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SCOC short coiled-coil protein [ Homo sapiens (human) ]

Gene ID: 60592, updated on 5-Mar-2024

Summary

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Official Symbol
SCOCprovided by HGNC
Official Full Name
short coiled-coil proteinprovided by HGNC
Primary source
HGNC:HGNC:20335
See related
Ensembl:ENSG00000153130 AllianceGenome:HGNC:20335
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SCOCO; UNC-69; HRIHFB2072
Summary
This gene encodes a short coiled-coiled domain-containing protein that localizes to the Golgi apparatus. The encoded protein interacts with ADP-ribosylation factor-like proteins. Pseudogenes of this gene are found on chromosomes 1 and 14. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Expression
Ubiquitous expression in brain (RPKM 55.6), thyroid (RPKM 34.6) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
4q31.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (140257308..140385728)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (143577068..143705503)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (141178462..141306882)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene mastermind like transcriptional coactivator 3 Neighboring gene uncharacterized LOC101927516 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:141071212-141072056 Neighboring gene H3K27ac hESC enhancer GRCh37_chr4:141072057-141072899 Neighboring gene Sharpr-MPRA regulatory region 8632 Neighboring gene uncharacterized LOC124900784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15708 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr4:141187913-141189112 Neighboring gene uncharacterized LOC124900785 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:141237061-141237740 Neighboring gene SCOC antisense RNA 1 Neighboring gene NADH:ubiquinone oxidoreductase subunit B4 pseudogene 9 Neighboring gene OCT4 hESC enhancer GRCh37_chr4:141294483-141294984 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:141334799-141335364 Neighboring gene ribosomal protein L14 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21935 Neighboring gene calmegin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:141418967-141419468 Neighboring gene MGAT4 family member D

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. Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity. Wirth M, et al. J Mol Biol, 2021 Jun 25. PMID 33845085, Free PMC Article
  2. Crystal structure of the human short coiled coil protein and insights into SCOC-FEZ1 complex formation. Behrens C, et al. PLoS One, 2013. PMID 24098481, Free PMC Article
  3. Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO). Alborghetti MR, et al. PLoS One, 2013. PMID 24116125, Free PMC Article
  4. Genome-wide association study of lifetime cannabis use based on a large meta-analytic sample of 32 330 subjects from the International Cannabis Consortium. Stringer S, et al. Transl Psychiatry, 2016 Mar 29. PMID 27023175, Free PMC Article
  5. ADP-ribosylation factors (ARFs) and ARF-like 1 (ARL1) have both specific and shared effectors: characterizing ARL1-binding proteins. Van Valkenburgh H, et al. J Biol Chem, 2001 Jun 22. PMID 11303027

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity.
    Title: Phosphorylation of the LIR Domain of SCOC Modulates ATG8 Binding Affinity and Specificity.
  2. SCOC SNPs were associated with lifetime cannabis use, but the association did not reach genome-wide significance. [Meta-Analysis]
    Title: Genome-wide association study of lifetime cannabis use based on a large meta-analytic sample of 32 330 subjects from the International Cannabis Consortium.
  3. SCOC forms a stable homogeneous complex with the coiled coil domain of FEZ1. SCOC dimerization and the SCOC surface residue R117 are important for this interaction.
    Title: Crystal structure of the human short coiled coil protein and insights into SCOC-FEZ1 complex formation.
  4. Studies indicate that FEZ1 (fasciculation and elongation protein zeta 1), SCOCO (short coiled-coil protein) and kinesins (kinesin heavy chain) are involved in biological transport process.
    Title: Structural analysis of intermolecular interactions in the kinesin adaptor complex fasciculation and elongation protein zeta 1/ short coiled-coil protein (FEZ1/SCOCO).
  5. The identification of SCOC and WAC as novel regulatory proteins with diverse functions in autophagy contributes towards a fuller understanding of autophagosome formation.
    Title: Genome-wide siRNA screen reveals amino acid starvation-induced autophagy requires SCOC and WAC.
  6. 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

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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 positive regulation of macroautophagy IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of protein complex stability IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
colocalizes_with endosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
colocalizes_with trans-Golgi network IBA
Inferred from Biological aspect of Ancestor
more info
  
colocalizes_with trans-Golgi network IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
short coiled-coil 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_001153446.1 → NP_001146918.1  short coiled-coil protein isoform 4

    See identical proteins and their annotated locations for NP_001146918.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and 5' coding region, compared to variant 1, resulting in an isoform (4) with a distinct and shorter N-terminus, compared to isoform 1. Variants 4, 5 and 6 encode the same isoform.
    Source sequence(s)
    AA213765, AF448857, DB204055
    Consensus CDS
    CCDS3750.1
    UniProtKB/Swiss-Prot
    Q9UIL1
    Related
    ENSP00000345262.4, ENST00000338517.8
    Conserved Domains (1) summary
    pfam10224
    Location:42 → 113
    DUF2205; Predicted coiled-coil protein (DUF2205)

