Human Gene CSMD2 (uc001bxn.1)
  Description: Homo sapiens CUB and Sushi multiple domains 2 (CSMD2), mRNA.
RefSeq Summary (NM_052896): The protein encoded by this gene is thought to be involved in the control of complement cascade of the immune system. Defects in this gene have been associated with schizophrenia. This gene may act as a tumor suppressor for colorectal cancer. [provided by RefSeq, Jan 2020].
Transcript (Including UTRs)
   Position: hg19 chr1:33,979,609-34,631,443 Size: 651,835 Total Exon Count: 70 Strand: -
Coding Region
   Position: hg19 chr1:33,985,118-34,631,414 Size: 646,297 Coding Exon Count: 69 

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 (chr1:33,979,609-34,631,443)mRNA (may differ from genome)Protein (3487 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMalacards
MGIneXtProtOMIMPubMedTreefamUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CSMD2_HUMAN
DESCRIPTION: RecName: Full=CUB and sushi domain-containing protein 2; AltName: Full=CUB and sushi multiple domains protein 2;
SUBCELLULAR LOCATION: Cell membrane; Single-pass membrane protein (Potential).
TISSUE SPECIFICITY: Weakly expressed in most tissues, except in brain. Expressed at intermediate level in brain, including cerebellum, substantia nigra, hippocampus and fetal brain. Overexpressed in some head and neck cancer cell lines.
SIMILARITY: Belongs to the CSMD family.
SIMILARITY: Contains 14 CUB domains.
SIMILARITY: Contains 26 Sushi (CCP/SCR) domains.
SEQUENCE CAUTION: Sequence=BAC04593.1; 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): CSMD2
CDC HuGE Published Literature: CSMD2
Positive Disease Associations: ADHD | attention-deficit hyperactivity disorder , Alcoholism , Attention Deficit Disorder with Hyperactivity , Brain , Brain structure , Inflammatory Bowel Diseases , Lipoproteins
Related Studies:
  1. ADHD | attention-deficit hyperactivity disorder
    Lesch ,et al. 2008, Molecular genetics of adult ADHD: converging evidence from genome-wide association and extended pedigree linkage studies, Journal of neural transmission (Vienna, Austria : 1996) 2008 115- 11 : 1573-85. [PubMed 18839057]
  2. Alcoholism
    , , . [PubMed 0]
  3. Alcoholism
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CSMD2
Diseases sorted by gene-association score: intermediate charcot-marie-tooth neuropathy (11), benign adult familial myoclonic epilepsy (9), long qt syndrome 1 (3), schizophrenia (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: 1.52 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 17.44 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 -3.8029-0.131 Picture PostScript Text
3' UTR -895.192615-0.342 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
IPR000859 - CUB
IPR000436 - Sushi_SCR_CCP

Pfam Domains:
PF00084 - Sushi repeat (SCR repeat)
PF00431 - CUB domain

SCOP Domains:
49854 - Spermadhesin, CUB domain
57535 - Complement control module/SCR domain

