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

Gene ID: 127495, updated on 5-Mar-2024

Summary

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 enable protein serine/threonine phosphatase activity. Predicted to be involved in signal transduction. Predicted to be located in M band. Predicted to be active in cytoplasm and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]
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

See LRRC39 in Genome Data Viewer
Location:
1p21.2
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (100148448..100179667, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (99996563..100027756, complement)
105.20220307 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

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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 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

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_001256385.2NP_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:79263
    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:85107
    LRR_RI; leucine-rich repeat [structural motif]
    pfam13855
    Location:84141
    LRR_8; Leucine rich repeat
  2. NM_001256386.2NP_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:37282
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:85107
    LRR_RI; leucine-rich repeat [structural motif]
  3. NM_001256387.2NP_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:37282
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:85107
    LRR_RI; leucine-rich repeat [structural motif]
  4. NM_144620.4NP_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:37282
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:85107
    LRR_RI; leucine-rich repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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_047445522.1XP_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_054334339.1XP_054190314.1  leucine-rich repeat-containing protein 39 isoform X1

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