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SCFD1 sec1 family domain containing 1 [ Homo sapiens (human) ]

Gene ID: 23256, updated on 4-Nov-2018

Summary

Official Symbol
SCFD1provided by HGNC
Official Full Name
sec1 family domain containing 1provided by HGNC
Primary source
HGNC:HGNC:20726
See related
Ensembl:ENSG00000092108 Vega:OTTHUMG00000029420
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
SLY1; RA410; SLY1P; STXBP1L2; C14orf163
Expression
Ubiquitous expression in thyroid (RPKM 19.4), testis (RPKM 13.5) and 25 other tissues See more
Orthologs

Genomic context

See SCFD1 in Genome Data Viewer
Location:
14q12
Exon count:
29
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (30622254..30735828)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (31091460..31205034)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC112267868 Neighboring gene G2E3 antisense RNA 1 Neighboring gene SYF2 pre-mRNA splicing factor pseudogene 1 Neighboring gene G2/M-phase specific E3 ubiquitin protein ligase Neighboring gene ubiquitin conjugating enzyme E2 C pseudogene 1 Neighboring gene ribosomal protein L12 pseudogene 5 Neighboring gene ribosomal protein L27 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of sec1 family domain containing 1 (SCFD1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Asparagine N-linked glycosylation, organism-specific biosystem (from REACTOME)
    Asparagine N-linked glycosylation, organism-specific biosystemN-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 rev...
  • COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystem (from REACTOME)
    COPII (Coat Protein 2) Mediated Vesicle Transport, organism-specific biosystemCOPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the ER-Golgi intermediate compartment (ERGIC). COPII-coated vesicles wer...
  • ER to Golgi Anterograde Transport, organism-specific biosystem (from REACTOME)
    ER to Golgi Anterograde Transport, organism-specific biosystemSecretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus for further processing.
  • Membrane Trafficking, organism-specific biosystem (from REACTOME)
    Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Transport to the Golgi and subsequent modification, organism-specific biosystem (from REACTOME)
    Transport to the Golgi and subsequent modification, organism-specific biosystemAt least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Martinez-Menarguez et al, 1999)....
  • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
    Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0917

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein N-terminus binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding ISS
Inferred from Sequence or Structural Similarity
more info
 
syntaxin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
COPII vesicle coating TAS
Traceable Author Statement
more info
 
cell morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
negative regulation of autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
post-Golgi vesicle-mediated transport ISS
Inferred from Sequence or Structural Similarity
more info
 
protein transport IEA
Inferred from Electronic Annotation
more info
 
regulation of ER to Golgi vesicle-mediated transport ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of protein transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
response to toxic substance IEP
Inferred from Expression Pattern
more info
PubMed 
retrograde vesicle-mediated transport, Golgi to ER ISS
Inferred from Sequence or Structural Similarity
more info
 
toxin transport IEA
Inferred from Electronic Annotation
more info
 
vesicle docking involved in exocytosis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi cisterna membrane IEA
Inferred from Electronic Annotation
more info
 
Golgi-associated vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 
cis-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
sec1 family domain-containing protein 1
Names
syntaxin-binding protein 1-like 2
vesicle transport-related protein

NCBI Reference Sequences (RefSeq)

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_001257376.1NP_001244305.1  sec1 family domain-containing protein 1 isoform c

    See identical proteins and their annotated locations for NP_001244305.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AK298622, BG212062, DA151789
    Consensus CDS
    CCDS58308.1
    UniProtKB/Swiss-Prot
    Q8WVM8
    Related
    ENSP00000379870.2, OTTHUMP00000244066, ENST00000396629.6, OTTHUMT00000409684
    Conserved Domains (1) summary
    pfam00995
    Location:1537
    Sec1; Sec1 family
  2. NM_001283031.1NP_001269960.1  sec1 family domain-containing protein 1 isoform d

