Free for academic non-profit institutions. Other users need a Commercial license

Aliases for RFTN1 Gene

Aliases for RFTN1 Gene

  • Raftlin, Lipid Raft Linker 1 2 3 5
  • Raft-Linking Protein 2 3 4
  • Cell Migration-Inducing Gene 2 Protein 3 4
  • Proliferation-Inducing Protein 10 3
  • Proliferation-Inducing Protein 9 3
  • KIAA0084 4
  • PIB10 3
  • MIG2 3
  • PIG9 3

External Ids for RFTN1 Gene

Previous GeneCards Identifiers for RFTN1 Gene

  • GC03M016333
  • GC03M016290

Summaries for RFTN1 Gene

GeneCards Summary for RFTN1 Gene

RFTN1 (Raftlin, Lipid Raft Linker 1) is a Protein Coding gene. Gene Ontology (GO) annotations related to this gene include double-stranded RNA binding. An important paralog of this gene is RFTN2.

UniProtKB/Swiss-Prot for RFTN1 Gene

  • May play a pivotal role in the formation and/or maintenance of lipid rafts. May regulate B-cell antigen receptor-mediated signaling.

Additional gene information for RFTN1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RFTN1 Gene

Genomics for RFTN1 Gene

GeneHancer (GH) Regulatory Elements for RFTN1 Gene

Promoters and enhancers for RFTN1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I016507 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 566 +1.5 1468 9.3 HDGF PKNOX1 SMAD1 NEUROD1 SIN3A YBX1 ZNF2 IRF4 YY1 ZNF121 RFTN1 OXNAD1 DPH3 PLCL2 GC03M015947
GH03I016368 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 24.7 +138.7 138704 13 HDGF PKNOX1 SMAD1 BMI1 YBX1 BATF KLF5 IRF4 ATF7 ETV6 RFTN1 DPH3 ENSG00000272529 GC03P016476 OXNAD1 GC03M015947
GH03I016467 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 23.2 +45.5 45498 2.8 SRF PKNOX1 ZNF687 ZNF362 JUNB FEZF1 ELF1 NR2F2 RELA OSR2 RFTN1 PLCL2 DPH3 GC03P016476 GC03M015947 ENSG00000272529
GH03I016479 Enhancer 1.4 Ensembl ENCODE dbSUPER 19.9 +31.1 31055 6.5 PKNOX1 FEZF1 ZNF2 ZNF121 ZNF213 KLF7 FOS RUNX3 RXRA ZNF662 ENSG00000270409 RFTN1 GC03P016476 GC03M015947
GH03I016473 Enhancer 1.3 Ensembl ENCODE dbSUPER 20.1 +37.5 37519 5.6 NSD2 FEZF1 ZNF121 ZNF213 FOS RUNX3 KLF13 JUNB ZNF662 TSHZ1 GC03P016476 ENSG00000270409 RFTN1 GC03M015947 ENSG00000272529
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around RFTN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RFTN1 gene promoter:

Genomic Locations for RFTN1 Gene

Genomic Locations for RFTN1 Gene
200,453 bases
Minus strand

Genomic View for RFTN1 Gene

Genes around RFTN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RFTN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RFTN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RFTN1 Gene

Proteins for RFTN1 Gene

  • Protein details for RFTN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q0D2G0
    • Q496Y2
    • Q4QQI7
    • Q5JB48
    • Q7Z7P2

    Protein attributes for RFTN1 Gene

    578 amino acids
    Molecular mass:
    63146 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAH51336.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=AAH69209.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA07644.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for RFTN1 Gene

Post-translational modifications for RFTN1 Gene

No data available for DME Specific Peptides for RFTN1 Gene

Domains & Families for RFTN1 Gene

Gene Families for RFTN1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RFTN1 Gene


Suggested Antigen Peptide Sequences for RFTN1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the raftlin family.
  • Belongs to the raftlin family.
genes like me logo Genes that share domains with RFTN1: view

Function for RFTN1 Gene

Molecular function for RFTN1 Gene

UniProtKB/Swiss-Prot Function:
May play a pivotal role in the formation and/or maintenance of lipid rafts. May regulate B-cell antigen receptor-mediated signaling.

Phenotypes From GWAS Catalog for RFTN1 Gene

Gene Ontology (GO) - Molecular Function for RFTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003725 double-stranded RNA binding IDA 21266579
genes like me logo Genes that share ontologies with RFTN1: view
genes like me logo Genes that share phenotypes with RFTN1: view

Animal Models for RFTN1 Gene

MGI Knock Outs for RFTN1:

Animal Model Products

CRISPR Products

miRNA for RFTN1 Gene

miRTarBase miRNAs that target RFTN1

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RFTN1 Gene

Localization for RFTN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RFTN1 Gene

Cell membrane; Lipid-anchor. Note=Associates with lipid rafts.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RFTN1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endosome 5
nucleus 2
cytosol 2
mitochondrion 1

Gene Ontology (GO) - Cellular Components for RFTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 21266579
GO:0005768 endosome IDA 21266579
GO:0005886 plasma membrane IDA,IEA 12805216
GO:0016020 membrane IEA --
GO:0043234 protein complex IDA 21266579
genes like me logo Genes that share ontologies with RFTN1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RFTN1 Gene

