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LRFN2 leucine rich repeat and fibronectin type III domain containing 2 [ Homo sapiens (human) ]

Gene ID: 57497, updated on 24-Nov-2022

Summary

Official Symbol
LRFN2provided by HGNC
Official Full Name
leucine rich repeat and fibronectin type III domain containing 2provided by HGNC
Primary source
HGNC:HGNC:21226
See related
Ensembl:ENSG00000156564 MIM:612808; AllianceGenome:HGNC:21226
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SALM1; FIGLER2; KIAA1246
Summary
Predicted to be involved in modulation of chemical synaptic transmission and regulation of postsynapse organization. Predicted to be located in plasma membrane. Predicted to be active in Schaffer collateral - CA1 synapse and cell surface. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Low expression observed in reference dataset See more
Orthologs
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Genomic context

See LRFN2 in Genome Data Viewer
Location:
6p21.2-p21.1
Exon count:
8
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (40391591..40587364, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (40219487..40415195, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (40359330..40555103, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9486 Neighboring gene testis development related 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:40387157-40387792 Neighboring gene RNA, U6 small nuclear 250, pseudogene Neighboring gene uncharacterized LOC105375051 Neighboring gene Sharpr-MPRA regulatory region 9042 Neighboring gene uncharacterized LOC101929535 Neighboring gene uncharacterized LOC105375052

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?

Phenotypes

EBI GWAS Catalog

Description
A genome-wide association meta-analysis identifies a novel locus at 17q11.2 associated with sporadic amyotrophic lateral sclerosis.
EBI GWAS Catalog
Genetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in modulation of chemical synaptic transmission IEA
Inferred from Electronic Annotation
more info
 
involved_in regulation of postsynapse organization IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in Schaffer collateral - CA1 synapse IEA
Inferred from Electronic Annotation
more info
 
is_active_in cell surface IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
is_active_in postsynaptic density membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in presynapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
leucine-rich repeat and fibronectin type-III domain-containing protein 2
Names
fibronectin type III, immunoglobulin and leucine rich repeat domains 2
synaptic adhesion-like molecule 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_020737.3NP_065788.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 precursor

    See identical proteins and their annotated locations for NP_065788.1

    Status: VALIDATED

    Source sequence(s)
    AB033072, AK291474, AL591063
    Consensus CDS
    CCDS34443.1
    UniProtKB/Swiss-Prot
    Q5SYP9, Q9ULH4
    Related
    ENSP00000345985.6, ENST00000338305.7
    Conserved Domains (5) summary
    smart00082
    Location:242286
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:5477
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:420493
    fn3; Fibronectin type III domain
    pfam13855
    Location:76136
    LRR_8; Leucine rich repeat
    cl11960
    Location:303376
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    40391591..40587364 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514761.3XP_011513063.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011513063.1

    UniProtKB/Swiss-Prot
    Q5SYP9, Q9ULH4
    Conserved Domains (5) summary
    smart00082
    Location:242286
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:5477
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:420493
    fn3; Fibronectin type III domain
    pfam13855
    Location:76136
    LRR_8; Leucine rich repeat
    cl11960
    Location:303376
    Ig; Immunoglobulin domain
  2. XM_011514762.3XP_011513064.1  leucine-rich repeat and fibronectin type-III domain-containing protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011513064.1

    UniProtKB/Swiss-Prot
    Q5SYP9, Q9ULH4
    Conserved Domains (5) summary
    smart00082
    Location:242286
    LRRCT; Leucine rich repeat C-terminal domain
    sd00033
    Location:5477
    LRR_RI; leucine-rich repeat [structural motif]
    pfam00041
    Location:420493
    fn3; Fibronectin type III domain
    pfam13855
    Location:76136
    LRR_8; Leucine rich repeat
    cl11960
    Location:303376
    Ig; Immunoglobulin domain

RNA

  1. XR_001743535.2 RNA Sequence

    Related
    ENST00000648418.1
  2. XR_007059281.1 RNA Sequence

  3. XR_926282.3 RNA Sequence

    Related
    ENST00000659707.1
  4. XR_926281.3 RNA Sequence

  5. XR_007059280.1 RNA Sequence

    Related
    ENST00000442781.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    40219487..40415195 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)