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

Gene ID: 54839, updated on 2-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
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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 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)

Genotypes

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

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