Q96DD0

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