Human Gene SDK1 (uc003smx.3) Description and Page Index
  Description: Homo sapiens sidekick cell adhesion molecule 1 (SDK1), transcript variant 1, mRNA.
RefSeq Summary (NM_152744): The protein encoded by this gene is a member of the immunoglobulin superfamily. The protein contains six immunoglobulin-like domains and thirteen fibronectin type III domains. Fibronectin type III domains are present in both extracellular and intracellular proteins and tandem repeats are known to contain binding sites for DNA, heparin and the cell surface. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016].
Transcript (Including UTRs)
   Position: hg19 chr7:3,341,080-4,308,631 Size: 967,552 Total Exon Count: 45 Strand: +
Coding Region
   Position: hg19 chr7:3,341,219-4,305,016 Size: 963,798 Coding Exon Count: 45 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:3,341,080-4,308,631)mRNA (may differ from genome)Protein (2213 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
  ID: SDK1_HUMAN
DESCRIPTION: RecName: Full=Protein sidekick-1; Flags: Precursor;
FUNCTION: Cell adhesion protein that guides axonal terminals to specific synapses in developing neurons. Dysregulation of this protein may play an important role in podocyte dysfunction in HIV- associated nephropathy.
SUBCELLULAR LOCATION: Membrane; Single-pass membrane protein (Potential).
TISSUE SPECIFICITY: Up-regulated in glomeruli in HIV-associated nephropathy. In diseased glomeruli, significantly overexpressed and the expression is no longer restricted to mesangial cells but includes podocytes and parietal epithelial cells.
SIMILARITY: Contains 13 fibronectin type-III domains.
SIMILARITY: Contains 6 Ig-like C2-type (immunoglobulin-like) domains.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SDK1
CDC HuGE Published Literature: SDK1
Positive Disease Associations: Blood Pressure Determination , Heart Failure , hypertension , Myocardial Infarction , Neuroblastoma , Platelet Aggregation , quantitative traits , Thyrotropin , Tunica Media
Related Studies:
  1. Blood Pressure Determination
    , , . [PubMed 0]
  2. Heart Failure
    , , . [PubMed 0]
  3. Heart Failure
    , , . [PubMed 0]
           more ... click here to view the complete list

-  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: 7.37 RPKM in Artery - Tibial
Total median expression: 85.99 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 -88.00139-0.633 Picture PostScript Text
3' UTR -1303.513615-0.361 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
IPR003961 - Fibronectin_type3
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR013098 - Ig_I-set
IPR003599 - Ig_sub
IPR003598 - Ig_sub2

Pfam Domains:
PF00041 - Fibronectin type III domain
PF00047 - Immunoglobulin domain
PF07679 - Immunoglobulin I-set domain
PF13895 - Immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin
49265 - Fibronectin type III

ModBase Predicted Comparative 3D Structure on Q7Z5N4
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 orthologGenome BrowserNo orthologGenome BrowserNo ortholog
Gene Details   Gene Details 
Gene Sorter   Gene Sorter 
  Ensembl WormBase 
  Protein Sequence Protein Sequence 
  Alignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0042802 identical protein binding

Biological Process:
GO:0007155 cell adhesion
GO:0007156 homophilic cell adhesion via plasma membrane adhesion molecules
GO:0007416 synapse assembly
GO:0010842 retina layer formation
GO:0045216 cell-cell junction organization
GO:0048148 behavioral response to cocaine
GO:0060998 regulation of dendritic spine development

Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0045202 synapse


-  Descriptions from all associated GenBank mRNAs
  AY310398 - Homo sapiens sidekick-like protein 1 (SDK1) mRNA, complete cds.
AK074083 - Homo sapiens mRNA for FLJ00154 protein.
AL833354 - Homo sapiens mRNA; cDNA DKFZp686M0535 (from clone DKFZp686M0535).
JD358793 - Sequence 339817 from Patent EP1572962.
AK074077 - Homo sapiens mRNA for FLJ00148 protein.
CQ873864 - Sequence 283 from Patent WO2004076622.
DD413701 - Regulation of Mammalian Cells.
AK055987 - Homo sapiens cDNA FLJ31425 fis, clone NT2NE2000455, weakly similar to Sdk (sidekick) protein.
JD042016 - Sequence 23040 from Patent EP1572962.
JD164360 - Sequence 145384 from Patent EP1572962.
JD300522 - Sequence 281546 from Patent EP1572962.
JD440666 - Sequence 421690 from Patent EP1572962.
JD401553 - Sequence 382577 from Patent EP1572962.
JD339194 - Sequence 320218 from Patent EP1572962.
JD321532 - Sequence 302556 from Patent EP1572962.
JD253050 - Sequence 234074 from Patent EP1572962.
JD146044 - Sequence 127068 from Patent EP1572962.
JD205103 - Sequence 186127 from Patent EP1572962.
JD066073 - Sequence 47097 from Patent EP1572962.
JD126167 - Sequence 107191 from Patent EP1572962.
JD143582 - Sequence 124606 from Patent EP1572962.
JD167004 - Sequence 148028 from Patent EP1572962.
JD489558 - Sequence 470582 from Patent EP1572962.
JD254790 - Sequence 235814 from Patent EP1572962.
JD513845 - Sequence 494869 from Patent EP1572962.
JD195043 - Sequence 176067 from Patent EP1572962.
JD153790 - Sequence 134814 from Patent EP1572962.
JD116567 - Sequence 97591 from Patent EP1572962.
JD057468 - Sequence 38492 from Patent EP1572962.
JD192499 - Sequence 173523 from Patent EP1572962.
JD098163 - Sequence 79187 from Patent EP1572962.
JD100854 - Sequence 81878 from Patent EP1572962.
AK055988 - Homo sapiens cDNA FLJ31426 fis, clone NT2NE2000470.
JD226761 - Sequence 207785 from Patent EP1572962.
AF131799 - Homo sapiens clone 25155 mRNA sequence.
JD398506 - Sequence 379530 from Patent EP1572962.
JD525429 - Sequence 506453 from Patent EP1572962.
JD151856 - Sequence 132880 from Patent EP1572962.
JD296643 - Sequence 277667 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q7Z5N4 (Reactome details) participates in the following event(s):

R-HSA-373745 SDK1 homophillic interaction
R-HSA-373756 SDK interactions
R-HSA-421270 Cell-cell junction organization
R-HSA-446728 Cell junction organization
R-HSA-1500931 Cell-Cell communication

-  Other Names for This Gene
  Alternate Gene Symbols: NM_152744, NP_689957, Q7Z5N4, Q8TEN9, Q8TEP5, Q96N44, SDK1_HUMAN
UCSC ID: uc003smx.3
RefSeq Accession: NM_152744
Protein: Q7Z5N4 (aka SDK1_HUMAN)
CCDS: CCDS34590.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_152744.3
exon count: 45CDS single in 3' UTR: no RNA size: 10397
ORF size: 6642CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 12925.00frame shift in genome: no % Coverage: 99.99
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 3751# strange splices: 0
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.