Human Gene SCYL3 (ENST00000367771.11_11) from GENCODE V47lift37
  Description: SCY1 like pseudokinase 3, transcript variant 1 (from RefSeq NM_020423.7)
Gencode Transcript: ENST00000367771.11_11
Gencode Gene: ENSG00000000457.14_14
Transcript (Including UTRs)
   Position: hg19 chr1:169,818,772-169,863,037 Size: 44,266 Total Exon Count: 13 Strand: -
Coding Region
   Position: hg19 chr1:169,822,854-169,857,981 Size: 35,128 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:169,818,772-169,863,037)mRNA (may differ from genome)Protein (688 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PACE1_HUMAN
DESCRIPTION: RecName: Full=Protein-associating with the carboxyl-terminal domain of ezrin; AltName: Full=Ezrin-binding protein PACE-1; AltName: Full=SCY1-like protein 3;
FUNCTION: May play a role in regulating cell adhesion/migration complexes in migrating cells.
SUBUNIT: Interacts with EZR/VIL2 C-terminal domain.
INTERACTION: P15311:EZR; NbExp=4; IntAct=EBI-1380680, EBI-1056902;
SUBCELLULAR LOCATION: Cytoplasm. Golgi apparatus. Cell projection, lamellipodium. Note=Colocalized with EZR/VIL2, actin and CD44 in lamellipodia.
TISSUE SPECIFICITY: Ubiquitously expressed.
DOMAIN: The protein kinase domain is predicted to be catalytically inactive.
PTM: May be myristoylated; myristoylation may target it to Golgi compartment.
PTM: Phosphorylated.
SIMILARITY: Belongs to the protein kinase superfamily.
SIMILARITY: Contains 4 HEAT repeats.
SIMILARITY: Contains 1 protein kinase domain.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.10 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 200.33 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -66.10159-0.416 Picture PostScript Text
3' UTR -1084.504082-0.266 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
IPR021133 - HEAT_type_2
IPR011009 - Kinase-like_dom
IPR000719 - Prot_kinase_cat_dom

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

ModBase Predicted Comparative 3D Structure on Q8IZE3
FrontTopSide
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 orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity

Biological Process:
GO:0006468 protein phosphorylation
GO:0016477 cell migration

Cellular Component:
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0030027 lamellipodium
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  BX647352 - Homo sapiens mRNA; cDNA DKFZp686J19244 (from clone DKFZp686J19244).
JD478501 - Sequence 459525 from Patent EP1572962.
JD543180 - Sequence 524204 from Patent EP1572962.
LF205424 - JP 2014500723-A/12927: Polycomb-Associated Non-Coding RNAs.
AL117233 - Novel human gene mapping to chomosome 1.
BC014662 - Homo sapiens SCY1-like 3 (S. cerevisiae), mRNA (cDNA clone MGC:23025 IMAGE:4852719), complete cds.
AK292507 - Homo sapiens cDNA FLJ76448 complete cds, highly similar to Homo sapiens SCY1-like 3 (S. cerevisiae) (SCYL3), transcript variant 2, mRNA.
AF540957 - Homo sapiens ezrin-binding partner PACE-1 mRNA, complete cds.
AY144493 - Homo sapiens ezrin-binding protein PACE-1 mRNA, complete cds; alternatively spliced.
JD026993 - Sequence 8017 from Patent EP1572962.
JD028959 - Sequence 9983 from Patent EP1572962.
JD118275 - Sequence 99299 from Patent EP1572962.
JD135344 - Sequence 116368 from Patent EP1572962.
AK304481 - Homo sapiens cDNA FLJ51470 complete cds, highly similar to Homo sapiens SCY1-like 3 (SCYL3), transcript variant 1, mRNA.
JD297607 - Sequence 278631 from Patent EP1572962.
JD094164 - Sequence 75188 from Patent EP1572962.
JD266958 - Sequence 247982 from Patent EP1572962.
KJ899315 - Synthetic construct Homo sapiens clone ccsbBroadEn_08709 SCYL3 gene, encodes complete protein.
KJ905514 - Synthetic construct Homo sapiens clone ccsbBroadEn_15121 SCYL3 gene, encodes complete protein.
DQ893468 - Synthetic construct clone IMAGE:100006098; FLH193486.01X; RZPDo839G0978D SCY1-like 3 (S. cerevisiae) (SCYL3) gene, encodes complete protein.
DQ896344 - Synthetic construct Homo sapiens clone IMAGE:100010804; FLH193482.01L; RZPDo839G0968D SCY1-like 3 (S. cerevisiae) (SCYL3) gene, encodes complete protein.
AB463242 - Synthetic construct DNA, clone: pF1KB8425, Homo sapiens SCYL3 gene for SCY1-like 3, without stop codon, in Flexi system.
AM393842 - Synthetic construct Homo sapiens clone IMAGE:100002438 for hypothetical protein (SCYL3 gene).
LF320374 - JP 2014500723-A/127877: Polycomb-Associated Non-Coding RNAs.
CU677085 - Synthetic construct Homo sapiens gateway clone IMAGE:100023393 5' read SCYL3 mRNA.
JD459847 - Sequence 440871 from Patent EP1572962.
LF320371 - JP 2014500723-A/127874: Polycomb-Associated Non-Coding RNAs.
JD064945 - Sequence 45969 from Patent EP1572962.
JD485514 - Sequence 466538 from Patent EP1572962.
JD285437 - Sequence 266461 from Patent EP1572962.
JD195231 - Sequence 176255 from Patent EP1572962.
JD225832 - Sequence 206856 from Patent EP1572962.
MA441001 - JP 2018138019-A/12927: Polycomb-Associated Non-Coding RNAs.
MA555951 - JP 2018138019-A/127877: Polycomb-Associated Non-Coding RNAs.
MA555948 - JP 2018138019-A/127874: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: A8K8Z2, ENST00000367771.1, ENST00000367771.10, ENST00000367771.2, ENST00000367771.3, ENST00000367771.4, ENST00000367771.5, ENST00000367771.6, ENST00000367771.7, ENST00000367771.8, ENST00000367771.9, NM_020423, PACE1, PACE1_HUMAN, Q5THA6, Q5THA8, Q8IZE3, Q8IZN9, Q96C56, Q9UBK6, uc318geo.1, uc318geo.2
UCSC ID: ENST00000367771.11_11
RefSeq Accession: NM_020423.7
Protein: Q8IZE3 (aka PACE1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.