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CSMD3 Gene(Protein Coding)

CUB And Sushi Multiple Domains 3

GCID:
GC08M112223
GIFtS:
50
Genes Participants
UDN Logo

Aliases for CSMD3 Gene

Aliases for CSMD3 Gene

  • CUB And Sushi Multiple Domains 3 2 3 5
  • CUB And Sushi Multiple Domains Protein 3 4
  • KIAA1894 4

External Ids for CSMD3 Gene

Previous GeneCards Identifiers for CSMD3 Gene

  • GC00U903104
  • GC08M112903
  • GC08M113191
  • GC08M113304
  • GC08M108554

Summaries for CSMD3 Gene

GeneCards Summary for CSMD3 Gene

CSMD3 (CUB And Sushi Multiple Domains 3) is a Protein Coding gene. Diseases associated with CSMD3 include Benign Adult Familial Myoclonic Epilepsy and Trichorhinophalangeal Syndrome, Type Ii. An important paralog of this gene is SVEP1.

No data available for Entrez Gene Summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CSMD3 Gene

Genomics for CSMD3 Gene

Products:

  1. Regulatory Element

Regulatory Elements for CSMD3 Gene

Enhancers for CSMD3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around CSMD3 on UCSC Golden Path with GeneCards custom track

Transcription factor binding sites by QIAGEN in the CSMD3 gene promoter:

Genomic Location for CSMD3 Gene

Chromosome:
8
Start:
112,222,928 bp from pter
End:
113,437,467 bp from pter
Size:
1,214,540 bases
Orientation:
Minus strand

Genomic View for CSMD3 Gene

Genes around CSMD3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CSMD3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CSMD3 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CSMD3 Gene

Proteins for CSMD3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for CSMD3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q7Z407-CSMD3_HUMAN
    Recommended name:
    CUB and sushi domain-containing protein 3
    Protein Accession:
    Q7Z407
    Secondary Accessions:
    • Q96PZ3

    Protein attributes for CSMD3 Gene

    Size:
    3707 amino acids
    Molecular mass:
    406000 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAO34702.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CSMD3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CSMD3 Gene

Proteomics data for CSMD3 Gene at MOPED

Protein Expression for CSMD3 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for CSMD3 Gene

  • Glycosylation at Asn 73, Asn 90, Asn 361, Asn 409, Asn 724, Asn 823, Asn 966, Asn 1092, Asn 1126, Asn 1171, Asn 1280, Asn 1536, Asn 1591, Asn 1709, Asn 1781, Asn 1929, Asn 2019, Asn 2155, Asn 2286, Asn 2291, Asn 2324, Asn 2495, Asn 2537, Asn 2711, Asn 2742, Asn 2862, Asn 2932, Asn 2952, Asn 3099, Asn 3158, Asn 3167, Asn 3194, Asn 3208, Asn 3218, Asn 3276, Asn 3364, Asn 3522, Asn 3529, Asn 3612, Asn 3618, and Asn 3627
  • Modification sites at PhosphoSitePlus

Other Protein References for CSMD3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for CSMD3 Gene

Domains & Families for CSMD3 Gene

Gene Families for CSMD3 Gene

HGNC:

Protein Domains for CSMD3 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for CSMD3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q7Z407

UniProtKB/Swiss-Prot:

CSMD3_HUMAN :
  • Contains 14 CUB domains.
  • Belongs to the CSMD family.
Domain:
  • Contains 14 CUB domains.
  • Contains 28 Sushi (CCP/SCR) domains.
Family:
  • Belongs to the CSMD family.
genes like me logo Genes that share domains with CSMD3: view

Function for CSMD3 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Phenotypes for CSMD3 Gene

GenomeRNAi human phenotypes for CSMD3:
genes like me logo Genes that share phenotypes with CSMD3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CSMD3

CRISPR Products

miRNA for CSMD3 Gene

miRTarBase miRNAs that target CSMD3

Inhibitory RNA Products

Flow Cytometry Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CSMD3 Gene

Localization for CSMD3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CSMD3 Gene

Cell membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for CSMD3 Gene COMPARTMENTS Subcellular localization image for CSMD3 gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for CSMD3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane IEA --
genes like me logo Genes that share ontologies with CSMD3: view

