U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    Lrfn1 leucine rich repeat and fibronectin type III domain containing 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 365222, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Symbol
    Lrfn1provided by RGD
    Full Name
    leucine rich repeat and fibronectin type III domain containing 1provided by RGD
    Primary source
    RGD:1304707
    See related
    EnsemblRapid:ENSRNOG00000019869 AllianceGenome:RGD:1304707
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Involved in regulation of postsynaptic density assembly. Is active in postsynaptic density membrane. Orthologous to human LRFN1 (leucine rich repeat and fibronectin type III domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Adrenal (RPKM 17.0), Brain (RPKM 9.6) and 6 other tissues See more
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See Lrfn1 in Genome Data Viewer
    Location:
    1q21
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (92866864..92888984)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (83742442..83761450)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (85290887..85308498, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene sterile alpha motif domain containing 4B Neighboring gene glia maturation factor, gamma Neighboring gene interferon, lambda 1 Neighboring gene interferon, lambda 3

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. SALM synaptic cell adhesion-like molecules regulate the differentiation of excitatory synapses. Ko J, et al. Neuron, 2006 Apr 20. PMID 16630835
    2. Comparative analysis of structure, expression and PSD95-binding capacity of Lrfn, a novel family of neuronal transmembrane proteins. Morimura N, et al. Gene, 2006 Oct 1. PMID 16828986
    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

    Pathways from PubChem

    Go to the top of the page

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by RGD

    Process Evidence Code Pubs
    involved_in regulation of postsynaptic density assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of postsynaptic density assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in postsynaptic density membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in postsynaptic density membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

    Go to the top of the page Help
    Preferred Names
    leucine-rich repeat and fibronectin type III domain-containing protein 1
    Names
    60S ribosomal protein L38-like
    synaptic adhesion-like molecule 2

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001127694.2 → NP_001121166.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 precursor

      See identical proteins and their annotated locations for NP_001121166.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    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_086019.1 Reference GRCr8

      Range
      92866864..92888984
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_008759174.4 → XP_008757396.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_008757396.1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    2. XM_017589472.3 → XP_017444961.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    3. XM_039084971.2 → XP_038940899.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    4. XM_017589473.3 → XP_017444962.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    5. XM_039084968.2 → XP_038940896.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P0C7J6
      Related
      ENSRNOP00000053905.2, ENSRNOT00000057073.7
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    6. XM_039084965.2 → XP_038940893.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    7. XM_039084966.2 → XP_038940894.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    8. XM_039084973.2 → XP_038940901.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    9. XM_006228628.5 → XP_006228690.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006228690.1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    10. XM_039084975.2 → XP_038940903.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    11. XM_017589471.3 → XP_017444960.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    12. XM_006228626.5 → XP_006228688.1  leucine-rich repeat and fibronectin type III domain-containing protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006228688.1

      UniProtKB/Swiss-Prot
      P0C7J6
      Conserved Domains (6) summary
      smart00082
      Location:252 → 284
      LRRCT; Leucine rich repeat C-terminal domain
      cd00063
      Location:426 → 500
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      sd00033
      Location:67 → 90
      LRR_RI; leucine-rich repeat [structural motif]
      cd00096
      Location:299 → 302
      Ig; Ig strand A [structural motif]
      cd21340
      Location:70 → 226
      PPP1R42; protein phosphatase 1 regulatory subunit 42
      cl11960
      Location:299 → 387
      Ig; Immunoglobulin domain

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001108910.1: Suppressed sequence

      Description
      NM_001108910.1: This RefSeq was removed because there is insufficient support for the transcript and protein.
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0C7J6.1 GenPept UniProtKB/Swiss-Prot:P0C7J6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous