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Aliases for CLDND1 Gene

Aliases for CLDND1 Gene

  • Claudin Domain Containing 1 2 3 5
  • Membrane Protein GENX-3745 3 4
  • C3orf4 3 4
  • Claudin Domain Containing 1 Protein 3
  • Claudin Domain-Containing Protein 1 3
  • Chromosome 3 Open Reading Frame 4 2
  • GENX-3745 3
  • Z38 3

External Ids for CLDND1 Gene

Previous HGNC Symbols for CLDND1 Gene

  • C3orf4

Previous GeneCards Identifiers for CLDND1 Gene

  • GC03M099718
  • GC03M098234
  • GC03M095606

Summaries for CLDND1 Gene

GeneCards Summary for CLDND1 Gene

CLDND1 (Claudin Domain Containing 1) is a Protein Coding gene.

Gene Wiki entry for CLDND1 Gene

Additional gene information for CLDND1 Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLDND1 Gene

Genomics for CLDND1 Gene

GeneHancer (GH) Regulatory Elements for CLDND1 Gene

Promoters and enhancers for CLDND1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I098521 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.6 584 2.4 HDGF PKNOX1 SMAD1 ZFP64 ARID4B SIN3A DMAP1 YBX1 ZBTB7B YY1 CLDND1 ENSG00000248839 OR5K2 CPOX
GH03I098573 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 7.2 -50.4 -50437 0.9 NFIB ZNF133 FEZF1 RAD21 ZNF366 ZNF143 ATF7 IKZF2 ZNF680 ZNF362 CPOX CLDND1 OR5H6 OR5H2 GC03M098547
GH03I098550 Enhancer 1.3 FANTOM5 ENCODE dbSUPER 2.2 -32.0 -31996 8.2 HDGF PKNOX1 SMAD1 IRF4 TCF12 GATA2 ATF7 RUNX3 RXRA JUNB CPOX GPR15 DCBLD2 ST3GAL6-AS1 OR5H6 CLDND1 OR5H2 GC03M098547
GH03I098560 Enhancer 1.6 FANTOM5 Ensembl ENCODE dbSUPER 1.3 -41.9 -41883 8.4 HDGF PKNOX1 SMAD1 RB1 BMI1 FEZF1 BATF KLF5 IRF4 ZNF143 CPOX OR5K2 ST3GAL6-AS1 ST3GAL6 GPR15 CLDND1 GC03M098547
GH03I098512 Enhancer 0.8 ENCODE dbSUPER 0.4 +9.9 9873 2.3 ZNF10 CEBPB REST FEZF1 EP300 JUND PRDM6 POLR2A FOS FOSL2 CPOX OR5K4 OR5K2 ENSG00000248839 CLDND1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLDND1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLDND1 gene promoter:

Genomic Locations for CLDND1 Gene

Genomic Locations for CLDND1 Gene
chr3:98,497,912-98,523,066
(GRCh38/hg38)
Size:
25,155 bases
Orientation:
Minus strand
chr3:98,216,756-98,241,910
(GRCh37/hg19)

Genomic View for CLDND1 Gene

Genes around CLDND1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLDND1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLDND1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLDND1 Gene

Proteins for CLDND1 Gene

  • Protein details for CLDND1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NY35-CLDN1_HUMAN
    Recommended name:
    Claudin domain-containing protein 1
    Protein Accession:
    Q9NY35
    Secondary Accessions:
    • B3KQR1
    • D3DN36
    • F2Z2D9
    • Q502Y8
    • Q6UVX2
    • Q9BUZ9
    • Q9NZZ5
    • Q9Y4S9

    Protein attributes for CLDND1 Gene

    Size:
    253 amino acids
    Molecular mass:
    28603 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF29137.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for CLDND1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLDND1 Gene

Post-translational modifications for CLDND1 Gene

  • Glycosylation at posLast=4242 and Asn72

No data available for DME Specific Peptides for CLDND1 Gene

Domains & Families for CLDND1 Gene

Gene Families for CLDND1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins
  • Transporters

Protein Domains for CLDND1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CLDND1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NY35

UniProtKB/Swiss-Prot:

CLDN1_HUMAN :
  • Belongs to the PMP-22/EMP/MP20 family.
Family:
  • Belongs to the PMP-22/EMP/MP20 family.
genes like me logo Genes that share domains with CLDND1: view

Function for CLDND1 Gene

Phenotypes From GWAS Catalog for CLDND1 Gene

genes like me logo Genes that share phenotypes with CLDND1: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone 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 CLDND1 Gene

Localization for CLDND1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLDND1 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLDND1 gene
Compartment Confidence
plasma membrane 3
cytoskeleton 2
nucleus 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Nucleoli (2)
  • Nucleus (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLDND1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009986 cell surface HDA 19581412
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0016324 apical plasma membrane IEA --
genes like me logo Genes that share ontologies with CLDND1: view

Pathways & Interactions for CLDND1 Gene

SuperPathways for CLDND1 Gene

No Data Available

Interacting Proteins for CLDND1 Gene

Gene Ontology (GO) - Biological Process for CLDND1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for CLDND1 Gene

