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

Gene ID: 127495, updated on 2-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
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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 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 Variation Viewer (GRCh37.p13)

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

Gene LinkOut

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