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    SFT2D1 SFT2 domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 113402, updated on 5-Mar-2024

    Summary

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    Official Symbol
    SFT2D1provided by HGNC
    Official Full Name
    SFT2 domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:21102
    See related
    Ensembl:ENSG00000198818 AllianceGenome:HGNC:21102
    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
    pRGR1; C6orf83
    Summary
    Predicted to be involved in protein transport and vesicle-mediated transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in prostate (RPKM 27.1), colon (RPKM 26.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SFT2D1 in Genome Data Viewer
    Location:
    6q27
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (166319728..166342545, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (167696648..167719464, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (166733216..166756033, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378118 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25429 Neighboring gene uncharacterized LOC107986669 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17774 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25430 Neighboring gene proline rich 18 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:166731429-166732174 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:166732175-166732919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25431 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25432 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 49 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17775 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:166755965-166756858 Neighboring gene uncharacterized LOC100289495 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:166761001-166762200 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:166776097-166776728 Neighboring gene mitochondrial pyruvate carrier 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25433 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17777

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Identification of host proteins required for HIV infection through a functional genomic screen. Brass AL, et al. Science, 2008 Feb 15. PMID 18187620
    2. Interrogating the protein interactomes of RAS isoforms identifies PIP5K1A as a KRAS-specific vulnerability. Adhikari H, et al. Nat Commun, 2018 Sep 7. PMID 30194290, Free PMC Article
    3. The DNA sequence and analysis of human chromosome 6. Mungall AJ, et al. Nature, 2003 Oct 23. PMID 14574404
    4. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of SFT2 domain containing 1 (SFT2D1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ11427, FLJ33476, MGC19825, DKFZp667D087

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endomembrane system IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in intracellular membrane-bounded organelle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    vesicle transport protein SFT2A
    Names
    SFT2 domain-containing protein 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_145169.3 → NP_660152.1  vesicle transport protein SFT2A

      See identical proteins and their annotated locations for NP_660152.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the protein.
      Source sequence(s)
      AL833217, BC018969, DB476616
      Consensus CDS
      CCDS5292.1
      UniProtKB/Swiss-Prot
      Q5TI64, Q8WV19, Q9UIC7
      Related
      ENSP00000354590.3, ENST00000361731.4
      Conserved Domains (1) summary
      pfam04178
      Location:38 → 155
      Got1; Got1/Sft2-like family

    RNA

    1. NR_130112.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL833217, BG706927, BI597156, DB476616

    2. NR_130113.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate internal exon and lacks two exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL833217, AW964442, BI597156, DB476616

    3. NR_130114.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate internal exon and lacks two exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL833217, BF223532, BI597156, DB476616

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      166319728..166342545 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      167696648..167719464 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WV19.1 GenPept UniProtKB/Swiss-Prot:Q8WV19

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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