Aliases for SFT2D1 Gene

Aliases for SFT2D1 Gene

  • SFT2 Domain Containing 1 2 3 5
  • PRGR1 2 3 4
  • SFT2 Domain-Containing Protein 1 3 4
  • Vesicle Transport Protein SFT2A 3 4
  • C6orf83 3 4
  • Chromosome 6 Open Reading Frame 83 2
  • MGC19825 2
  • SFT2D1 5

External Ids for SFT2D1 Gene

Previous HGNC Symbols for SFT2D1 Gene

  • C6orf83

Previous GeneCards Identifiers for SFT2D1 Gene

  • GC06M166704
  • GC06M166654
  • GC06M164204
  • GC06M166736

Summaries for SFT2D1 Gene

GeneCards Summary for SFT2D1 Gene

SFT2D1 (SFT2 Domain Containing 1) is a Protein Coding gene. An important paralog of this gene is SFT2D2.

UniProtKB/Swiss-Prot Summary for SFT2D1 Gene

  • May be involved in fusion of retrograde transport vesicles derived from an endocytic compartment with the Golgi complex.

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SFT2D1 Gene

Genomics for SFT2D1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SFT2D1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J166340 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 275.3 -0.4 -421 4.1 SP1 ZNF207 MYC ZNF600 SSRP1 ZNF580 ZNF592 KLF9 POLR2A NFIC SFT2D1 LOC100289495 lnc-PRR18-1 HNRNPA1P49 PRR18 MPC1 RF00994-972
GH06J166341 Enhancer 0.3 ENCODE 250.7 +1.9 1948 0.2 POLR2A LOC100289495 SFT2D1 lnc-PRR18-1 MPC1 PRR18 HSALNG0055092
GH06J166317 Enhancer 1.1 Ensembl ENCODE dbSUPER 30.4 +24.0 23972 2.1 POLR2A NFIC ZIC2 MAFF ELF1 ZNF316 RBM22 MYNN MAFK PRDM10 SFT2D1 MPC1 HNRNPA1P49 piR-55029-014 HSALNG0055088 PRR18
GH06J166330 Enhancer 1.3 Ensembl ENCODE dbSUPER 19 +9.2 9176 6 SP1 ZNF600 IKZF1 MYC POLR2A NFIC ZIC2 NONO BCL11A REST HNRNPA1P49 HSALNG0055090 HSALNG0055091 SFT2D1 MPC1 PRR18 HSALNG0055092 HSALNG0055089 lnc-PRR18-1
GH06J166381 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 11.8 -40.2 -40225 3.6 BCLAF1 SP1 ZNF207 ZNF600 MYC SSRP1 ZNF580 ZNF592 ZMYM3 KLF9 ENSG00000261420 MPC1 lnc-MPC1-2 PRR18 SFT2D1 piR-40666-016
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SFT2D1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SFT2D1

Top Transcription factor binding sites by QIAGEN in the SFT2D1 gene promoter:
  • AP-4
  • c-Ets-1
  • E47
  • En-1
  • FOXC1
  • IRF-2
  • Meis-1
  • Meis-1a
  • Meis-1b
  • POU2F1c

Genomic Locations for SFT2D1 Gene

Latest Assembly
chr6:166,319,728-166,342,576
(GRCh38/hg38)
Size:
22,849 bases
Orientation:
Minus strand

Previous Assembly
chr6:166,733,216-166,756,033
(GRCh37/hg19 by Entrez Gene)
Size:
22,818 bases
Orientation:
Minus strand

chr6:166,733,216-166,756,079
(GRCh37/hg19 by Ensembl)
Size:
22,864 bases
Orientation:
Minus strand

Genomic View for SFT2D1 Gene

Genes around SFT2D1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SFT2D1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SFT2D1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SFT2D1 Gene

Proteins for SFT2D1 Gene

  • Protein details for SFT2D1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WV19-SFT2A_HUMAN
    Recommended name:
    Vesicle transport protein SFT2A
    Protein Accession:
    Q8WV19
    Secondary Accessions:
    • Q5TI64
    • Q9UIC7

    Protein attributes for SFT2D1 Gene

    Size:
    159 amino acids
    Molecular mass:
    17804 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF18564.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for SFT2D1 Gene

Post-translational modifications for SFT2D1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SFT2D1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SFT2D1 Gene

Domains & Families for SFT2D1 Gene

Gene Families for SFT2D1 Gene

Human Protein Atlas (HPA):
  • Predicted membrane proteins

Protein Domains for SFT2D1 Gene

Suggested Antigen Peptide Sequences for SFT2D1 Gene

GenScript: Design optimal peptide antigens:
  • SFT2D1 protein (Q4G178_HUMAN)
  • pRGR1 (SFT2A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8WV19

UniProtKB/Swiss-Prot:

SFT2A_HUMAN :
  • Belongs to the SFT2 family.
Family:
  • Belongs to the SFT2 family.
genes like me logo Genes that share domains with SFT2D1: view

Function for SFT2D1 Gene

Molecular function for SFT2D1 Gene

UniProtKB/Swiss-Prot Function:
May be involved in fusion of retrograde transport vesicles derived from an endocytic compartment with the Golgi complex.

