Human Gene SUSD1 (uc004bfu.3)
  Description: Homo sapiens sushi domain containing 1 (SUSD1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:114,803,061-114,937,556 Size: 134,496 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr9:114,803,772-114,937,515 Size: 133,744 Coding Exon Count: 17 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:114,803,061-114,937,556)mRNA (may differ from genome)Protein (747 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMalacardsMGI
neXtProtPubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SUSD1_HUMAN
DESCRIPTION: RecName: Full=Sushi domain-containing protein 1; Flags: Precursor;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein (Potential).
SIMILARITY: Contains 3 EGF-like domains.
SIMILARITY: Contains 2 Sushi (CCP/SCR) domains.
SEQUENCE CAUTION: Sequence=BAB15149.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAB71259.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=CAI12348.2; Type=Erroneous gene model prediction; Sequence=CAI95300.2; Type=Erroneous gene model prediction;

-  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): SUSD1
CDC HuGE Published Literature: SUSD1
Positive Disease Associations: Amyotrophic lateral sclerosis , Iron
Related Studies:
  1. Amyotrophic lateral sclerosis
    Schymick ,et al. 2007, Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data, Lancet neurology 2007 6- 4 : 322-8. [PubMed 17362836]
  2. Amyotrophic Lateral Sclerosis
    Jennifer C Schymick et al. Lancet neurology 2007, Genome-wide genotyping in amyotrophic lateral sclerosis and neurologically normal controls: first stage analysis and public release of data., Lancet neurology. [PubMed 17362836]
    We generated publicly available genotype data for sporadic ALS patients and controls. No single locus was definitively associated with increased risk of developing disease, although potentially associated candidate SNPs were identified.
  3. Iron
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: SUSD1
Diseases sorted by gene-association score: tic disorder (2)

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

+  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: 6.12 RPKM in Kidney - Cortex
Total median expression: 125.80 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 -17.7041-0.432 Picture PostScript Text
3' UTR -219.72711-0.309 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
IPR016060 - Complement_control_module
IPR000742 - EG-like_dom
IPR001881 - EGF-like_Ca-bd
IPR013032 - EGF-like_CS
IPR000152 - EGF-type_Asp/Asn_hydroxyl_site
IPR018097 - EGF_Ca-bd_CS
IPR000436 - Sushi_SCR_CCP

Pfam Domains:
PF00084 - Sushi repeat (SCR repeat)
PF07645 - Calcium-binding EGF domain
PF12661 - Human growth factor-like EGF

SCOP Domains:
57535 - Complement control module/SCR domain
57196 - EGF/Laminin

ModBase Predicted Comparative 3D Structure on Q6UWL2
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 orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005509 calcium ion binding

Cellular Component:
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  BC021125 - Homo sapiens sushi domain containing 1, mRNA (cDNA clone IMAGE:3956128), partial cds.
AK025486 - Homo sapiens cDNA: FLJ21833 fis, clone HEP01592.
AY358746 - Homo sapiens clone DNA96031 GRGP2438 (UNQ2438) mRNA, complete cds.
AK056704 - Homo sapiens cDNA FLJ32142 fis, clone PLACE5000068, weakly similar to C4B-BINDING PROTEIN PRECURSOR (C4BP).
AL137432 - Homo sapiens mRNA; cDNA DKFZp761E1824 (from clone DKFZp761E1824); partial cds.
BC060770 - Homo sapiens sushi domain containing 1, mRNA (cDNA clone MGC:71518 IMAGE:30348765), complete cds.
BC052314 - Homo sapiens sushi domain containing 1, mRNA (cDNA clone IMAGE:6646273), partial cds.
AK292868 - Homo sapiens cDNA FLJ75182 complete cds.
JD528072 - Sequence 509096 from Patent EP1572962.
JD469290 - Sequence 450314 from Patent EP1572962.
JD266198 - Sequence 247222 from Patent EP1572962.
JD087555 - Sequence 68579 from Patent EP1572962.
JD440028 - Sequence 421052 from Patent EP1572962.
JD134541 - Sequence 115565 from Patent EP1572962.
JD283026 - Sequence 264050 from Patent EP1572962.
JD158597 - Sequence 139621 from Patent EP1572962.
JD233619 - Sequence 214643 from Patent EP1572962.
JD418622 - Sequence 399646 from Patent EP1572962.
JD561713 - Sequence 542737 from Patent EP1572962.
JD360380 - Sequence 341404 from Patent EP1572962.
JD114589 - Sequence 95613 from Patent EP1572962.
JD427477 - Sequence 408501 from Patent EP1572962.
JD234411 - Sequence 215435 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A1A4C5, A8KA03, NM_022486, NP_071931, Q5T8V6, Q5T8V7, Q6P9G7, Q6UWL2, Q8WU83, Q96DM9, Q9H6V2, Q9NTA7, SUSD1_HUMAN, UNQ2438/PRO4999
UCSC ID: uc004bfu.3
RefSeq Accession: NM_022486
Protein: Q6UWL2 (aka SUSD1_HUMAN)
CCDS: CCDS65105.1, CCDS65106.1, CCDS6783.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_022486.3
exon count: 17CDS single in 3' UTR: no RNA size: 3010
ORF size: 2244CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4688.00frame shift in genome: no % Coverage: 99.53
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.