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    LRRC49 leucine rich repeat containing 49 [ Homo sapiens (human) ]

    Gene ID: 54839, updated on 27-Nov-2024

    Summary

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    Official Symbol
    LRRC49provided by HGNC
    Official Full Name
    leucine rich repeat containing 49provided by HGNC
    Primary source
    HGNC:HGNC:25965
    See related
    Ensembl:ENSG00000137821 MIM:620497; AllianceGenome:HGNC:25965
    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
    Also known as
    PGs4; CSTPP2
    Summary
    Located in centriolar satellite. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in heart (RPKM 8.5), testis (RPKM 7.2) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRRC49 in Genome Data Viewer
    Location:
    15q23
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (70853378..71053658)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (68676342..68876951)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (71145717..71345997)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uveal autoantigen with coiled-coil domains and ankyrin repeats Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:71002570-71003070 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71005595-71006134 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:71010983-71011484 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6609 Neighboring gene ribosomal protein L29 pseudogene 30 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:71145885-71146386 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71163033-71163588 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71163589-71164146 Neighboring gene La ribonucleoprotein 6, translational regulator Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9701 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:71170236-71170412 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71184427-71185125 Neighboring gene keratin 8 pseudogene 9 Neighboring gene THAP domain containing 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71281950-71282450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:71282451-71282951 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:71315600-71316198 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr15:71364462-71365661 Neighboring gene uncharacterized LOC105370886 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr15:71377897-71378512 Neighboring gene ribosomal protein L5 pseudogene 3

    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. Silencing of LRRC49 and THAP10 genes by bidirectional promoter hypermethylation is a frequent event in breast cancer. De Souza Santos E, et al. Int J Oncol, 2008 Jul. PMID 18575747
    2. Regulators of tubulin polyglutamylation control nuclear shape and cilium disassembly by balancing microtubule and actin assembly. Wang L, et al. Cell Res, 2022 Feb. PMID 34782749, Free PMC Article
    3. Tubulin polyglutamylase enzymes are members of the TTL domain protein family. Janke C, et al. Science, 2005 Jun 17. PMID 15890843
    4. The MYO6 interactome reveals adaptor complexes coordinating early endosome and cytoskeletal dynamics. O'Loughlin T, et al. EMBO Rep, 2018 Apr. PMID 29467281, Free PMC Article
    5. Proximity interactions of the ubiquitin ligase Mind bomb 1 reveal a role in regulation of epithelial polarity complex proteins. Dho SE, et al. Sci Rep, 2019 Aug 28. PMID 31462741, Free PMC Article

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20156

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in centriolar satellite IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in microtubule IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat-containing protein 49
    Names
    centriolar satellite-associated tubulin polyglutamylase complex regulator 2
    centriolar satellite-associated tubulin polyglutamylation protein 2
    polyglutamylase subunit 4
    tubulin polyglutamylase complex subunit 4

    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_001199017.3 → NP_001185946.1  leucine-rich repeat-containing protein 49 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC013752, AC084703, AC090868
      Consensus CDS
      CCDS58376.1
      UniProtKB/TrEMBL
      B7Z7G0
      Related
      ENSP00000453273.1, ENST00000560369.5
      Conserved Domains (3) summary
      sd00033
      Location:119 → 140
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:163 → 203
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:206 → 261
      LRR_8; Leucine rich repeat

    2. NM_001199018.3 → NP_001185947.1  leucine-rich repeat-containing protein 49 isoform 3

      See identical proteins and their annotated locations for NP_001185947.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site and contains an alternate exon in the 5' region, 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)
      AC013752, AC084703, AC090868
      Consensus CDS
      CCDS55971.1
      UniProtKB/TrEMBL
      B7Z7G0
      Related
      ENSP00000414065.2, ENST00000443425.6
      Conserved Domains (3) summary
      sd00033
      Location:70 → 91
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:114 → 154
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:157 → 212
      LRR_8; Leucine rich repeat

    3. NM_001284357.2 → NP_001271286.1  leucine-rich repeat-containing protein 49 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and contains multiple differences in the 5' coding region, compared to variant 1, including initiation of translation at an alternate start codon. The encoded isoform (4) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC013752, AC084703, AC090868
      Consensus CDS
      CCDS61694.1
      UniProtKB/TrEMBL
      B7Z7G0
      Related
      ENSP00000439600.2, ENST00000544974.6
      Conserved Domains (3) summary
      sd00033
      Location:104 → 125
      LRR_RI; leucine-rich repeat [structural motif]
      pfam12799
      Location:148 → 188
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:191 → 246
      LRR_8; Leucine rich repeat

    4. NM_001363732.2 → NP_001350661.1  leucine-rich repeat-containing protein 49 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC013752, AC084703, AC090868
      Consensus CDS
      CCDS86472.1
      UniProtKB/TrEMBL
      H0YKE9, H0YNV5
      Related
      ENSP00000454170.1, ENST00000560691.5

    5. NM_017691.5 → NP_060161.2  leucine-rich repeat-containing protein 49 isoform 2

      See identical proteins and their annotated locations for NP_060161.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
      Source sequence(s)
      AC013752, AC084703, AC090868
      Consensus CDS
      CCDS32282.1
      UniProtKB/Swiss-Prot
      B3KVX1, B7Z366, F5H1J4, G5E9T5, H0YLN4, Q8IUZ0, Q9NXM6
      UniProtKB/TrEMBL
      B7Z7G0
      Related
      ENSP00000260382.4, ENST00000260382.10
      Conserved Domains (2) summary
      sd00033
      Location:114 → 135
      LRR_RI; leucine-rich repeat [structural motif]
      NF033189
      Location:69 → 275
      internalin_A; class 1 internalin InlA

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      70853378..71053658
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      68676342..68876951
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IUZ0.2 GenPept UniProtKB/Swiss-Prot:Q8IUZ0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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