ModBase Predicted Comparative 3D Structure on Q7Z408
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 Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AY210418 - Homo sapiens CUB and sushi multiple domains 2 (CSMD2) mRNA, complete cds.
AB212622 - Homo sapiens mRNA for CSMD2 protein, complete cds.
AK127722 - Homo sapiens cDNA FLJ45822 fis, clone NT2RP8001604, moderately similar to Homo sapiens CUB and Sushi multiple domains 1 (CSMD1).
AK291019 - Homo sapiens cDNA FLJ77945 complete cds.
AK122603 - Homo sapiens cDNA FLJ16011 fis, clone NT2RP7004027, weakly similar to BONE MORPHOGENETIC PROTEIN 1 PRECURSOR (EC 3.4.24.-).
KJ903642 - Synthetic construct Homo sapiens clone ccsbBroadEn_13036 CSMD2 gene, encodes complete protein.
AB067471 - Homo sapiens mRNA for KIAA1884 protein, partial cds.
JD556808 - Sequence 537832 from Patent EP1572962.
AK095627 - Homo sapiens cDNA FLJ38308 fis, clone FCBBF3019085, weakly similar to E-SELECTIN PRECURSOR.
JD116213 - Sequence 97237 from Patent EP1572962.
JD392424 - Sequence 373448 from Patent EP1572962.
JD482949 - Sequence 463973 from Patent EP1572962.
JD121740 - Sequence 102764 from Patent EP1572962.
JD354223 - Sequence 335247 from Patent EP1572962.
JD393992 - Sequence 375016 from Patent EP1572962.
JD391353 - Sequence 372377 from Patent EP1572962.
JD164322 - Sequence 145346 from Patent EP1572962.
JD166961 - Sequence 147985 from Patent EP1572962.
JD437581 - Sequence 418605 from Patent EP1572962.
JD363116 - Sequence 344140 from Patent EP1572962.
JD445682 - Sequence 426706 from Patent EP1572962.
JD203013 - Sequence 184037 from Patent EP1572962.
JD506953 - Sequence 487977 from Patent EP1572962.
JD061572 - Sequence 42596 from Patent EP1572962.
JD548896 - Sequence 529920 from Patent EP1572962.
JD393600 - Sequence 374624 from Patent EP1572962.
JD049295 - Sequence 30319 from Patent EP1572962.
JD383119 - Sequence 364143 from Patent EP1572962.
JD324961 - Sequence 305985 from Patent EP1572962.
JD061222 - Sequence 42246 from Patent EP1572962.
JD101182 - Sequence 82206 from Patent EP1572962.
JD552037 - Sequence 533061 from Patent EP1572962.
JD063917 - Sequence 44941 from Patent EP1572962.
JD494066 - Sequence 475090 from Patent EP1572962.
JD349332 - Sequence 330356 from Patent EP1572962.
JD304014 - Sequence 285038 from Patent EP1572962.
JD501874 - Sequence 482898 from Patent EP1572962.
JD492566 - Sequence 473590 from Patent EP1572962.
JD103591 - Sequence 84615 from Patent EP1572962.
JD467906 - Sequence 448930 from Patent EP1572962.
JD549123 - Sequence 530147 from Patent EP1572962.
JD311198 - Sequence 292222 from Patent EP1572962.
JD456016 - Sequence 437040 from Patent EP1572962.
JD232718 - Sequence 213742 from Patent EP1572962.
JD283804 - Sequence 264828 from Patent EP1572962.
JD261442 - Sequence 242466 from Patent EP1572962.
JD375760 - Sequence 356784 from Patent EP1572962.
JD407145 - Sequence 388169 from Patent EP1572962.
JD453799 - Sequence 434823 from Patent EP1572962.
JD519940 - Sequence 500964 from Patent EP1572962.
JD040730 - Sequence 21754 from Patent EP1572962.
AK022620 - Homo sapiens cDNA FLJ12558 fis, clone NT2RM4000787.
BC031871 - Homo sapiens CUB and Sushi multiple domains 2, mRNA (cDNA clone IMAGE:5167721), complete cds.
JD062435 - Sequence 43459 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B1AM50, CSMD2_HUMAN, KIAA1884, NM_052896, NP_443128, Q5VT59, Q7Z408, Q8N963, Q96Q03, Q9H4V7, Q9H4V8, Q9H4V9, Q9H4W0, Q9H4W1, Q9H4W2, Q9H4W3, Q9H4W4, Q9HCY5, Q9HCY6, Q9HCY7
UCSC ID: uc001bxn.1
RefSeq Accession: NM_052896
Protein: Q7Z408 (aka CSMD2_HUMAN or CSM2_HUMAN)
CCDS: CCDS380.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_052896.3
exon count: 70CDS single in 3' UTR: no RNA size: 13108
ORF size: 10464CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 19540.00frame 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.