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LRRC6 leucine rich repeat containing 6 [ Homo sapiens (human) ]

Gene ID: 23639, updated on 7-Jun-2020

Summary

Official Symbol
LRRC6provided by HGNC
Official Full Name
leucine rich repeat containing 6provided by HGNC
Primary source
HGNC:HGNC:16725
See related
Ensembl:ENSG00000129295 MIM:614930
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
LRTP; tilB; TSLRP; CILD19
Summary
The protein encoded by this gene contains several leucine-rich repeat domains and appears to be involved in the motility of cilia. Defects in this gene are a cause of primary ciliary dyskinesia-19 (CILD19). Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 4, 11 and 22. [provided by RefSeq, Apr 2016]
Expression
Broad expression in testis (RPKM 4.7), kidney (RPKM 2.2) and 17 other tissues See more
Orthologs

Genomic context

See LRRC6 in Genome Data Viewer
Location:
8q24.22
Exon count:
17
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (132570416..132685039, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (133584201..133687863, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375765 Neighboring gene Helicobacter pylori responsive 1 Neighboring gene uncharacterized LOC105375767 Neighboring gene transmembrane protein 71 Neighboring gene PHD finger protein 20 like 1 Neighboring gene thyroglobulin Neighboring gene ribosomal protein L21 pseudogene 78

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
molecular_function ND
No biological Data available
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cerebrospinal fluid circulation IEA
Inferred from Electronic Annotation
more info
 
cilium movement IMP
Inferred from Mutant Phenotype
more info
PubMed 
epithelial cilium movement involved in determination of left/right asymmetry IMP
Inferred from Mutant Phenotype
more info
PubMed 
flagellated sperm motility IMP
Inferred from Mutant Phenotype
more info
PubMed 
inner dynein arm assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
male gonad development ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
motile cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
outer dynein arm assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to cilium IEA
Inferred from Electronic Annotation
more info
 
regulation of protein binding IEA
Inferred from Electronic Annotation
more info
 
reproductive system development IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
apical cytoplasm IEA
Inferred from Electronic Annotation
more info
 
cilium IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
extracellular region IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
protein tilB homolog
Names
protein TILB homolog
seahorse
testis-specific leucine-rich repeat protein

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_033068.1 RefSeqGene

    Range
    5073..110200
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001321961.2NP_001308890.1  protein tilB homolog isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AF216667, AL041128, BC047286, BM981867, CA426602, DA570320
    UniProtKB/Swiss-Prot
    Q86X45
    Conserved Domains (5) summary
    smart00446
    Location:128146
    LRRcap; occurring C-terminal to leucine-rich repeats
    cd00116
    Location:20194
    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 ...
    sd00031
    Location:4667
    LRR_1; leucine-rich repeat [structural motif]
    pfam12799
    Location:4686
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:4698
    LRR_8; Leucine rich repeat
  2. NM_001321962.2NP_001308891.1  protein tilB homolog isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) lacks two alternate in-frame exons in the 5' coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform a.
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA310108, DA570320
    UniProtKB/Swiss-Prot
    Q86X45
    Conserved Domains (1) summary
    smart00446
    Location:4664
    LRRcap; occurring C-terminal to leucine-rich repeats
  3. NM_001321963.2NP_001308892.1  protein tilB homolog isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) contains an alternate 5' terminal exon, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a. Variants 5, 6 and 7 all encode isoform d.
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA570320
    UniProtKB/Swiss-Prot
    Q86X45
    Conserved Domains (1) summary
    smart00446
    Location:826
    LRRcap; occurring C-terminal to leucine-rich repeats
  4. NM_001321964.2NP_001308893.1  protein tilB homolog isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) contains an alternate 5' terminal exon, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a. Variants 5, 6 and 7 all encode isoform d.
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA570320
    UniProtKB/Swiss-Prot
    Q86X45
    Conserved Domains (1) summary
    smart00446
    Location:826
    LRRcap; occurring C-terminal to leucine-rich repeats
  5. NM_001321965.2NP_001308894.1  protein tilB homolog isoform d

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) contains an alternate 5' terminal exon and lacks an alternate exon in the 5' region, and it thus differs in its 5' UTR and initiates translation from an downstream in-frame start codon, compared to variant 1. The encoded isoform (d) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA570320, DR002710
    UniProtKB/Swiss-Prot
    Q86X45
    Conserved Domains (1) summary
    smart00446
    Location:826
    LRRcap; occurring C-terminal to leucine-rich repeats
  6. NM_001321966.2NP_001308895.1  protein tilB homolog isoform e

