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Lrch4 leucine rich repeats and calponin homology domain containing 4 [ Rattus norvegicus (Norway rat) ]

Gene ID: 360779, updated on 2-Nov-2024

Summary

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Official Symbol
Lrch4provided by RGD
Official Full Name
leucine rich repeats and calponin homology domain containing 4provided by RGD
Primary source
RGD:1306145
See related
EnsemblRapid:ENSRNOG00000001402 AllianceGenome:RGD:1306145
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to be involved in membrane raft assembly and positive regulation of toll-like receptor signaling pathway. Predicted to be located in plasma membrane. Predicted to be active in PML body. Orthologous to human LRCH4 (leucine rich repeats and calponin homology domain containing 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Thymus (RPKM 114.1), Spleen (RPKM 90.4) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Lrch4 in Genome Data Viewer
Location:
12q12
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 12 NC_086030.1 (24694364..24709354, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 12 NC_051347.1 (19057582..19072573, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 12 NC_005111.4 (22127387..22138436, complement)

Chromosome 12 - NC_086030.1Genomic Context describing neighboring genes Neighboring gene ArfGAP with FG repeats 2 Neighboring gene insulin receptor substrate 3 Neighboring gene Sin3A-associated protein 25 Neighboring gene F-box protein 24 Neighboring gene procollagen C-endopeptidase enhancer

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Identification and characterization of SAP25, a novel component of the mSin3 corepressor complex. Shiio Y, et al. Mol Cell Biol, 2006 Feb. PMID 16449650, Free PMC Article
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by RGD

Process Evidence Code Pubs
involved_in membrane raft assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of toll-like receptor signaling pathway ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
is_active_in PML body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in PML body ISO
Inferred from Sequence Orthology
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
leucine-rich repeat and calponin homology domain-containing protein 4
Names
leucine-rich repeats and calponin homology (CH) domain containing 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_001127551.1 → NP_001121023.1  leucine-rich repeat and calponin homology domain-containing protein 4

    See identical proteins and their annotated locations for NP_001121023.1

    Status: PROVISIONAL

    Source sequence(s)
    BC166781
    UniProtKB/TrEMBL
    B2RYH6, E9PSW6
    Related
    ENSRNOP00000001899.6, ENSRNOT00000001899.7
    Conserved Domains (6) summary
    cd00116
    Location:103 → 245
    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:46 → 69
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00307
    Location:539 → 630
    CH; Calponin homology (CH) domain
    pfam02377
    Location:265 → 408
    Dishevelled; Dishevelled specific domain
    pfam12799
    Location:92 → 131
    LRR_4; Leucine Rich repeats (2 copies)
    pfam13855
    Location:138 → 194
    LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

  1. NC_086030.1 Reference GRCr8

    Range
    24694364..24709354 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_063271483.1 → XP_063127553.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X15

  2. XM_006249175.5 → XP_006249237.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X3

    See identical proteins and their annotated locations for XP_006249237.1

    UniProtKB/TrEMBL
    A6J009, E9PSW6
    Related
    ENSRNOP00000093054.2, ENSRNOT00000115724.2
    Conserved Domains (4) summary
    COG4886
    Location:74 → 255
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    PRK10263
    Location:332 → 496
    PRK10263; DNA translocase FtsK; Provisional
    sd00033
    Location:46 → 69
    LRR_RI; leucine-rich repeat [structural motif]
    cd21273
    Location:535 → 641
    CH_LRCH4; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 4

  3. XM_039089579.2 → XP_038945507.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X4

    UniProtKB/TrEMBL
    E9PSW6
    Conserved Domains (4) summary
    PRK15370
    Location:46 → 273
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    PHA03247
    Location:259 → 486
    PHA03247; large tegument protein UL36; Provisional
    sd00033
    Location:46 → 72
    LRR_RI; leucine-rich repeat [structural motif]
    cd21273
    Location:527 → 633
    CH_LRCH4; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 4

  4. XM_039089578.2 → XP_038945506.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X2

    UniProtKB/TrEMBL
    E9PSW6
    Conserved Domains (4) summary
    COG4886
    Location:25 → 264
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    PRK10263
    Location:341 → 505
    PRK10263; DNA translocase FtsK; Provisional
    sd00033
    Location:46 → 72
    LRR_RI; leucine-rich repeat [structural motif]
    cd21273
    Location:544 → 650
    CH_LRCH4; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 4

  5. XM_039089577.2 → XP_038945505.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X1

    UniProtKB/TrEMBL
    E9PSW6
    Conserved Domains (4) summary
    PHA03247
    Location:280 → 507
    PHA03247; large tegument protein UL36; Provisional
    COG4886
    Location:25 → 264
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:46 → 72
    LRR_RI; leucine-rich repeat [structural motif]
    cd21273
    Location:548 → 654
    CH_LRCH4; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 4

  6. XM_063271476.1 → XP_063127546.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X7

  7. XM_063271475.1 → XP_063127545.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X5

  8. XM_017598386.3 → XP_017453875.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X10

    UniProtKB/TrEMBL
    E9PSW6

  9. XM_063271478.1 → XP_063127548.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X9

  10. XM_063271477.1 → XP_063127547.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X8

  11. XM_039089580.2 → XP_038945508.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X6

    UniProtKB/TrEMBL
    E9PSW6
    Conserved Domains (4) summary
    PHA03247
    Location:280 → 507
    PHA03247; large tegument protein UL36; Provisional
    COG4886
    Location:25 → 264
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:46 → 72
    LRR_RI; leucine-rich repeat [structural motif]
    cd21205
    Location:551 → 662
    CH_LRCH; calponin homology (CH) domain found in the leucine-rich repeat and calponin homology domain-containing protein family

  12. XM_063271480.1 → XP_063127550.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X13

  13. XM_063271479.1 → XP_063127549.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X11

  14. XM_063271482.1 → XP_063127552.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X15

  15. XM_063271481.1 → XP_063127551.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X14

    UniProtKB/TrEMBL
    A0A8I6APG5

  16. XM_039089581.2 → XP_038945509.1  leucine-rich repeat and calponin homology domain-containing protein 4 isoform X12

    UniProtKB/TrEMBL
    E9PSW6
    Related
    ENSRNOP00000095598.2, ENSRNOT00000094748.2
    Conserved Domains (4) summary
    PHA03247
    Location:217 → 444
    PHA03247; large tegument protein UL36; Provisional
    COG4886
    Location:20 → 201
    LRR; Leucine-rich repeat (LRR) protein [Transcription]
    sd00033
    Location:39 → 61
    LRR_RI; leucine-rich repeat [structural motif]
    cd21273
    Location:485 → 591
    CH_LRCH4; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 4
Nucleotide Protein Strain
Heading Accession and Version

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