Pathways & Interactions for CSMD3 Gene

SuperPathways for CSMD3 Gene

PathCards logoMore details on SuperPathways for CSMD3
No Data Available

Gene Ontology (GO) - Biological Process for CSMD3 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for CSMD3 Gene

Drugs & Compounds for CSMD3 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for CSMD3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for CSMD3 Gene

(12) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(22) Selected AceView cDNA sequences:
(10) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CSMD3 Gene

CUB and Sushi multiple domains 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for CSMD3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16a · 16b ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^
SP1: -
SP2: - - -
SP3: - - - -
SP4:
SP5:
SP6: - -

ExUns: 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45a · 45b ^ 46 ^ 47 ^
SP1:
SP2:
SP3:
SP4: - -
SP5:
SP6:

ExUns: 48 ^ 49 ^ 50 ^ 51 ^ 52a · 52b ^ 53 ^ 54 ^ 55 ^ 56 ^ 57 ^ 58 ^ 59 ^ 60 ^ 61 ^ 62 ^ 63 ^ 64 ^ 65 ^ 66 ^ 67 ^ 68 ^ 69 ^ 70 ^ 71 ^ 72
SP1: -
SP2: -
SP3: - -
SP4: -
SP5:
SP6:

Relevant External Links for CSMD3 Gene

GeneLoc Exon Structure for
CSMD3
ECgene alternative splicing isoforms for
CSMD3

Expression for CSMD3 Gene

Products:

  1. Primer

mRNA expression in normal human tissues for CSMD3 Gene

mRNA expression in normal human tissues for CSMD3 Gene
mRNA expression by BioGPS for CSMD3 GenemRNA expression by GTEx for CSMD3 Gene

mRNA differential expression in normal tissues according to GTEx for CSMD3 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x5.8), Brain - Hypothalamus (x5.5), Brain - Anterior cingulate cortex (BA24) (x5.0), Brain - Frontal Cortex (BA9) (x4.8), Brain - Amygdala (x4.4), and Brain - Cortex (x4.2).

Protein differential expression in normal tissues from HIPED for CSMD3 Gene

This gene is overexpressed in Pancreatic juice (45.1) and Urine (23.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CSMD3 Gene



SOURCE GeneReport for Unigene cluster for CSMD3 Gene Hs.91381

mRNA Expression by UniProt/SwissProt for CSMD3 Gene

Q7Z407-CSMD3_HUMAN
Tissue specificity: Weakly expressed in most tissues, except in brain. Expressed at intermediate level in brain, including cerebellum, substantia nigra, thalamus, spinal cord, hippocampus and fetal brain. Also expressed in testis.
genes like me logo Genes that share expression patterns with CSMD3: view

Protein tissue co-expression partners for CSMD3 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery for CSMD3 Gene

Orthologs for CSMD3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CSMD3 Gene

Organism Taxonomy Gene Similarity Type Details
dog
(Canis familiaris)
 Mammalia CSMD3 35
  • 94.8 (n)
  • 98.46 (a)
CSMD3 36
  • 98 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Csmd3 35
  • 91.14 (n)
  • 97.52 (a)
Csmd3 16
Csmd3 36
  • 98 (a)
 OneToOne
chimpanzee
(Pan troglodytes)
 Mammalia CSMD3 35
  • 99.53 (n)
  • 99.54 (a)
CSMD3 36
  • 100 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Csmd3 35
  • 90.26 (n)
  • 97.01 (a)
cow
(Bos Taurus)
 Mammalia CSMD3 36
  • 93 (a)
 OneToOne
oppossum
(Monodelphis domestica)
 Mammalia CSMD3 36
  • 97 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia CSMD3 36
  • 67 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves CSMD3 35
  • 84.64 (n)
  • 93.36 (a)
CSMD3 36
  • 94 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia CSMD3 36
  • 92 (a)
 OneToOne
zebrafish
(Danio rerio)
 Actinopterygii LOC572419 35
  • 72.17 (n)
  • 82.61 (a)
CSMD3 (1 of 3) 36
  • 81 (a)
 OneToMany
CSMD3 (2 of 3) 36
  • 76 (a)
 OneToMany
CSMD3 (3 of 3) 36
  • 34 (a)
 OneToMany
Species with no ortholog for CSMD3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CSMD3 Gene