Drugs & Compounds for CLDND1 Gene

No Compound Related Data Available

Transcripts for CLDND1 Gene

Unigene Clusters for CLDND1 Gene

Claudin domain containing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for CLDND1 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4a · 4b · 4c · 4d ^ 5a · 5b · 5c ^ 6a · 6b ^ 7a · 7b · 7c ^ 8a · 8b · 8c · 8d ^ 9a · 9b · 9c ·
SP1: - - - - - - - - - - -
SP2: - - - - - - - - -
SP3: - - - - - - - - - -
SP4: - - - - - - - - - - - - - - -
SP5: - - - - - - - - -
SP6: - - - - - - - - - -
SP7: - - - - - - - - - - -
SP8: - - - - - - - - - - -
SP9: - - - - - - - - -
SP10: - - - - - - - -
SP11: - - - - - - - - - -
SP12: - - - - - - - - - - - - -
SP13: - - - - - - - - - - -
SP14: - - - - - - - - -
SP15: - - - - - - -
SP16: - - - - - -
SP17: - - - - - - - -
SP18: - - - - - -
SP19: - - - -
SP20: - - - - - - - - - - - - - - -
SP21: - - - - - -
SP22: - - - - - - - - - - -
SP23: - - - - -
SP24: - - -
SP25: - - - - - - - - -
SP26: - - - - - - -
SP27: - -
SP28:

ExUns: 9d ^ 10a · 10b · 10c · 10d · 10e · 10f · 10g
SP1: -
SP2: -
SP3: -
SP4: -
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:
SP11:
SP12: -
SP13: -
SP14:
SP15:
SP16:
SP17: -
SP18:
SP19: -
SP20: -
SP21:
SP22:
SP23:
SP24:
SP25:
SP26:
SP27:
SP28: -

Relevant External Links for CLDND1 Gene

GeneLoc Exon Structure for
CLDND1
ECgene alternative splicing isoforms for
CLDND1

Expression for CLDND1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLDND1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLDND1 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (x10.9) and Brain - Substantia nigra (x5.7).

Protein differential expression in normal tissues from HIPED for CLDND1 Gene

This gene is overexpressed in Spinal cord (23.0), Frontal cortex (14.7), and Placenta (6.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for CLDND1 Gene



Protein tissue co-expression partners for CLDND1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLDND1 Gene:

CLDND1

SOURCE GeneReport for Unigene cluster for CLDND1 Gene:

Hs.531371

mRNA Expression by UniProt/SwissProt for CLDND1 Gene:

Q9NY35-CLDN1_HUMAN
Tissue specificity: Widely distributed in the adult CNS with highest expression in the corpus callosum, caudate nucleus, cerebral cortex, medulla, putamen, spinal cord, substantia nigra and subthalamic nucleus. Weak expression was detected in the adult heart.

Evidence on tissue expression from TISSUES for CLDND1 Gene

  • Nervous system(5)
  • Blood(4.3)
  • Eye(4.3)
  • Liver(4.3)
  • Kidney(2.8)
genes like me logo Genes that share expression patterns with CLDND1: view

Primer Products

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for CLDND1 Gene

Orthologs for CLDND1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CLDND1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLDND1 33 34
  • 99.76 (n)
cow
(Bos Taurus)
Mammalia CLDND1 33 34
  • 93.02 (n)
dog
(Canis familiaris)
Mammalia CLDND1 33 34
  • 92.39 (n)
mouse
(Mus musculus)
Mammalia Cldn25 33 34
  • 86.35 (n)
Cldnd1 16
rat
(Rattus norvegicus)
Mammalia Cldnd1 33
  • 85.64 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia CLDND1 34
  • 83 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia CLDND1 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLDND1 33 34
  • 74.06 (n)
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 75 (a)
OneToMany
-- 34
  • 65 (a)
OneToMany
tropical clawed frog
(Silurana tropicalis)
Amphibia cldnd1 33
  • 60.64 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC554386 33
  • 57.35 (n)
CLDND1 (1 of 2) 34
  • 51 (a)
OneToMany
CLDND1 (2 of 2) 34
  • 51 (a)
OneToMany
Species where no ortholog for CLDND1 was found in the sources mined by GeneCards:
  • 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLDND1 Gene

ENSEMBL:
Gene Tree for CLDND1 (if available)
TreeFam:
Gene Tree for CLDND1 (if available)

Paralogs for CLDND1 Gene

No data available for Paralogs for CLDND1 Gene

Variants for CLDND1 Gene

Sequence variations from dbSNP and Humsavar for CLDND1 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000142068 -- 98,517,753(-) C/G intron_variant
rs1000180428 -- 98,522,687(-) C/G 5_prime_UTR_variant, intron_variant
rs1000249989 -- 98,515,072(-) C/A downstream_transcript_variant
rs1000257217 -- 98,522,973(-) C/G 5_prime_UTR_variant
rs1000514714 -- 98,521,497(-) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for CLDND1 Gene

Variant ID Type Subtype PubMed ID
nsv834775 CNV gain 17160897
nsv834774 CNV loss 17160897
nsv591065 CNV gain 21841781
dgv293n21 CNV loss 19592680

Variation tolerance for CLDND1 Gene

Residual Variation Intolerance Score: 42% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.50; 10.96% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLDND1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLDND1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLDND1 Gene

Disorders for CLDND1 Gene

Additional Disease Information for CLDND1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for CLDND1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLDND1 Gene

Publications for CLDND1 Gene

  1. Prognostic significance of long noncoding RNA Z38 as a candidate biomarker in breast cancer. (PMID: 28247935) Nie ZL … Wang SK (Journal of clinical laboratory analysis 2018) 2 3 58
  2. Signal sequence and keyword trap in silico for selection of full-length human cDNAs encoding secretion or membrane proteins from oligo-capped cDNA libraries. (PMID: 16303743) Otsuki T … Isogai T (DNA research : an international journal for rapid publication of reports on genes and genomes 2005) 3 4 58
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 58
  5. Characterization of tissue expression and full-length coding sequence of a novel human gene mapping at 3q12.1 and transcribed in oligodendrocytes. (PMID: 12036590) Fayein NA … Devignes MD (Gene 2002) 3 4 58

Products for CLDND1 Gene

Sources for CLDND1 Gene

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