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

    Gene ID: 360779, updated on 6-Jun-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
    Ensembl: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 act upstream of or within negative regulation of transcription, DNA-templated. Predicted to be located in cytoplasm. 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, Apr 2022]
    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
    • 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
      ENSRNOP00000001899.5, ENSRNOT00000001899.6
      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
      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

      UniProtKB/TrEMBL
      E9PSW6

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

      UniProtKB/TrEMBL
      E9PSW6

    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

      UniProtKB/TrEMBL
      E9PSW6

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

      UniProtKB/TrEMBL
      E9PSW6

    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

      UniProtKB/TrEMBL
      E9PSW6

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

      UniProtKB/TrEMBL
      E9PSW6

    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, E9PSW6

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

      UniProtKB/TrEMBL
      E9PSW6
      Related
      ENSRNOP00000095598.1
      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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