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SCYL2 SCY1 like pseudokinase 2 [ Homo sapiens (human) ]

Gene ID: 55681, updated on 15-Jun-2019

Summary

Official Symbol
SCYL2provided by HGNC
Official Full Name
SCY1 like pseudokinase 2provided by HGNC
Primary source
HGNC:HGNC:19286
See related
Ensembl:ENSG00000136021 MIM:616365
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
CVAK104
Summary
The protein encoded by this gene associates with clathrin-coated complexes at the plasma membrane and with endocytic coated vesicles. The encoded protein phosphorylates the beta2 subunit of the plasma membrane adapter complex AP2 and interacts with clathrin, showing involvement in clathrin-dependent pathways between the trans-Golgi network and the endosomal system. In addition, this protein has a role in the Wnt signaling pathway by targeting frizzled 5 (Fzd5) for lysosomal degradation. Two transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Dec 2015]
Expression
Ubiquitous expression in colon (RPKM 12.7), esophagus (RPKM 10.5) and 25 other tissues See more
Orthologs

Genomic context

See SCYL2 in Genome Data Viewer
Location:
12q23.1
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (100267140..100341724)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (100660918..100735502)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene microRNA 1827 Neighboring gene DEP domain containing 4 Neighboring gene actin related protein 6 Neighboring gene solute carrier family 17 member 8 Neighboring gene nuclear receptor subfamily 1 group H member 4

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 FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association study identifies a novel susceptibility locus at 12q23.1 for lung squamous cell carcinoma in han chinese.
NHGRI GWA Catalog

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of SCY1-like 2 (SCYL2) by siRNA enhances HIV-1 release in transfected HeLa cells PubMed

Protein interactions

Protein Gene Interaction Pubs
Nef nef Genome-wide shRNA screening identifies SCYL2, which is required for HIV-1 Nef-induced downregulation of CD4 in HeLa CD4+ cells PubMed
Vpu vpu IFN-alpha and IFN-beta increases SCYL2 expression and the increase induces PP2A-mediated dephosphorylation of Vpu, suggesting that SCYL2 affects Vpu function through a phosphorylation-dependent mechanism PubMed
vpu Both the kinase-like domain (residues 1-375) and the clathrin-binding domain (residues 697-929) of SCYL2 are required for its anti-Vpu activity PubMed
vpu SCYL2 inhibits Vpu-induced BST2 and CD4 reduction at the cell surface by suppressing the phosphorylation of Vpu at positions Ser-52 and Ser-56 PubMed
vpu In vitro protein-protein interaction analysis identifies a Vpu-binding host protein SCYL2, which inhibits the particle release of Vpu-positive HIV-1, but not Vpu-deficient HIV-1 PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10074, KIAA1360

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase activity IEA
Inferred from Electronic Annotation
more info
 
signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IEA
Inferred from Electronic Annotation
more info
 
clathrin-coated vesicle IEA
Inferred from Electronic Annotation
more info
 
endosome membrane IEA
Inferred from Electronic Annotation
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
SCY1-like protein 2
Names
SCY1-like 2
SCY1-like, kinase-like 2
coated vesicle-associated kinase of 104 kDa

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_001317784.1NP_001304713.1  SCY1-like protein 2 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AB037781, BC011525, CN337316, DA234206
    Consensus CDS
    CCDS9076.1
    UniProtKB/Swiss-Prot
    Q6P3W7
    Conserved Domains (2) summary
    cd14011
    Location:38329
    PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
    sd00044
    Location:373403
    HEAT; HEAT repeat [structural motif]
  2. NM_001330253.1NP_001317182.1  SCY1-like protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate in-frame exon in its central coding region, compared to variant 1. The encoded isoform (2) has the same N- and C-termini, but is longer than isoform 1. Both variants 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AB037781, BC063798, CN337316, DB127407
    Consensus CDS
    CCDS81726.1
    UniProtKB/Swiss-Prot
    Q6P3W7
    UniProtKB/TrEMBL
    A0A0U1RQQ9
  3. NM_001330254.1NP_001317183.1  SCY1-like protein 2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and contains an alternate in-frame exon in its central coding region, compared to variant 1. The encoded isoform (2) has the same N- and C-termini, but is longer than isoform 1. Both variants 3 and 4 encode the same isoform (2).
    Source sequence(s)
    AB037781, BC011525, CN337316, DA234206
    Consensus CDS
    CCDS81726.1
    UniProtKB/Swiss-Prot
    Q6P3W7
    UniProtKB/TrEMBL
    A0A0U1RQQ9
    Related
    ENSP00000489123.1, ENST00000635101.1
  4. NM_001330256.1NP_001317185.1  SCY1-like protein 2 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and contains two alternate exons compared to variant 1. This variant represents translation initiation at a downstream start codon compared to variant 1; the 5'-most initiation codon, as used in variant 1, is associated with a truncated ORF that would render the transcript a candidate for nonsense-mediated decay (NMD). Leaky scanning may allow translation initiation at the downstream start codon to encode an isoform (3) that has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AB037781, AC026110, BC011525, CN337316, DA234206, DB261340
    UniProtKB/Swiss-Prot
    Q6P3W7
  5. NM_017988.6NP_060458.3  SCY1-like protein 2 isoform 1

    See identical proteins and their annotated locations for NP_060458.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1. Both variants 1 and 2 encode the same protein.
    Source sequence(s)
    AB037781, AC026110, BC063798, CN337316, DB127407
    Consensus CDS
    CCDS9076.1
    UniProtKB/Swiss-Prot
    Q6P3W7
    Related
    ENSP00000354061.2, ENST00000360820.6
    Conserved Domains (2) summary
    cd14011
    Location:38329
    PK_SCY1_like; Pseudokinase domain of Scy1-like proteins
    sd00044
    Location:373403
    HEAT; HEAT repeat [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    100267140..100341724
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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