ENSEMBL:
Gene Tree for CSMD3 (if available)
TreeFam:
Gene Tree for CSMD3 (if available)

Paralogs for CSMD3 Gene

Paralogs for CSMD3 Gene

(9) SIMAP similar genes for CSMD3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with CSMD3: view

Variants for CSMD3 Gene

Sequence variations from dbSNP and Humsavar for CSMD3 Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs2219898 - 113,173,774(-) TGCAT(A/G)GCCAA reference, missense
rs2193430 - 112,289,515(-) CTGGC(A/C/G)TTCCT reference, missense
rs1592624 - 112,228,859(+) TTGAT(G/T)TGAAG reference, missense
VAR_035688 A colorectal cancer sample
VAR_035689 A colorectal cancer sample

Structural Variations from Database of Genomic Variants (DGV) for CSMD3 Gene

Variant ID Type Subtype PubMed ID
dgv7856n71 CNV Loss 21882294
nsv891323 CNV Loss 21882294
nsv518270 CNV Loss 19592680
nsv831427 CNV Loss 17160897
nsv891324 CNV Gain 21882294
nsv891325 CNV Loss 21882294
nsv524089 CNV Gain 19592680
nsv891326 CNV Loss 21882294
nsv891327 CNV Gain 21882294
dgv7857n71 CNV Loss 21882294
nsv891331 CNV Loss 21882294
nsv465766 CNV Loss 19166990
nsv6352 CNV Insertion 18451855
nsv511403 CNV Loss 21212237
nsv512060 CNV Loss 21212237
esv2674135 CNV Deletion 23128226
esv25527 CNV Loss 19812545
nsv511390 CNV Loss 21212237
nsv512061 CNV Loss 21212237
esv2670906 CNV Deletion 23128226
dgv187e180 CNV Deletion 20482838
dgv188e180 CNV Loss 20482838
esv28758 CNV Loss 19812545
nsv831428 CNV Gain 17160897
esv2666384 CNV Deletion 23128226
esv2660416 CNV Deletion 23128226
nsv507482 CNV Insertion 20534489
nsv831429 CNV Loss 17160897

Variation tolerance for CSMD3 Gene

Residual Variation Intolerance Score: 0.133% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 13.94; 95.97% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CSMD3 Gene

Human Gene Mutation Database (HGMD)
CSMD3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CSMD3 Gene

Disorders for CSMD3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for CSMD3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
benign adult familial myoclonic epilepsy
  • adcme
trichorhinophalangeal syndrome, type ii
  • lennox-gastaut syndrome
autistic disorder
  • autism
- elite association - COSMIC cancer census association via MalaCards
Search CSMD3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for CSMD3

Genetic Association Database (GAD)
CSMD3
Human Genome Epidemiology (HuGE) Navigator
CSMD3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CSMD3
genes like me logo Genes that share disorders with CSMD3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CSMD3 Gene

Publications for CSMD3 Gene

  1. A novel giant gene CSMD3 encoding a protein with CUB and sushi multiple domains: a candidate gene for benign adult familial myoclonic epilepsy on human chromosome 8q23.3-q24.1. (PMID: 12943675) Shimizu A. … Shimizu N. (Biochem. Biophys. Res. Commun. 2003) 3 4 23 67
  2. Identification of two new members of the CSMD gene family. (PMID: 12906867) Lau W.L. … Scholnick S.B. (Genomics 2003) 3 23
  3. Probing nuclear pore complex architecture with proximity-dependent biotinylation. (PMID: 24927568) Kim D.I. … Roux K.J. (Proc. Natl. Acad. Sci. U.S.A. 2014) 3
  4. A genome-wide association study (GWAS) for bronchopulmonary dysplasia. (PMID: 23897914) Wang H. … O'Brodovich H.M. (Pediatrics 2013) 3
  5. Genome-wide association study of periodontal pathogen colonization. (PMID: 22699663) Divaris K. … Offenbacher S. (J. Dent. Res. 2012) 3

Products for CSMD3 Gene

Sources for CSMD3 Gene

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