Human Gene SEC23IP (uc001leu.2)
  Description: Homo sapiens SEC23 interacting protein (SEC23IP), transcript variant 1, mRNA.
RefSeq Summary (NM_007190): This gene encodes a member of the phosphatidic acid preferring-phospholipase A1 family. The encoded protein is localized to endoplasmic reticulum exit sites and plays a critical role in ER-Golgi transport as part of the multimeric coat protein II complex. An orthologous gene in frogs is required for normal neural crest cell development, suggesting that this gene may play a role in Waardenburg syndrome neural crest defects. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011].
Transcript (Including UTRs)
   Position: hg19 chr10:121,652,085-121,704,170 Size: 52,086 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg19 chr10:121,652,295-121,693,279 Size: 40,985 Coding Exon Count: 18 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsMalaCards
CTDGene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein Structure
Other SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:121,652,085-121,704,170)mRNA (may differ from genome)Protein (1000 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
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MGIneXtProtOMIMPubMedReactomeTreefam
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: S23IP_HUMAN
DESCRIPTION: RecName: Full=SEC23-interacting protein; AltName: Full=p125;
FUNCTION: Plays a role in the organization of endoplasmic reticulum exit sites.
SUBUNIT: Interacts with SEC23A.
SUBCELLULAR LOCATION: Cytoplasmic vesicle, COPII-coated vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Endoplasmic reticulum (Probable).
TISSUE SPECIFICITY: Ubiquitously expressed with stronger levels detected in heart, liver and skeletal muscle.
SIMILARITY: Belongs to the PA-PLA1 family.
SIMILARITY: Contains 1 DDHD domain.
SIMILARITY: Contains 1 SAM (sterile alpha motif) domain.
CAUTION: Although belonging to the PA-PL1 family, does not seem to have any phospholipase activity.
SEQUENCE CAUTION: Sequence=AAP35401.1; Type=Frameshift; Positions=471;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SEC23IP
CDC HuGE Published Literature: SEC23IP
Positive Disease Associations: Body Mass Index , C-Reactive Protein , Carotid Artery Diseases , Cholesterol, LDL , Echocardiography , Electrocardiography , Glomerular Filtration Rate , Heart Rate , Hematocrit , Sleep , Waist-Hip Ratio
Related Studies:
  1. Body Mass Index
    , , . [PubMed 0]
  2. Body Mass Index
    , , . [PubMed 0]
  3. C-Reactive Protein
    Emelia J Benjamin et al. BMC medical genetics 2007, Genome-wide association with select biomarker traits in the Framingham Heart Study., BMC medical genetics. [PubMed 17903293]
    The Framingham GWAS represents a resource to describe potentially novel genetic influences on systemic biomarker variability. The newly described associations will need to be replicated in other studies.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SEC23IP
Diseases sorted by gene-association score: waardenburg's syndrome (7)

-  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: 13.91 RPKM in Cells - Cultured fibroblasts
Total median expression: 356.16 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 -87.90210-0.419 Picture PostScript Text
3' UTR -1189.364093-0.291 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
IPR004177 - DDHD
IPR001660 - SAM
IPR013761 - SAM/pointed
IPR021129 - SAM_type1

Pfam Domains:
PF00536 - SAM domain (Sterile alpha motif)
PF02862 - DDHD domain

SCOP Domains:
47769 - SAM/Pointed domain

ModBase Predicted Comparative 3D Structure on Q9Y6Y8
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 orthologGenome BrowserGenome BrowserGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsemblFlyBase  
 Protein SequenceProtein SequenceProtein Sequence  
 AlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0004620 phospholipase activity
GO:0005515 protein binding
GO:0046872 metal ion binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0007030 Golgi organization
GO:0048208 COPII vesicle coating