    See identical proteins and their annotated locations for NP_001269960.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an exon in the 5' region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus, compared to isoform a. Variants 4 and 6 encode the same isoform (d).
    Source sequence(s)
    AK299222, BG212062, DB105324
    UniProtKB/TrEMBL
    B7Z5N7
    Conserved Domains (1) summary
    pfam00995
    Location:3444
    Sec1; Sec1 family
  3. NM_001283032.1NP_001269961.1  sec1 family domain-containing protein 1 isoform e

    See identical proteins and their annotated locations for NP_001269961.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks an exon in the 5' region and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (e) is shorter and has a distinct N-terminus, compared to isoform a.
    Source sequence(s)
    AF067205, AK301406, BG212062, BX325898, DB105324
    UniProtKB/Swiss-Prot
    Q8WVM8
    UniProtKB/TrEMBL
    B7Z738
    Conserved Domains (1) summary
    pfam00995
    Location:16570
    Sec1; Sec1 family
  4. NM_001283033.1NP_001269962.1  sec1 family domain-containing protein 1 isoform d

    See identical proteins and their annotated locations for NP_001269962.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) lacks three exons in the 5' region and initiates translation at an alternate downstream start codon, compared to variant 1. The encoded isoform (d) has a shorter N-terminus, compared to isoform a. Variants 4 and 6 encode the same isoform (d).
    Source sequence(s)
    AK307960, BG212062, DB105324, DN993082
    UniProtKB/TrEMBL
    B7Z5N7
    Conserved Domains (1) summary
    pfam00995
    Location:3444
    Sec1; Sec1 family
  5. NM_016106.3NP_057190.2  sec1 family domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_057190.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AB020724, BG212062, DB105324
    Consensus CDS
    CCDS9639.1
    UniProtKB/Swiss-Prot
    Q8WVM8
    Related
    ENSP00000390783.2, OTTHUMP00000178786, ENST00000458591.6, OTTHUMT00000276612
    Conserved Domains (1) summary
    pfam00995
    Location:44629
    Sec1; Sec1 family
  6. NM_182835.2NP_878255.1  sec1 family domain-containing protein 1 isoform b

    See identical proteins and their annotated locations for NP_878255.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (b) has a shorter N-terminus, compared to isoform a.
    Source sequence(s)
    AK316212, BG212062, DB105324
    Consensus CDS
    CCDS45092.1
    UniProtKB/Swiss-Prot
    Q8WVM8
    Related
    ENSP00000443010.2, OTTHUMP00000244059, ENST00000544052.6, OTTHUMT00000073326
    Conserved Domains (1) summary
    pfam00995
    Location:2562
    Sec1; Sec1 family

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    30622254..30735828
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011536587.3XP_011534889.1  sec1 family domain-containing protein 1 isoform X2

    Conserved Domains (1) summary
    pfam00995
    Location:44462
    Sec1; Sec1 family
  2. XM_011536588.3XP_011534890.1  sec1 family domain-containing protein 1 isoform X3

    Conserved Domains (1) summary
    pfam00995
    Location:44414
    Sec1; Sec1 family
  3. XM_011536589.2XP_011534891.1  sec1 family domain-containing protein 1 isoform X4

    Conserved Domains (1) summary
    pfam00995
    Location:44414
    Sec1; Sec1 family
  4. XM_017021113.2XP_016876602.1  sec1 family domain-containing protein 1 isoform X5

  5. XM_005267469.2XP_005267526.1  sec1 family domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_005267526.1

    Conserved Domains (1) summary
    pfam00995
    Location:19437
    Sec1; Sec1 family

RNA

  1. XR_429299.3 RNA Sequence

    Related
    ENST00000311943.11
  2. XR_001750201.1 RNA Sequence

    Related
    ENST00000484733.6, OTTHUMT00000073325
  3. XR_001750202.2 RNA Sequence

  4. XR_002957538.1 RNA Sequence

  5. XR_002957540.1 RNA Sequence

  6. XR_002957539.1 RNA Sequence

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