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

Gene ID: 23256, updated on 8-Jul-2021

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 MIM:618207
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
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Genomic context

See SCFD1 in Genome Data Viewer
Location:
14q12
Exon count:
29
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (30622254..30735850)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (31091460..31205056)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What'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 PubChem

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
enables protein N-terminus binding IEA
Inferred from Electronic Annotation
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-containing complex binding ISS
Inferred from Sequence or Structural Similarity
more info
 
enables syntaxin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables syntaxin binding ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
involved_in cell morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in negative regulation of autophagosome assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in post-Golgi vesicle-mediated transport ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of ER to Golgi vesicle-mediated transport ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in regulation of protein transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in response to hypoxia IEA
Inferred from Electronic Annotation
more info
 
involved_in response to toxic substance IEP
Inferred from Expression Pattern
more info
PubMed 
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in toxin transport IEA
Inferred from Electronic Annotation
more info
 
involved_in vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
located_in Golgi cisterna membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in Golgi membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in Golgi-associated vesicle ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in cis-Golgi network IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
 
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
 
located_in 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)

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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_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, ENST00000396629.6
    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
    Related
    ENSP00000504658.1, ENST00000676520.1
    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
    Related
    ENSP00000502860.1, ENST00000676674.1
    Conserved Domains (1) summary
    pfam00995
    Location:3444
    Sec1; Sec1 family
  5. NM_016106.4NP_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, AL121852, BG212062
    Consensus CDS
    CCDS9639.1
    UniProtKB/Swiss-Prot
    Q8WVM8
    Related
    ENSP00000390783.2, ENST00000458591.7
    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, ENST00000544052.6
    Conserved Domains (1) summary
    pfam00995
    Location:1562
    Sec1; Sec1 family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    30622254..30735850
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Related
    ENSP00000503287.1, ENST00000679102.1
    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

    Related
    ENSP00000504309.1, ENST00000678760.1
    Conserved Domains (1) summary
    pfam00995
    Location:44414
    Sec1; Sec1 family
  4. XM_017021113.2XP_016876602.1  sec1 family domain-containing protein 1 isoform X5

    Related
    ENSP00000504339.1, ENST00000678475.1
  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

    Related
    ENSP00000504124.1, ENST00000677340.1
    Conserved Domains (1) summary
    pfam00995
    Location:19604
    Sec1; Sec1 family

RNA

  1. XR_429299.3 RNA Sequence

    Related
    ENST00000677637.1
  2. XR_001750201.1 RNA Sequence

    Related
    ENST00000676834.1
  3. XR_001750202.2 RNA Sequence

    Related
    ENST00000678516.1
  4. XR_002957538.1 RNA Sequence

    Related
    ENST00000678396.1
  5. XR_002957540.1 RNA Sequence

    Related
    ENST00000679096.1
  6. XR_002957539.1 RNA Sequence

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