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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
  • RAFTLIN 3
  • 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. 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.

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

Genomics for RFTN1 Gene

Regulatory Elements for RFTN1 Gene

Enhancers for RFTN1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F016368 1.5 FANTOM5 Ensembl ENCODE 24.7 +138.7 138705 13.0 HDGF TBP PKNOX1 TBL1XR1 WRNIP1 YBX1 BMI1 RAD21 ZBTB40 RFX5 RFTN1 DPH3 ENSG00000272529 GC03P016476
GH03F016467 1.4 FANTOM5 Ensembl ENCODE 23.2 +45.5 45499 2.8 HDGF PKNOX1 FEZF1 YBX1 RAD21 ZNF143 ZNF207 ETV6 CREM ZNF362 RFTN1 PLCL2 DPH3 GC03P016476 ENSG00000272529
GH03F016503 1.5 FANTOM5 Ensembl ENCODE 19.7 +9.4 9447 1.2 HDGF PKNOX1 ATF1 ARNT ZNF766 GATA2 JUNB NCOA1 TBX21 SMARCA4 RFTN1 DPH3 OXNAD1 PLCL2 GC03M015947
GH03F016386 1.3 FANTOM5 Ensembl ENCODE 20.1 +125.8 125762 3.7 HDGF YBX1 ZFHX2 POLR2A EED EGR2 MTA2 JUNB TBX21 NR2F2 RFTN1 ENSG00000272529 GC03P016476
GH03F016479 1.3 Ensembl ENCODE 19.9 +31.1 31056 6.5 PKNOX1 SIN3A FEZF1 ZNF2 ZNF121 ZNF143 FOS KLF7 ZNF263 JUNB RFTN1 ENSG00000270409 GC03P016476 GC03M015947
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RFTN1 on UCSC Golden Path with GeneCards custom track

Promoters for RFTN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001358662 926 2601 HDGF PKNOX1 WRNIP1 SIN3A GLIS2 ZNF143 JUNB TBX21 PBX2 GLIS1

Genomic Location for RFTN1 Gene

Chromosome:
3
Start:
16,313,574 bp from pter
End:
16,514,026 bp from pter
Size:
200,453 bases
Orientation:
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:
    Q14699-RFTN1_HUMAN
    Recommended name:
    Raftlin
    Protein Accession:
    Q14699
    Secondary Accessions:
    • Q0D2G0
    • Q496Y2
    • Q4QQI7
    • Q5JB48
    • Q7Z7P2

    Protein attributes for RFTN1 Gene

    Size:
    578 amino acids
    Molecular mass:
    63146 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • 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

  • Ubiquitination at Lys 147
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for RFTN1
  • Cloud-Clone Corp. Antibodies for RFTN1
  • Santa Cruz Biotechnology (SCBT) Antibodies for RFTN1

No data available for DME Specific Peptides for RFTN1 Gene

Domains & Families for RFTN1 Gene

Protein Domains for RFTN1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for RFTN1 Gene

Graphical View of Domain Structure for InterPro Entry

Q14699

UniProtKB/Swiss-Prot:

RFTN1_HUMAN :
  • Belongs to the raftlin family.
Family:
  • Belongs to the raftlin family.
genes like me logo Genes that share domains with RFTN1: view

No data available for Gene Families for RFTN1 Gene

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.

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

  • Taconic Biosciences Mouse Models for RFTN1

miRNA for RFTN1 Gene

miRTarBase miRNAs that target RFTN1

Inhibitory RNA Products

Flow Cytometry 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

COMPARTMENTS
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 IEA,IDA 12805216
GO:0016020 membrane IEA --
GO:0043234 protein complex IDA 21266579
genes like me logo Genes that share ontologies with RFTN1: view

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 IEA,ISS --
GO:0032596 protein transport into membrane raft IEA,ISS --
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

Transcripts for RFTN1 Gene

Unigene Clusters for RFTN1 Gene

Raftlin, lipid raft linker 1:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry 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: - -
SP6:
SP7: - - - - -
SP8: - - - - - -
SP9: -
SP10: - - -
SP11: - -

ExUns: 18d
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for RFTN1 Gene

GeneLoc Exon Structure for
RFTN1
ECgene alternative splicing isoforms for
RFTN1

Expression for RFTN1 Gene

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



Protein tissue co-expression partners for RFTN1 Gene

NURSA nuclear receptor signaling pathways regulating expression of RFTN1 Gene:

RFTN1

SOURCE GeneReport for Unigene cluster for RFTN1 Gene:

Hs.98910

mRNA Expression by UniProt/SwissProt for RFTN1 Gene:

Q14699-RFTN1_HUMAN
Tissue specificity: Specifically expressed by B-cells (at protein level).
genes like me logo Genes that share expression patterns with RFTN1: view

Primer Products

No data available for mRNA differential expression in normal tissues 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
chimpanzee
(Pan troglodytes)
Mammalia RFTN1 34 35
  • 99.54 (n)
dog
(Canis familiaris)
Mammalia RFTN1 34 35
  • 86.06 (n)
mouse
(Mus musculus)
Mammalia Rftn1 34 16 35
  • 78.52 (n)
rat
(Rattus norvegicus)
Mammalia Rftn1 34
  • 78.33 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RFTN1 35
  • 62 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RFTN1 35
  • 60 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RFTN1 35
  • 56 (a)
OneToOne
chicken
(Gallus gallus)
Aves RFTN1 34 35
  • 68.72 (n)
lizard
(Anolis carolinensis)
Reptilia RFTN1 35
  • 50 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rftn1 34
  • 60.54 (n)
zebrafish
(Danio rerio)
Actinopterygii RFTN1 (2 of 2) 35
  • 33 (a)
OneToMany
rftn1a 35
  • 26 (a)
OneToMany
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

ENSEMBL:
Gene Tree for RFTN1 (if available)
TreeFam:
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.org 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 Sequence Context AA Info Type
rs10212328 -- 16,372,511(+) AAGCA(C/G)AAATG intron-variant, nc-transcript-variant, utr-variant-3-prime
rs10454232 -- 16,493,590(+) CCGCC(C/T)CCTTG intron-variant
rs1050604 -- 16,316,201(-) CTACT(C/T)TTGCA intron-variant, utr-variant-3-prime
rs1050626 -- 16,315,897(-) CTCTT(A/C/T)TCTTG intron-variant, utr-variant-3-prime
rs10510447 -- 16,361,608(+) CTGAC(A/C)TGCAG 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)

Relevant External Links for RFTN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RFTN1

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

Disorders for RFTN1 Gene

Relevant External Links for RFTN1

Genetic Association Database (GAD)
RFTN1
Human Genome Epidemiology (HuGE) Navigator
RFTN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RFTN1

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. (EMBO J. 2003) 2 3 4 22 64
  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. … Nomura N. (DNA Res. 1995) 2 3 4 64
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  4. Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. (PMID: 20395239) Macgregor S. … Mackey D.A. (Hum. Mol. Genet. 2010) 3 46 64
  5. Common body mass index-associated variants confer risk of extreme obesity. (PMID: 19553259) Cotsapas C. … Daly M.J. (Hum. Mol. Genet. 2009) 3 46 64

Products for RFTN1 Gene

Sources for RFTN1 Gene

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