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

Gene ID: 113402, updated on 27-Nov-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 located in several cellular components, including cytoplasm; endomembrane system; and intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in prostate (RPKM 27.1), colon (RPKM 26.8) and 25 other tissues See more
Orthologs
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (166319728..166342545, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (167696648..167719464, complement)
RS_2024_09 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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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)

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_2024_08

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

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