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Aliases for NCLN Gene

Aliases for NCLN Gene

  • Nicalin 2 3 3 5
  • Nicastrin-Like Protein 2 3 4
  • Nicalin Homolog (Zebrafish) 2
  • Nicalin Homolog 3
  • NET59 3

External Ids for NCLN Gene

Previous GeneCards Identifiers for NCLN Gene

  • GC19P003139
  • GC19P002952

Summaries for NCLN Gene

GeneCards Summary for NCLN Gene

NCLN (Nicalin) is a Protein Coding gene.

UniProtKB/Swiss-Prot for NCLN Gene

  • May antagonize Nodal signaling and subsequent organization of axial structures during mesodermal patterning.

Gene Wiki entry for NCLN Gene

Additional gene information for NCLN Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NCLN Gene

Genomics for NCLN Gene

Regulatory Elements for NCLN Gene

Enhancers for NCLN Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H003183 1.4 ENCODE dbSUPER 29.7 +2.0 1980 7 HDGF PKNOX1 ARNT ARID4B SIN3A YY1 ZNF766 ZNF207 ZNF143 SP3 NCLN SF3A2 APBA3 ENSG00000267139 CACTIN-AS1 ZNF77 ENSG00000268670 CACTIN ZNF57 GC19M003196
GH19H003210 0.9 ENCODE 44.6 +25.3 25325 0 HNRNPUL1 HDGF PKNOX1 PTBP1 RB1 ZNF76 KLF17 ZNF2 RAD21 ZNF121 NCLN SF3A2 CACTIN-AS1 CACTIN ZNF77 S1PR4 TLE6 APBA3 GC19M003196 CELF5
GH19H002968 1.5 FANTOM5 Ensembl ENCODE 21.5 -213.7 -213652 6 PKNOX1 FEZF1 TCF12 ZNF121 ZNF766 GLIS2 GATA2 ATF7 NCOA1 REST NCLN TLE6 TLE2 AES ZNF77 GNA11 LOC101928631 ZNF57 S1PR4 ENSG00000267283
GH19H003178 1.1 ENCODE dbSUPER 26.4 -5.7 -5688 3 HDGF PKNOX1 TBL1XR1 SIN3A BMI1 ETV6 RUNX3 IKZF2 SMARCA5 SMAD5 NCLN GNA15 GC19M003171
GH19H003193 0.9 ENCODE 30.2 +8.4 8438 0 HDAC1 TBP ATF1 NFIB ARNT ZBTB40 TCF12 EGR1 RCOR1 EGR2 NCLN CELF5 ZNF77 GC19M003196
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NCLN on UCSC Golden Path with GeneCards custom track

Promoters for NCLN Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000106009 337 1801 PKNOX1 ARNT ARID4B SIN3A YY1 ZNF766 ZNF207 ZNF143 SP3 MXD4

Genomic Location for NCLN Gene

Chromosome:
19
Start:
3,185,563 bp from pter
End:
3,209,575 bp from pter
Size:
24,013 bases
Orientation:
Plus strand

Genomic View for NCLN Gene

Genes around NCLN on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for NCLN Gene

Proteins for NCLN Gene

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

    Protein Symbol:
    Q969V3-NCLN_HUMAN
    Recommended name:
    Nicalin
    Protein Accession:
    Q969V3
    Secondary Accessions:
    • D6W613
    • O75252
    • Q6FI60
    • Q6ZMB7
    • Q8TAT7
    • Q96H48
    • Q96IS7
    • Q9BQH9
    • Q9BTX4
    • Q9NPP2

    Protein attributes for NCLN Gene

    Size:
    563 amino acids
    Molecular mass:
    62974 Da
    Quaternary structure:
    • Forms a complex with NOMO2 and TMEM147, resulting in a stabilization of the 3 proteins, which are otherwise quickly degraded by the proteasome. Due to the strong similarity between NOMO1, NOMO2 and NOMO3, probably also interacts with NOMO1 and NOMO3. Participates in a large protein complex, which is not related to the gamma-secretase complex.
    SequenceCaution:
    • Sequence=AAH03076.2; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH25926.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAB66502.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Alternative splice isoforms for NCLN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NCLN Gene

Post-translational modifications for NCLN Gene

  • Ubiquitination at Lys99, Lys471, and Lys491
  • Glycosylation at Asn241 and Asn428
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for NCLN Gene

Domains & Families for NCLN Gene

Gene Families for NCLN Gene

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

Protein Domains for NCLN Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for NCLN Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q969V3

UniProtKB/Swiss-Prot:

NCLN_HUMAN :
  • Belongs to the nicastrin family.
Family:
  • Belongs to the nicastrin family.
genes like me logo Genes that share domains with NCLN: view

Function for NCLN Gene

Molecular function for NCLN Gene

UniProtKB/Swiss-Prot Function:
May antagonize Nodal signaling and subsequent organization of axial structures during mesodermal patterning.

