Human Gene SCYL2 (uc001thn.3) Description and Page Index
  Description: Homo sapiens SCY1-like 2 (S. cerevisiae) (SCYL2), mRNA.
RefSeq Summary (NM_017988): 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].
Transcript (Including UTRs)
   Position: hg19 chr12:100,661,549-100,733,914 Size: 72,366 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr12:100,676,749-100,732,950 Size: 56,202 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:100,661,549-100,733,914)mRNA (may differ from genome)Protein (929 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=SCY1-like protein 2; AltName: Full=Coated vesicle-associated kinase of 104 kDa;
FUNCTION: Component of AP2-containing clathrin coated structures at the plasma membrane or of endocytic coated vesicles. According to PubMed:15809293, probable serine/threonine-protein kinase that phosphorylates, in vitro, the beta2-subunit of the plasma membrane adapter complex AP2 and other proteins in presence of poly-L- lysine. According to PubMed:16914521, has no detectable kinase activity in vitro. May regulate clathrin-dependent trafficking between the TGN and/or the endosomal system.
SUBUNIT: Interacts with clathrin and AP2B1; the interaction mediates the association with the AP-2 complex.
SUBCELLULAR LOCATION: Cytoplasm, perinuclear region. Cytoplasmic vesicle, clathrin-coated vesicle. Golgi apparatus, trans-Golgi network membrane. Endosome membrane. Note=According to PubMed:15809293, plasma membrane-associated in clathrin-coated vesicles. According to PubMed:16914521, colocalizes to the trans- Golgi network (TGN) and to endosomal membranes with clathrin, transferrin and plasma membrane adapter AP1 and AP3 complexes.
PTM: According to PubMed:15809293, autophosphorylated in presence of poly-L-lysine.
SIMILARITY: Belongs to the protein kinase superfamily.
SIMILARITY: Contains 1 HEAT repeat.
SIMILARITY: Contains 1 protein kinase domain.
SEQUENCE CAUTION: Sequence=BAA91778.1; Type=Erroneous initiation; Sequence=BAB14869.1; Type=Erroneous initiation; Sequence=BAB55194.1; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: SCYL2
Diseases sorted by gene-association score: cataract 8, multiple types (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 10.99 RPKM in Pituitary
Total median expression: 383.34 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -8.2050-0.164 Picture PostScript Text
3' UTR -218.06964-0.226 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011989 - ARM-like
IPR016024 - ARM-type_fold
IPR011009 - Kinase-like_dom
IPR000719 - Prot_kinase_cat_dom

Pfam Domains:
PF00069 - Protein kinase domain
PF07714 - Protein tyrosine kinase

SCOP Domains:
48371 - ARM repeat
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on Q6P3W7
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene Details  Gene DetailsGene DetailsGene Details
Gene Sorter  Gene SorterGene SorterGene Sorter
  Protein SequenceProtein SequenceProtein SequenceProtein Sequence

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004672 protein kinase activity
GO:0005102 receptor binding
GO:0005515 protein binding
GO:0005524 ATP binding

Biological Process:
GO:0002092 positive regulation of receptor internalization
GO:0006468 protein phosphorylation
GO:0008333 endosome to lysosome transport
GO:0090090 negative regulation of canonical Wnt signaling pathway
GO:2000286 receptor internalization involved in canonical Wnt signaling pathway
GO:2000370 positive regulation of clathrin-dependent endocytosis

Cellular Component:
GO:0005737 cytoplasm
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0030136 clathrin-coated vesicle
GO:0031410 cytoplasmic vesicle
GO:0048471 perinuclear region of cytoplasm

-  Descriptions from all associated GenBank mRNAs
  AK000936 - Homo sapiens cDNA FLJ10074 fis, clone HEMBA1001744, weakly similar to SCY1 PROTEIN.
BC011525 - Homo sapiens SCY1-like 2 (S. cerevisiae), mRNA (cDNA clone IMAGE:3873314), with apparent retained intron.
AK125091 - Homo sapiens cDNA FLJ43101 fis, clone CTONG2006798, weakly similar to Serine/threonine protein kinase.
AK292980 - Homo sapiens cDNA FLJ78687 complete cds, highly similar to Homo sapiens SCY1-like 2 (SCYL2), mRNA.
BC063798 - Homo sapiens SCY1-like 2 (S. cerevisiae), mRNA (cDNA clone MGC:70725 IMAGE:6473586), complete cds.
KJ894234 - Synthetic construct Homo sapiens clone ccsbBroadEn_03628 SCYL2 gene, encodes complete protein.
AB462923 - Synthetic construct DNA, clone: pF1KSDA1360, Homo sapiens SCYL2 gene for SCY1-like 2, without stop codon, in Flexi system.
AB037781 - Homo sapiens mRNA for KIAA1360 protein, partial cds.
AK027551 - Homo sapiens cDNA FLJ14645 fis, clone NT2RP2001839, weakly similar to SCY1 PROTEIN.
AK024274 - Homo sapiens cDNA FLJ14212 fis, clone NT2RP3003500, weakly similar to SCY1 PROTEIN.
BC012387 - Homo sapiens SCY1-like 2 (S. cerevisiae), mRNA (cDNA clone IMAGE:3882729), partial cds.
AK001597 - Homo sapiens cDNA FLJ10735 fis, clone NT2RP3001407, weakly similar to SCY1 PROTEIN.
AK026160 - Homo sapiens cDNA: FLJ22507 fis, clone HRC11710.
JD363107 - Sequence 344131 from Patent EP1572962.
JD527831 - Sequence 508855 from Patent EP1572962.
AL133044 - Homo sapiens mRNA; cDNA DKFZp566D124 (from clone DKFZp566D124).
JD551068 - Sequence 532092 from Patent EP1572962.
DQ570951 - Homo sapiens piRNA piR-31063, complete sequence.
JD066233 - Sequence 47257 from Patent EP1572962.
JD236072 - Sequence 217096 from Patent EP1572962.
JD037785 - Sequence 18809 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A8KAB5, CVAK104, KIAA1360, NM_017988, NP_060458, Q6P3W7, Q96EF4, Q96ST4, Q9H7V5, Q9NVH3, Q9P2I7, SCYL2_HUMAN
UCSC ID: uc001thn.3
RefSeq Accession: NM_017988
Protein: Q6P3W7 (aka SCYL2_HUMAN)
CCDS: CCDS9076.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_017988.4
exon count: 18CDS single in 3' UTR: no RNA size: 3818
ORF size: 2790CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5780.00frame shift in genome: no % Coverage: 99.63
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.