Phenotypes From GWAS Catalog for SFT2D1 Gene

Gene Ontology (GO) - Molecular Function for SFT2D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 32296183
genes like me logo Genes that share ontologies with SFT2D1: view
genes like me logo Genes that share phenotypes with SFT2D1: view

miRNA for SFT2D1 Gene

miRTarBase miRNAs that target SFT2D1

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SFT2D1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for SFT2D1 Gene

Localization for SFT2D1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SFT2D1 Gene

Membrane. Multi-pass membrane protein.

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 SFT2D1 gene
Compartment Confidence
plasma membrane 3
nucleus 2
cytosol 2
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SFT2D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with SFT2D1: view

Pathways & Interactions for SFT2D1 Gene

PathCards logo

SuperPathways for SFT2D1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SFT2D1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport IEA --
genes like me logo Genes that share ontologies with SFT2D1: view

No data available for Pathways by source and SIGNOR curated interactions for SFT2D1 Gene

Drugs & Compounds for SFT2D1 Gene

No Compound Related Data Available

Transcripts for SFT2D1 Gene

mRNA/cDNA for SFT2D1 Gene

1 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SFT2D1

Alternative Splicing Database (ASD) splice patterns (SP) for SFT2D1 Gene

No ASD Table

Relevant External Links for SFT2D1 Gene

GeneLoc Exon Structure for
SFT2D1

Expression for SFT2D1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SFT2D1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Tonsil (Hematopoietic System)

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SFT2D1 Gene



Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SFT2D1

SOURCE GeneReport for Unigene cluster for SFT2D1 Gene:

Hs.487143

Evidence on tissue expression from TISSUES for SFT2D1 Gene

  • Nervous system(3)
genes like me logo Genes that share expression patterns with SFT2D1: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SFT2D1 Gene

Orthologs for SFT2D1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for SFT2D1 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SFT2D1 29 30
  • 98.95 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Gm12166 30
  • 91 (a)
OneToMany
Sft2d1 29 16 30
  • 86.29 (n)
OneToMany
Dog
(Canis familiaris)
Mammalia SFT2D1 29 30
  • 90.99 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SFT2D1 29 30
  • 87.84 (n)
OneToMany
-- 30
  • 79 (a)
OneToMany
Rat
(Rattus norvegicus)
Mammalia Sft2d1 29
  • 86.37 (n)
Oppossum
(Monodelphis domestica)
Mammalia SFT2D1 30
  • 84 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia SFT2D1 30
  • 70 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SFT2D1 29 30
  • 76.1 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SFT2D1 30
  • 73 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sft2d1 29
  • 73.38 (n)
Str.11136 29
Zebrafish
(Danio rerio)
Actinopterygii sft2d1 29 30
  • 67.71 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta CG5104 29 30
  • 59.33 (n)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea F27D4.7 30
  • 31 (a)
OneToMany
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G24170 29
  • 47.96 (n)
Rice
(Oryza sativa)
Liliopsida Os01g0219100 29
  • 49.89 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 46 (a)
OneToMany
Species where no ortholog for SFT2D1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
  • 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 Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for SFT2D1 Gene

ENSEMBL:
Gene Tree for SFT2D1 (if available)
TreeFam:
Gene Tree for SFT2D1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SFT2D1: view image
Alliance of Genome Resources:
Additional Orthologs for SFT2D1

Paralogs for SFT2D1 Gene

Paralogs for SFT2D1 Gene

(1) SIMAP similar genes for SFT2D1 Gene using alignment to 2 proteins:

  • SFT2A_HUMAN
  • Q4G178_HUMAN
genes like me logo Genes that share paralogs with SFT2D1: view

Variants for SFT2D1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SFT2D1 Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs11551053 -- p.Ile109Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SFT2D1 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SFT2D1 Gene

Variant ID Type Subtype PubMed ID
nsv981205 CNV duplication 23825009

Variation tolerance for SFT2D1 Gene

Residual Variation Intolerance Score: 70.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.72; 15.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SFT2D1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SFT2D1
Leiden Open Variation Database (LOVD)
SFT2D1

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SFT2D1 Gene

Disorders for SFT2D1 Gene

Additional Disease Information for SFT2D1

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for SFT2D1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for SFT2D1 Gene

Publications for SFT2D1 Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  2. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. Interrogating the protein interactomes of RAS isoforms identifies PIP5K1A as a KRAS-specific vulnerability. (PMID: 30194290) Adhikari H … Counter CM (Nature communications 2018) 3
  5. Initial characterization of the human central proteome. (PMID: 21269460) Burkard TR … Colinge J (BMC systems biology 2011) 4

Products for SFT2D1 Gene

Sources for SFT2D1 Gene