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) contains an alternate 5' terminal exon, and it thus differs in its 5' UTR and initiates translation from a downstream in-frame start codon, and it also lacks an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (e) is shorter at the N-terminus, compared to isoform a.
    Source sequence(s)
    AF216667, AL041128, BC047286, BM981867, CA426602, DA359044, DA570320
    UniProtKB/Swiss-Prot
    Q86X45
    Conserved Domains (2) summary
    cd00298
    Location:192240
    ACD_sHsps_p23-like; This domain family includes the alpha-crystallin domain (ACD) of alpha-crystallin-type small heat shock proteins (sHsps) and a similar domain found in p23-like proteins. sHsps are small stress induced proteins with monomeric masses between 12 -43 kDa, ...
    smart00446
    Location:826
    LRRcap; occurring C-terminal to leucine-rich repeats
  7. NM_012472.6NP_036604.2  protein tilB homolog isoform a

    See identical proteins and their annotated locations for NP_036604.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (a).
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA570320
    Consensus CDS
    CCDS6365.1
    UniProtKB/Swiss-Prot
    Q86X45
    Related
    ENSP00000484634.1, ENST00000620350.5
    Conserved Domains (2) summary
    sd00031
    Location:4667
    LRR_1; leucine-rich repeat [structural motif]
    pfam14580
    Location:1163
    LRR_9; Leucine-rich repeat

RNA

  1. NR_073525.3 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site and includes an additional exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, BC027589, BC047286, BM981867, CA426602, DA570320
  2. NR_135905.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (9) contains an additional internal exon but lacks a different internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA570320, DR002710
  3. NR_135906.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (10) lacks three internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA310108, DA570320, DA789153
  4. NR_135907.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (11) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, BC047286, BM981867, BU674822, CA426602, DA570320
  5. NR_135908.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12) lacks four internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, AL041128, BC047286, BM981867, CA426602, DA310108, DA570320, DA789153
  6. NR_135909.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (13) contains an alternate 5' terminal exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, BC047286, BM981867, BU674822, CA426602, DA359044, DA570320
  7. NR_135910.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (14) contains an alternate 5' terminal exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, which is in-frame with the coding sequence of variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, BC047286, BM981867, BU674822, CA426602, DA570320
  8. NR_135911.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (15) contains an alternate 5' terminal exon and lacks three internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, which is in-frame with the coding sequence of variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA570320, DA789153
  9. NR_135912.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (16) contains an alternate 5' terminal exon and lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, which is in-frame with the coding sequence of variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA570320, DA789153, DR002710
  10. NR_135913.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (17) contains an alternate 5' terminal exon and lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, which is in-frame with the coding sequence of variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AF216667, BC047286, BM981867, CA426602, DA570320, DA789153, DR002710

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    132570416..132685039 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011516950.2XP_011515252.1  protein tilB homolog isoform X2

    Conserved Domains (5) summary
    smart00446
    Location:134152
    LRRcap; occurring C-terminal to leucine-rich repeats
    cd00116
    Location:5200
    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 ...
    sd00031
    Location:5273
    LRR_1; leucine-rich repeat [structural motif]
    pfam12799
    Location:5292
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:52104
    LRR_8; Leucine rich repeat
  2. XM_006716538.3XP_006716601.2  protein tilB homolog isoform X1

    Conserved Domains (5) summary
    smart00446
    Location:134152
    LRRcap; occurring C-terminal to leucine-rich repeats
    cd00116
    Location:5200
    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 ...
    sd00031
    Location:5273
    LRR_1; leucine-rich repeat [structural motif]
    pfam12799
    Location:5292
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:52104
    LRR_8; Leucine rich repeat
  3. XM_017013298.1XP_016868787.1  protein tilB homolog isoform X4

    Conserved Domains (1) summary
    smart00446
    Location:826
    LRRcap; occurring C-terminal to leucine-rich repeats
  4. XM_017013297.1XP_016868786.1  protein tilB homolog isoform X4

    Conserved Domains (1) summary
    smart00446
    Location:826
    LRRcap; occurring C-terminal to leucine-rich repeats
  5. XM_017013296.1XP_016868785.1  protein tilB homolog isoform X3

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