Human Gene SUSD5 (uc003cfo.1)
  Description: Homo sapiens sushi domain containing 5 (SUSD5), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:33,191,537-33,260,707 Size: 69,171 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr3:33,194,234-33,260,289 Size: 66,056 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:33,191,537-33,260,707)mRNA (may differ from genome)Protein (629 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsGeneNetworkH-INV
HGNCHPRDLynxMGIneXtProtPubMed
TreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SUSD5_HUMAN
DESCRIPTION: RecName: Full=Sushi domain-containing protein 5; Flags: Precursor;
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
SIMILARITY: Contains 1 Link domain.
SIMILARITY: Contains 1 Sushi (CCP/SCR) domain.
SEQUENCE CAUTION: Sequence=BAA25453.1; Type=Erroneous initiation;

-  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): SUSD5
CDC HuGE Published Literature: SUSD5
Positive Disease Associations: Tunica Media
Related Studies:
  1. Tunica Media
    , , . [PubMed 0]

-  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: 109.98 RPKM in Artery - Aorta
Total median expression: 304.43 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 -207.50418-0.496 Picture PostScript Text
3' UTR -810.212697-0.300 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
IPR016186 - C-type_lectin-like
IPR016187 - C-type_lectin_fold
IPR016060 - Complement_control_module
IPR000538 - Link
IPR000436 - Sushi_SCR_CCP

Pfam Domains:
PF00193 - Extracellular link domain

SCOP Domains:
56436 - C-type lectin-like
57535 - Complement control module/SCR domain

ModBase Predicted Comparative 3D Structure on O60279
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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:0005540 hyaluronic acid binding

Biological Process:
GO:0007155 cell adhesion
GO:0007219 Notch signaling pathway

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


-  Descriptions from all associated GenBank mRNAs
  AB011099 - Homo sapiens KIAA0527 mRNA for KIAA0527 protein.
JD488694 - Sequence 469718 from Patent EP1572962.
JD088804 - Sequence 69828 from Patent EP1572962.
JD063196 - Sequence 44220 from Patent EP1572962.
JD236378 - Sequence 217402 from Patent EP1572962.
JD559812 - Sequence 540836 from Patent EP1572962.
JD300198 - Sequence 281222 from Patent EP1572962.
JD091082 - Sequence 72106 from Patent EP1572962.
JD358175 - Sequence 339199 from Patent EP1572962.
JD189546 - Sequence 170570 from Patent EP1572962.
JD502796 - Sequence 483820 from Patent EP1572962.
JD233270 - Sequence 214294 from Patent EP1572962.
JD051820 - Sequence 32844 from Patent EP1572962.
JD257426 - Sequence 238450 from Patent EP1572962.
JD305242 - Sequence 286266 from Patent EP1572962.
JD068017 - Sequence 49041 from Patent EP1572962.
JD290347 - Sequence 271371 from Patent EP1572962.
JD074206 - Sequence 55230 from Patent EP1572962.
JD555004 - Sequence 536028 from Patent EP1572962.
JD298978 - Sequence 280002 from Patent EP1572962.
JD334732 - Sequence 315756 from Patent EP1572962.
JD434637 - Sequence 415661 from Patent EP1572962.
JD177602 - Sequence 158626 from Patent EP1572962.
JD357870 - Sequence 338894 from Patent EP1572962.
JD081488 - Sequence 62512 from Patent EP1572962.
JD311663 - Sequence 292687 from Patent EP1572962.
JD379616 - Sequence 360640 from Patent EP1572962.
JD342072 - Sequence 323096 from Patent EP1572962.
JD397314 - Sequence 378338 from Patent EP1572962.
JD397315 - Sequence 378339 from Patent EP1572962.
JD070009 - Sequence 51033 from Patent EP1572962.
JD514047 - Sequence 495071 from Patent EP1572962.
JD121114 - Sequence 102138 from Patent EP1572962.
JD381331 - Sequence 362355 from Patent EP1572962.
JD381332 - Sequence 362356 from Patent EP1572962.
JD070010 - Sequence 51034 from Patent EP1572962.
JD514048 - Sequence 495072 from Patent EP1572962.
JD536583 - Sequence 517607 from Patent EP1572962.
JD444163 - Sequence 425187 from Patent EP1572962.
JD532596 - Sequence 513620 from Patent EP1572962.
JD273319 - Sequence 254343 from Patent EP1572962.
JD148400 - Sequence 129424 from Patent EP1572962.
JD148399 - Sequence 129423 from Patent EP1572962.
JD063879 - Sequence 44903 from Patent EP1572962.
JD282460 - Sequence 263484 from Patent EP1572962.
JD324663 - Sequence 305687 from Patent EP1572962.
JD481716 - Sequence 462740 from Patent EP1572962.
JD067760 - Sequence 48784 from Patent EP1572962.
AK295869 - Homo sapiens cDNA FLJ56620 complete cds.
JD369399 - Sequence 350423 from Patent EP1572962.
JD068168 - Sequence 49192 from Patent EP1572962.
DQ589690 - Homo sapiens piRNA piR-56802, complete sequence.
DQ587181 - Homo sapiens piRNA piR-54293, complete sequence.
JD391737 - Sequence 372761 from Patent EP1572962.
JD461097 - Sequence 442121 from Patent EP1572962.
JD478014 - Sequence 459038 from Patent EP1572962.
JD103983 - Sequence 85007 from Patent EP1572962.
JD419569 - Sequence 400593 from Patent EP1572962.
JD256681 - Sequence 237705 from Patent EP1572962.
JD114935 - Sequence 95959 from Patent EP1572962.
JD409246 - Sequence 390270 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: KIAA0527, NM_015551, NP_056366, O60279, SUSD5_HUMAN
UCSC ID: uc003cfo.1
RefSeq Accession: NM_015551
Protein: O60279 (aka SUSD5_HUMAN)
CCDS: CCDS46787.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_015551.1
exon count: 5CDS single in 3' UTR: no RNA size: 5005
ORF size: 1890CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3980.00frame 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.