Cellular Component:
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005793 endoplasmic reticulum-Golgi intermediate compartment
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0012507 ER to Golgi transport vesicle membrane
GO:0016020 membrane
GO:0030134 ER to Golgi transport vesicle
GO:0031410 cytoplasmic vesicle
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AB019435 - Homo sapiens mRNA for putative phospholipase, complete cds.
AK021846 - Homo sapiens cDNA FLJ11784 fis, clone HEMBA1006031, highly similar to Homo sapiens mRNA for putative phospholipase.
AK314592 - Homo sapiens cDNA, FLJ95426.
JD490226 - Sequence 471250 from Patent EP1572962.
AK301517 - Homo sapiens cDNA FLJ55643 complete cds, highly similar to SEC23-interacting protein.
AK001135 - Homo sapiens cDNA FLJ10273 fis, clone HEMBB1001137, highly similar to SEC23-interacting protein.
BC063800 - Homo sapiens SEC23 interacting protein, mRNA (cDNA clone MGC:70759 IMAGE:6514739), complete cds.
BC002540 - Homo sapiens cDNA clone IMAGE:3138899, containing frame-shift errors.
AF116723 - Homo sapiens MSTP053 mRNA, complete cds.
BX649119 - Homo sapiens mRNA; cDNA DKFZp686N1929 (from clone DKFZp686N1929).
AB384691 - Synthetic construct DNA, clone: pF1KB0668, Homo sapiens SEC23IP gene for SEC23-interacting protein, complete cds, without stop codon, in Flexi system.
CU687818 - Synthetic construct Homo sapiens gateway clone IMAGE:100022836 5' read SEC23IP mRNA.
KJ904671 - Synthetic construct Homo sapiens clone ccsbBroadEn_14065 SEC23IP gene, encodes complete protein.
BT006755 - Homo sapiens Sec23-interacting protein p125 mRNA, complete cds.
AK000698 - Homo sapiens cDNA FLJ20691 fis, clone KAIA2759, highly similar to AB019435 Homo sapiens mRNA for putative phospholipase.
AK023238 - Homo sapiens cDNA FLJ13176 fis, clone NT2RP3003846, highly similar to SEC23-interacting protein.
AK307286 - Homo sapiens cDNA, FLJ97234.
JD552408 - Sequence 533432 from Patent EP1572962.
JD086389 - Sequence 67413 from Patent EP1572962.
JD113023 - Sequence 94047 from Patent EP1572962.
JD022549 - Sequence 3573 from Patent EP1572962.
JD032233 - Sequence 13257 from Patent EP1572962.
JD037830 - Sequence 18854 from Patent EP1572962.
JD114169 - Sequence 95193 from Patent EP1572962.
JD534997 - Sequence 516021 from Patent EP1572962.
JD538856 - Sequence 519880 from Patent EP1572962.
JD539149 - Sequence 520173 from Patent EP1572962.
JD020748 - Sequence 1772 from Patent EP1572962.
JD033782 - Sequence 14806 from Patent EP1572962.
JD027387 - Sequence 8411 from Patent EP1572962.
JD481867 - Sequence 462891 from Patent EP1572962.
JD481868 - Sequence 462892 from Patent EP1572962.

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

Protein Q9Y6Y8 (Reactome details) participates in the following event(s):

R-HSA-204008 SEC31:SEC13 and v-SNARE recruitment
R-HSA-5694441 CSNK1D phosphorylates SEC23
R-HSA-5694439 COPII coat binds TRAPPCII and RAB1:GDP
R-HSA-203973 Vesicle budding
R-HSA-5694418 RAB1:GTP binds USO1 and GORASP1:GOLGA2
R-HSA-5694409 Nucleotide exchange on RAB1
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: D3DRD2, MSTP053, NM_007190, NP_009121, Q8IXH5, Q9BUK5, Q9Y6Y8, S23IP_HUMAN
UCSC ID: uc001leu.2
RefSeq Accession: NM_007190
Protein: Q9Y6Y8 (aka S23IP_HUMAN or S23I_HUMAN)
CCDS: CCDS7618.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_007190.3
exon count: 19CDS single in 3' UTR: no RNA size: 7306
ORF size: 3003CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 6179.00frame shift in genome: no % Coverage: 100.00
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
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.