Pathways & Interactions for RFTN1 Gene

SuperPathways for RFTN1 Gene

No Data Available

Interacting Proteins for RFTN1 Gene

Gene Ontology (GO) - Biological Process for RFTN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001765 membrane raft assembly IMP 12805216
GO:0002457 T cell antigen processing and presentation ISS,IEA --
GO:0032596 protein transport into membrane raft ISS,IEA --
GO:0032620 interleukin-17 production IEA,ISS --
GO:0033227 dsRNA transport IMP 21266579
genes like me logo Genes that share ontologies with RFTN1: view

No data available for Pathways by source and SIGNOR curated interactions for RFTN1 Gene

Drugs & Compounds for RFTN1 Gene

No Compound Related Data Available

Transcripts for RFTN1 Gene

Unigene Clusters for RFTN1 Gene

Raftlin, lipid raft linker 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for RFTN1 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c · 12d ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b · 18c ·
SP1: - - - - - - - -
SP2: - - - - -
SP3: - - - - - - -
SP4: - - - - - -
SP5: - -
SP7: - - - - -
SP8: - - - - - -
SP9: -
SP10: - - -
SP11: - -

ExUns: 18d

Relevant External Links for RFTN1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RFTN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RFTN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RFTN1 Gene

This gene is overexpressed in Breast (39.7) and Lymph node (15.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for RFTN1 Gene

Protein tissue co-expression partners for RFTN1 Gene

NURSA nuclear receptor signaling pathways regulating expression of RFTN1 Gene:


SOURCE GeneReport for Unigene cluster for RFTN1 Gene:


mRNA Expression by UniProt/SwissProt for RFTN1 Gene:

Tissue specificity: Specifically expressed by B-cells (at protein level).

Evidence on tissue expression from TISSUES for RFTN1 Gene

  • Liver(4.2)
  • Bone marrow(4.1)
  • Nervous system(2.9)
  • Lymph node(2.3)
  • Spleen(2.1)
genes like me logo Genes that share expression patterns with RFTN1: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RFTN1 Gene

Orthologs for RFTN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for RFTN1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RFTN1 33 34
  • 99.54 (n)
(Canis familiaris)
Mammalia RFTN1 33 34
  • 86.06 (n)
(Mus musculus)
Mammalia Rftn1 33 16 34
  • 78.52 (n)
(Rattus norvegicus)
Mammalia Rftn1 33
  • 78.33 (n)
(Ornithorhynchus anatinus)
Mammalia RFTN1 34
  • 62 (a)
(Monodelphis domestica)
Mammalia RFTN1 34
  • 60 (a)
(Bos Taurus)
Mammalia RFTN1 34
  • 56 (a)
(Gallus gallus)
Aves RFTN1 33 34
  • 68.72 (n)
(Anolis carolinensis)
Reptilia RFTN1 34
  • 50 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rftn1 33
  • 60.54 (n)
(Danio rerio)
Actinopterygii RFTN1 (2 of 2) 34
  • 33 (a)
rftn1a 34
  • 26 (a)
Species where no ortholog for RFTN1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RFTN1 Gene

Gene Tree for RFTN1 (if available)
Gene Tree for RFTN1 (if available)

Paralogs for RFTN1 Gene

Paralogs for RFTN1 Gene

(1) SIMAP similar genes for RFTN1 Gene using alignment to 9 proteins: Pseudogenes for RFTN1 Gene

genes like me logo Genes that share paralogs with RFTN1: view

Variants for RFTN1 Gene

Sequence variations from dbSNP and Humsavar for RFTN1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000001162 -- 16,511,162(-) G/T intron_variant
rs1000008174 -- 16,474,307(-) C/A intron_variant
rs1000009079 -- 16,513,952(-) C/G upstream_transcript_variant
rs1000037621 -- 16,504,573(-) G/A intron_variant
rs1000039465 -- 16,348,614(-) C/A/T intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RFTN1 Gene

Variant ID Type Subtype PubMed ID
nsv834625 CNV gain 17160897
nsv834623 CNV gain 17160897
nsv1142353 CNV tandem duplication 24896259
nsv1139097 CNV deletion 24896259
nsv1072242 CNV deletion 25765185
esv7245 CNV gain 19470904
esv3430328 CNV duplication 20981092
esv3353629 CNV duplication 20981092
esv2724973 CNV deletion 23290073
esv2724971 CNV deletion 23290073
esv2659741 CNV deletion 23128226

Variation tolerance for RFTN1 Gene

Residual Variation Intolerance Score: 48.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.50; 82.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RFTN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RFTN1 Gene

Disorders for RFTN1 Gene

Additional Disease Information for RFTN1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for RFTN1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RFTN1 Gene

Publications for RFTN1 Gene

  1. The B cell-specific major raft protein, Raftlin, is necessary for the integrity of lipid raft and BCR signal transduction. (PMID: 12805216) Saeki K … Yoshimura A (The EMBO journal 2003) 2 3 4 22 58
  2. Prediction of the coding sequences of unidentified human genes. III. The coding sequences of 40 new genes (KIAA0081-KIAA0120) deduced by analysis of cDNA clones from human cell line KG-1. (PMID: 7788527) Nagase T … Kotani H (DNA research : an international journal for rapid publication of reports on genes and genomes 1995) 2 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. (PMID: 20395239) Macgregor S … Mackey DA (Human molecular genetics 2010) 3 44 58
  5. Sequential use of transcriptional profiling, expression quantitative trait mapping, and gene association implicates MMP20 in human kidney aging. (PMID: 19834535) Wheeler HE … Kim SK (PLoS genetics 2009) 3 44 58

Products for RFTN1 Gene

Sources for RFTN1 Gene

Loading form....