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    RFTN1 raftlin, lipid raft linker 1 [ Homo sapiens (human) ]

    Gene ID: 23180, updated on 3-Dec-2024

    Summary

    Official Symbol
    RFTN1provided by HGNC
    Official Full Name
    raftlin, lipid raft linker 1provided by HGNC
    Primary source
    HGNC:HGNC:30278
    See related
    Ensembl:ENSG00000131378 MIM:618210; AllianceGenome:HGNC:30278
    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
    MIG2; PIG9; PIB10; RAFTLIN
    Summary
    Enables double-stranded RNA binding activity. Involved in B cell receptor signaling pathway; membrane raft assembly; and positive regulation of growth rate. Acts upstream of or within dsRNA transport; response to exogenous dsRNA; and toll-like receptor 3 signaling pathway. Located in endosome; membrane raft; and plasma membrane. Part of protein-containing complex. Biomarker of glaucoma. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in lymph node (RPKM 35.0), fat (RPKM 23.7) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See RFTN1 in Genome Data Viewer
    Location:
    3p24.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (16315845..16513699, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (16317057..16514836, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (16357352..16555206, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14113 Neighboring gene oxidoreductase NAD binding domain containing 1 Neighboring gene uncharacterized LOC107986065 Neighboring gene THAP domain containing 5 pseudogene 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14114 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16343021-16343602 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16343603-16344182 Neighboring gene Sharpr-MPRA regulatory region 2856 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:16377723-16378222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19541 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14116 Neighboring gene uncharacterized LOC124906220 Neighboring gene NANOG hESC enhancer GRCh37_chr3:16497386-16497905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19544 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19545 Neighboring gene uncharacterized LOC124906219 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16524187-16525039 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19546 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19547 Neighboring gene NANOG hESC enhancer GRCh37_chr3:16539919-16540420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19548 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19549 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19550 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14118 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14117 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19551 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:16556589-16556764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16557992-16558492 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:16558493-16558993 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19552 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:16577170-16577365 Neighboring gene long intergenic non-protein coding RNA 690 Neighboring gene deleted in azoospermia like

    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
    Common body mass index-associated variants confer risk of extreme obesity.
    EBI GWAS Catalog
    Genome-wide association identifies ATOH7 as a major gene determining human optic disc size.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ23866, KIAA0084, MGC44480, MGC141678

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables double-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in B cell receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in T cell antigen processing and presentation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in T cell receptor signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within dsRNA transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in membrane raft assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of growth rate IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of interleukin-17 production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein localization to membrane raft ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein transport into membrane raft ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within response to exogenous dsRNA IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within toll-like receptor 3 signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    raftlin
    Names
    cell migration-inducing gene 2 protein
    proliferation-inducing protein 10
    proliferation-inducing protein 9
    raft-linking protein

    NCBI Reference Sequences (RefSeq)

    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_015150.2NP_055965.1  raftlin

      See identical proteins and their annotated locations for NP_055965.1

      Status: VALIDATED

      Source sequence(s)
      AU138240, BC032349, D42043
      Consensus CDS
      CCDS33712.1
      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
      Related
      ENSP00000334153.4, ENST00000334133.9
      Conserved Domains (1) summary
      pfam15250
      Location:1471
      Raftlin; Raftlin

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      16315845..16513699 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017006007.3XP_016861496.1  raftlin isoform X4

    2. XM_047447783.1XP_047303739.1  raftlin isoform X4

    3. XM_005264985.2XP_005265042.1  raftlin isoform X2

      See identical proteins and their annotated locations for XP_005265042.1

      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
      Conserved Domains (1) summary
      pfam15250
      Location:1471
      Raftlin; Raftlin
    4. XM_011533530.2XP_011531832.1  raftlin isoform X2

      See identical proteins and their annotated locations for XP_011531832.1

      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
      Conserved Domains (1) summary
      pfam15250
      Location:1471
      Raftlin; Raftlin
    5. XM_047447780.1XP_047303736.1  raftlin isoform X2

      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
    6. XM_005264986.3XP_005265043.1  raftlin isoform X2

      See identical proteins and their annotated locations for XP_005265043.1

      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
      Related
      ENSP00000403926.1, ENST00000432519.5
      Conserved Domains (1) summary
      pfam15250
      Location:1471
      Raftlin; Raftlin
    7. XM_006713069.2XP_006713132.1  raftlin isoform X2

      See identical proteins and their annotated locations for XP_006713132.1

      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
      Conserved Domains (1) summary
      pfam15250
      Location:1471
      Raftlin; Raftlin
    8. XM_047447781.1XP_047303737.1  raftlin isoform X3

    9. XM_047447779.1XP_047303735.1  raftlin isoform X1

      UniProtKB/TrEMBL
      G3XAJ6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      16317057..16514836 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345829.1XP_054201804.1  raftlin isoform X4

    2. XM_054345830.1XP_054201805.1  raftlin isoform X4

    3. XM_054345824.1XP_054201799.1  raftlin isoform X2

      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
    4. XM_054345827.1XP_054201802.1  raftlin isoform X2

      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
    5. XM_054345826.1XP_054201801.1  raftlin isoform X2

      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
    6. XM_054345825.1XP_054201800.1  raftlin isoform X2

      UniProtKB/Swiss-Prot
      Q0D2G0, Q14699, Q496Y2, Q4QQI7, Q5JB48, Q7Z7P2
      UniProtKB/TrEMBL
      G3XAJ6
    7. XM_054345828.1XP_054201803.1  raftlin isoform X3

    8. XM_054345823.1XP_054201798.1  raftlin isoform X1

      UniProtKB/TrEMBL
      G3XAJ6