  2. NM_001153484.2 → NP_001146956.2  short coiled-coil protein isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC093671
    Consensus CDS
    CCDS54806.2
    UniProtKB/TrEMBL
    A0A0C4DGB0
    Related
    ENSP00000477352.2, ENST00000608372.6
    Conserved Domains (1) summary
    pfam10224
    Location:13 → 73
    DUF2205; Predicted coiled-coil protein (DUF2205)

  3. NM_001153552.2 → NP_001147024.2  short coiled-coil protein isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter compared to isoform 1.
    Source sequence(s)
    AC093671
    Consensus CDS
    CCDS54807.2
    UniProtKB/TrEMBL
    A0A804E055
    Related
    ENSP00000426649.2, ENST00000506597.2
    Conserved Domains (1) summary
    pfam10224
    Location:1 → 45
    DUF2205; Predicted coiled-coil protein (DUF2205)

  4. NM_001153585.1 → NP_001147057.1  short coiled-coil protein isoform 4

    See identical proteins and their annotated locations for NP_001147057.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and 5' coding region, compared to variant 1, resulting in an isoform (4) with a distinct and shorter N-terminus, compared to isoform 1. Variants 4, 5 and 6 encode the same isoform.
    Source sequence(s)
    AA213765, BC016511, DA625782
    Consensus CDS
    CCDS3750.1
    UniProtKB/Swiss-Prot
    Q9UIL1
    Related
    ENSP00000377753.3, ENST00000394203.7
    Conserved Domains (1) summary
    pfam10224
    Location:42 → 113
    DUF2205; Predicted coiled-coil protein (DUF2205)

  5. NM_001153635.1 → NP_001147107.1  short coiled-coil protein isoform 5

    See identical proteins and their annotated locations for NP_001147107.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR, has multiple differences in the coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (5) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AA213765, BC062684, BG151522, DB204055
    UniProtKB/Swiss-Prot
    Q9UIL1
    Conserved Domains (1) summary
    pfam10224
    Location:42 → 112
    DUF2205; Predicted coiled-coil protein (DUF2205)

  6. NM_001153663.1 → NP_001147135.1  short coiled-coil protein isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
    Source sequence(s)
    AA213765, BC016511, CN367654, DB465370
    UniProtKB/Swiss-Prot
    B7WPH7, D3DNY7, E9PB65, Q6P5T9, Q7L2Y0, Q7Z4P2, Q96JY9, Q9BZB2, Q9UIL1
    Conserved Domains (1) summary
    pfam10224
    Location:79 → 149
    DUF2205; Predicted coiled-coil protein (DUF2205)

  7. NM_001153690.1 → NP_001147162.1  short coiled-coil protein isoform 6

    Status: REVIEWED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR, has multiple differences in the coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (6) has a distinct N-terminus and is shorter than isoform 1.
    Source sequence(s)
    AA213765, BC016511, BU070009, DA625782
    UniProtKB/Swiss-Prot
    Q9UIL1
    Conserved Domains (1) summary
    pfam10224
    Location:40 → 85
    DUF2205; Predicted coiled-coil protein (DUF2205)

  8. NM_032547.3 → NP_115936.2  short coiled-coil protein isoform 4

    See identical proteins and their annotated locations for NP_115936.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, compared to variant 1, resulting in an isoform (4) with a distinct and shorter N-terminus, compared to isoform 1. Variants 4, 5 and 6 encode the same isoform.
    Source sequence(s)
    AA213765, AC093671, AC114771, AK027797
    Consensus CDS
    CCDS3750.1
    UniProtKB/Swiss-Prot
    Q9UIL1
    Related
    ENSP00000377755.3, ENST00000394205.7
    Conserved Domains (1) summary
    pfam10224
    Location:42 → 113
    DUF2205; Predicted coiled-coil protein (DUF2205)

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_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    140257308..140385728
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047416067.1 → XP_047272023.1  short coiled-coil protein isoform X1

    UniProtKB/TrEMBL
    A0A0C4DGB0
    Related
    ENSP00000426810.1, ENST00000506322.5

  2. XM_047416068.1 → XP_047272024.1  short coiled-coil protein isoform X2

    UniProtKB/TrEMBL
    A0A804E055

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    143577068..143705503
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350699.1 → XP_054206674.1  short coiled-coil protein isoform X1

    UniProtKB/TrEMBL
    A0A0C4DGB0

  2. XM_054350700.1 → XP_054206675.1  short coiled-coil protein isoform X2

    UniProtKB/TrEMBL
    A0A804E055
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UIL1.2 GenPept UniProtKB/Swiss-Prot:Q9UIL1

Gene LinkOut

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