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    SCFD2 sec1 family domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 152579, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SCFD2provided by HGNC
    Official Full Name
    sec1 family domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:30676
    See related
    Ensembl:ENSG00000184178 AllianceGenome:HGNC:30676
    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
    STXBP1L1
    Summary
    Predicted to be involved in intracellular protein transport and vesicle-mediated transport. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in brain (RPKM 1.5), adrenal (RPKM 1.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SCFD2 in Genome Data Viewer
    Location:
    4q12
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (52872982..53366061, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (56359861..56853303, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (53739149..54232228, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15428 Neighboring gene uncharacterized LOC124900700 Neighboring gene Sharpr-MPRA regulatory region 13979 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:53733886-53734386 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:53734387-53734887 Neighboring gene NANOG hESC enhancer GRCh37_chr4:53739270-53739771 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr4:53739925-53740884 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:53743608-53744108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21558 Neighboring gene RAS like family 11 member B Neighboring gene uncharacterized LOC101928658 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:53816447-53817384 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15429 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21559 Neighboring gene uncharacterized LOC124900701 Neighboring gene VISTA enhancer hs1668 Neighboring gene VISTA enhancer hs1460 Neighboring gene NANOG hESC enhancer GRCh37_chr4:54102933-54103444 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr4:54103445-54103956 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:54122352-54122863 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:54140029-54140243 Neighboring gene RNA, U6 small nuclear 310, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:54195258-54195835 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21561 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21562 Neighboring gene uncharacterized LOC105377654 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:54243526-54244074 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:54244075-54244623 Neighboring gene factor interacting with PAPOLA and CPSF1 Neighboring gene LNX1 antisense RNA 1 Neighboring gene ligand of numb-protein X 1

    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. PSF Promotes ER-Positive Breast Cancer Progression via Posttranscriptional Regulation of ESR1 and SCFD2. Mitobe Y, et al. Cancer Res, 2020 Jun 1. PMID 32213542
    2. PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2. Takeiwa T, et al. Sci Rep, 2022 Jun 9. PMID 35681031, Free PMC Article
    3. Genome-wide association identifies ATOH7 as a major gene determining human optic disc size. Macgregor S, et al. Hum Mol Genet, 2010 Jul 1. PMID 20395239, Free PMC Article
    4. Genome-wide association study of smoking behaviours in patients with COPD. Siedlinski M, et al. Thorax, 2011 Oct. PMID 21685187, Free PMC Article
    5. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Ceccarelli DF, et al. Structure, 2019 Jun 4. PMID 31056421, Free PMC Article

    See all (29) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2.
      Title: PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2.
    2. PSF Promotes ER-Positive Breast Cancer Progression via Posttranscriptional Regulation of ESR1 and SCFD2.
      Title: PSF Promotes ER-Positive Breast Cancer Progression via Posttranscriptional Regulation of ESR1 and SCFD2.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome-wide association identifies ATOH7 as a major gene determining human optic disc size.
    EBI GWAS Catalog
    Genome-wide association study of smoking behaviours in patients with COPD.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ21060, FLJ39514

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sec1 family domain-containing protein 2
    Names
    syntaxin binding protein 1-like 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_152540.4 → NP_689753.2  sec1 family domain-containing protein 2

      See identical proteins and their annotated locations for NP_689753.2

      Status: VALIDATED

      Source sequence(s)
      AY299407
      Consensus CDS
      CCDS33984.1
      UniProtKB/Swiss-Prot
      Q8N5F3, Q8N8H0, Q8WU76, Q96ED3
      Related
      ENSP00000384182.3, ENST00000401642.8
      Conserved Domains (1) summary
      cl15415
      Location:572 → 665
      Sec1; Sec1 family

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      52872982..53366061 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007787.3 → XP_016863276.1  sec1 family domain-containing protein 2 isoform X4

    2. XM_047449646.1 → XP_047305602.1  sec1 family domain-containing protein 2 isoform X2

    3. XM_017007786.3 → XP_016863275.1  sec1 family domain-containing protein 2 isoform X1

    4. XM_011534376.4 → XP_011532678.1  sec1 family domain-containing protein 2 isoform X5

    5. XM_011534375.4 → XP_011532677.1  sec1 family domain-containing protein 2 isoform X3

    6. XM_047449647.1 → XP_047305603.1  sec1 family domain-containing protein 2 isoform X7

    7. XM_011534378.4 → XP_011532680.1  sec1 family domain-containing protein 2 isoform X6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      56359861..56853303 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348996.1 → XP_054204971.1  sec1 family domain-containing protein 2 isoform X4

    2. XM_054348994.1 → XP_054204969.1  sec1 family domain-containing protein 2 isoform X2

    3. XM_054348993.1 → XP_054204968.1  sec1 family domain-containing protein 2 isoform X1

    4. XM_054348997.1 → XP_054204972.1  sec1 family domain-containing protein 2 isoform X5

    5. XM_054348995.1 → XP_054204970.1  sec1 family domain-containing protein 2 isoform X3

    6. XM_054348999.1 → XP_054204974.1  sec1 family domain-containing protein 2 isoform X7

    7. XM_054348998.1 → XP_054204973.1  sec1 family domain-containing protein 2 isoform X6

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8WU76.2 GenPept UniProtKB/Swiss-Prot:Q8WU76

    Gene LinkOut

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

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