Phenotypes From GWAS Catalog for NCLN Gene

Gene Ontology (GO) - Molecular Function for NCLN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17261586
genes like me logo Genes that share ontologies with NCLN: view
genes like me logo Genes that share phenotypes with NCLN: view

Animal Model Products

CRISPR Products

miRNA for NCLN Gene

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for NCLN
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for NCLN Gene

Localization for NCLN Gene

Subcellular locations from UniProtKB/Swiss-Prot for NCLN Gene

Endoplasmic reticulum membrane; Single-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 NCLN gene
Compartment Confidence
endoplasmic reticulum 5
plasma membrane 2
nucleus 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Lipid droplets (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for NCLN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005783 endoplasmic reticulum IEA --
GO:0005789 endoplasmic reticulum membrane IEA,IDA 20538592
GO:0016020 membrane IEA,IDA 19946888
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with NCLN: view

Pathways & Interactions for NCLN Gene

No Data Available

Gene Ontology (GO) - Biological Process for NCLN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0009966 regulation of signal transduction IBA --
GO:0031648 protein destabilization IMP 20538592
GO:0043254 regulation of protein complex assembly IMP 20538592
genes like me logo Genes that share ontologies with NCLN: view

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

Drugs & Compounds for NCLN Gene

No Compound Related Data Available

Transcripts for NCLN Gene

Unigene Clusters for NCLN Gene

Nicalin:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for NCLN
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11a · 11b ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17a · 17b · 17c · 17d ^
SP1: - - - - -
SP2: - - -
SP3: - - -
SP4: - - - - - -
SP5: - -
SP6: - -
SP7:
SP8:

ExUns: 18
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:

Relevant External Links for NCLN Gene

GeneLoc Exon Structure for
NCLN
ECgene alternative splicing isoforms for
NCLN

Expression for NCLN Gene

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

Protein differential expression in normal tissues from HIPED for NCLN Gene

This gene is overexpressed in Neutrophil (7.6) and Peripheral blood mononuclear cells (6.3).

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



Protein tissue co-expression partners for NCLN Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of NCLN Gene:

NCLN

SOURCE GeneReport for Unigene cluster for NCLN Gene:

Hs.657032

mRNA Expression by UniProt/SwissProt for NCLN Gene:

Q969V3-NCLN_HUMAN
Tissue specificity: Highly expressed in pancreas and skeletal muscle and, at lower levels, in heart.

Evidence on tissue expression from TISSUES for NCLN Gene

  • Nervous system(4.6)
  • Kidney(4.2)
  • Intestine(3.1)
genes like me logo Genes that share expression patterns with NCLN: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for NCLN Gene

Orthologs for NCLN Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for NCLN Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NCLN 34 33
  • 98.64 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NCLN 34 33
  • 90.29 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia NCLN 34
  • 90 (a)
OneToOne
cow
(Bos Taurus)
Mammalia NCLN 34 33
  • 89.09 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Ncln 33
  • 87.21 (n)
mouse
(Mus musculus)
Mammalia Ncln 34 16 33
  • 87.15 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NCLN 34
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves NCLN 34 33
  • 73.5 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NCLN 34
  • 83 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia ncln 33
  • 72.86 (n)
Str.1209 33
zebrafish
(Danio rerio)
Actinopterygii ncl1 34 33
  • 73.65 (n)
OneToOne
wufb07e09 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002549 33
  • 53.46 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4972 34 33
  • 48.2 (n)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea nra-2 34 33
  • 41.38 (n)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G44330 33
  • 44.56 (n)
rice
(Oryza sativa)
Liliopsida Os08g0102100 33
  • 46.09 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10535 34
  • 36 (a)
OneToOne
Species where no ortholog for NCLN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for NCLN Gene

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

Paralogs for NCLN Gene

No data available for Paralogs for NCLN Gene

Variants for NCLN Gene

Sequence variations from dbSNP and Humsavar for NCLN Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type
rs1057519322 Likely pathogenic 3,193,404(+) CCTCC(C/T)AGGGC reference, stop-gained
rs1000074661 -- 3,187,070(+) CATAC(C/T)CACGC intron-variant
rs1000159681 -- 3,203,295(+) AAGAG(A/C/T)GAAAC intron-variant
rs1000170373 -- 3,202,594(+) TGAGA(A/C/T)GTTTC intron-variant
rs1000205794 -- 3,200,490(+) TATTT(C/T)TAGTA intron-variant

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

Variant ID Type Subtype PubMed ID
nsv509716 CNV insertion 20534489
nsv953948 CNV deletion 24416366

Variation tolerance for NCLN Gene

Residual Variation Intolerance Score: 16.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.43; 81.95% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NCLN Gene

Human Gene Mutation Database (HGMD)
NCLN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
NCLN

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

Disorders for NCLN Gene

Relevant External Links for NCLN

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NCLN

No disorders were found for NCLN Gene.

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

Publications for NCLN Gene

  1. The Nicastrin-like protein Nicalin regulates assembly and stability of the Nicalin-nodal modulator (NOMO) membrane protein complex. (PMID: 17261586) Haffner C … Haass C (The Journal of biological chemistry 2007) 2 3 22 60
  2. Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PMID: 11230166) Wiemann S … Poustka A (Genome research 2001) 2 3 4 60
  3. Transmembrane protein 147 (TMEM147) is a novel component of the Nicalin-NOMO protein complex. (PMID: 20538592) Dettmer U … Haffner C (The Journal of biological chemistry 2010) 3 4 60
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  5. The DNA sequence and biology of human chromosome 19. (PMID: 15057824) Grimwood J … Lucas SM (Nature 2004) 3 4 60

Products for NCLN Gene

Sources for NCLN Gene

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