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Lrch1 leucine-rich repeats and calponin homology (CH) domain containing 1 [ Mus musculus (house mouse) ]

Gene ID: 380916, updated on 2-Nov-2024

Summary

Official Symbol
Lrch1provided by MGI
Official Full Name
leucine-rich repeats and calponin homology (CH) domain containing 1provided by MGI
Primary source
MGI:MGI:2443390
See related
Ensembl:ENSMUSG00000068015 AllianceGenome:MGI:2443390
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
Chdc1; mKIAA1016; 4832412D13Rik
Summary
Involved in cellular response to chemokine; negative regulation of GTPase activity; and negative regulation of T cell migration. Predicted to be active in cytoplasm. Is expressed in several structures, including cardiovascular system; central nervous system; genitourinary system; gut; and hemolymphoid system gland. Used to study multiple sclerosis. Orthologous to human LRCH1 (leucine rich repeats and calponin homology domain containing 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in bladder adult (RPKM 4.8), lung adult (RPKM 4.8) and 28 other tissues See more
Orthologs
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Genomic context

See Lrch1 in Genome Data Viewer
Location:
14 D3; 14 39.39 cM
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 14 NC_000080.7 (74992113..75185447, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 14 NC_000080.6 (74754673..74948007, complement)

Chromosome 14 - NC_000080.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E5454 Neighboring gene tubulin, alpha 1C pseudogene Neighboring gene esterase D/formylglutathione hydrolase Neighboring gene STARR-positive B cell enhancer ABC_E5455 Neighboring gene predicted gene, 52135 Neighboring gene STARR-positive B cell enhancer ABC_E9901 Neighboring gene STARR-positive B cell enhancer ABC_E8571 Neighboring gene predicted gene 10847 Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:75346402-75346511 Neighboring gene CapStarr-seq enhancer MGSCv37_chr14:75346543-75346730 Neighboring gene STARR-positive B cell enhancer ABC_E5456 Neighboring gene STARR-seq mESC enhancer starr_37134 Neighboring gene predicted gene 4278 Neighboring gene STARR-positive B cell enhancer ABC_E10834 Neighboring gene STARR-positive B cell enhancer ABC_E757 Neighboring gene RUN and cysteine rich domain containing beclin 1 interacting protein like Neighboring gene predicted gene, 57618

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1)  1 citation
  • Targeted (2) 

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
involved_in cellular response to chemokine IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in cellular response to chemokine IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cellular response to chemokine ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of GTPase activity IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of GTPase activity ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of T cell migration IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in negative regulation of T cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in negative regulation of T cell migration ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 

General protein information

Preferred Names
leucine-rich repeat and calponin homology domain-containing protein 1

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_001033439.3NP_001028611.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001028611.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC135083, AC154621, BB612742, BC028469
    Consensus CDS
    CCDS36976.1
    UniProtKB/Swiss-Prot
    E9QLJ4, P62046
    UniProtKB/TrEMBL
    Q3UP01
    Related
    ENSMUSP00000086363.6, ENSMUST00000088970.7
    Conserved Domains (4) summary
    cd00116
    Location:106220
    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:6688
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00307
    Location:591698
    CH; Calponin homology (CH) domain
    pfam13855
    Location:178258
    LRR_8; Leucine rich repeat
  2. NM_001252132.1NP_001239061.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 3' coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    AK143909, AK160965, BB612742, BC028469
    Consensus CDS
    CCDS88714.1
    UniProtKB/TrEMBL
    A0A2I3BQ16, Q3UP01
    Related
    ENSMUSP00000154004.2, ENSMUST00000228252.2
    Conserved Domains (4) summary
    cd00116
    Location:106220
    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:6688
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00307
    Location:564671
    CH; Calponin homology (CH) domain
    pfam13855
    Location:178258
    LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000080.7 Reference GRCm39 C57BL/6J

    Range
    74992113..75185447 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017316067.2XP_017171556.2  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X6

    UniProtKB/TrEMBL
    Q3UP01
    Conserved Domains (4) summary
    PRK15370
    Location:162365
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    smart00033
    Location:702807
    CH; Calponin homology domain
    sd00031
    Location:376387
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:167189
    LRR_RI; leucine-rich repeat [structural motif]
  2. XM_006519156.3XP_006519219.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X4

    UniProtKB/TrEMBL
    Q3UP01
    Conserved Domains (4) summary
    PRK15370
    Location:162365
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    smart00033
    Location:729834
    CH; Calponin homology domain
    sd00031
    Location:376387
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:167189
    LRR_RI; leucine-rich repeat [structural motif]
  3. XM_036158691.1XP_036014584.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X8

    UniProtKB/TrEMBL
    Q3UP01
    Conserved Domains (5) summary
    PRK15370
    Location:162365
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    COG5271
    Location:402655
    MDN1; Midasin, AAA ATPase with vWA domain, involved in ribosome maturation [Translation, ribosomal structure and biogenesis]
    sd00031
    Location:376387
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:167189
    LRR_RI; leucine-rich repeat [structural motif]
    cd21270
    Location:635746
    CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1
  4. XM_036158690.1XP_036014583.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X3

    UniProtKB/TrEMBL
    Q3UP01
    Conserved Domains (4) summary
    PRK15370
    Location:162365
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00031
    Location:376387
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:167189
    LRR_RI; leucine-rich repeat [structural motif]
    cd21270
    Location:697808
    CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1
  5. XM_006519158.4XP_006519221.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X7

    UniProtKB/TrEMBL
    Q3UP01
    Conserved Domains (4) summary
    PRK15370
    Location:162365
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    smart00033
    Location:667756
    CH; Calponin homology domain
    sd00031
    Location:376387
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:167189
    LRR_RI; leucine-rich repeat [structural motif]
  6. XM_006519155.4XP_006519218.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    Q3UP01
    Conserved Domains (4) summary
    PRK15370
    Location:162365
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    smart00033
    Location:702791
    CH; Calponin homology domain
    sd00031
    Location:376387
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:167189
    LRR_RI; leucine-rich repeat [structural motif]
  7. XM_006519157.4XP_006519220.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X5

    UniProtKB/TrEMBL
    Q3UP01
    Conserved Domains (4) summary
    PRK15370
    Location:162365
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    smart00033
    Location:694783
    CH; Calponin homology domain
    sd00031
    Location:376387
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:167189
    LRR_RI; leucine-rich repeat [structural motif]
  8. XM_006519154.4XP_006519217.3  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    Q3UP01
    Conserved Domains (4) summary
    PRK15370
    Location:162365
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    smart00033
    Location:729818
    CH; Calponin homology domain
    sd00031
    Location:376387
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:167189
    LRR_RI; leucine-rich repeat [structural motif]
  9. XM_036158693.1XP_036014586.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X10

    Conserved Domains (1) summary
    cd21270
    Location:382493
    CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1
  10. XM_036158692.1XP_036014585.1  leucine-rich repeat and calponin homology domain-containing protein 1 isoform X9

    Conserved Domains (3) summary
    sd00031
    Location:222
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:178
    LRR_8; Leucine rich repeat
    cd21270
    Location:446557
    CH_LRCH1; calponin homology (CH) domain found in leucine-rich repeat and calponin homology domain-containing protein 1

RNA

  1. XR_001781129.2 RNA Sequence