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Aliases for NICN1 Gene

Aliases for NICN1 Gene

  • Nicolin 1 2 3 5
  • Tubulin Polyglutamylase Complex Subunit 5 3 4
  • NPCEDRG 3 4
  • PGs5 3 4
  • Nicolin-1 3

External Ids for NICN1 Gene

Previous GeneCards Identifiers for NICN1 Gene

  • GC03P048862
  • GC03M049314
  • GC03M049419
  • GC03M049435

Summaries for NICN1 Gene

Entrez Gene Summary for NICN1 Gene

  • This protein encoded by this gene localizes to the nucleus and is expressed in numerous tissues including brain, testis, liver, and kidney. This refseq contains genomic sequence in its 3' UTR which is not supported by experimental evidence. Computer predictions indicate that this region of the 3' UTR contains hairpin-forming self-complementary sequence which is possibly excised after transcription. This gene has a pseudogene on chromosome X. [provided by RefSeq, Jul 2008]

GeneCards Summary for NICN1 Gene

NICN1 (Nicolin 1) is a Protein Coding gene. An important paralog of this gene is ENSG00000283189.

No data available for CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for NICN1 Gene

Genomics for NICN1 Gene

Regulatory Elements for NICN1 Gene

Enhancers for NICN1 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
GH03G049338 1.9 FANTOM5 ENCODE dbSUPER 15.6 +83.3 83277 14.7 MLX CREB3L1 ZFP64 DMAP1 YY1 SLC30A9 ZNF143 ZNF263 SP3 NFYC AMT QRICH1 IMPDH2 DALRD3 RHOA WDR6 NICN1 USP4 ENSG00000230454 RHOA-IT1
GH03G050257 2 FANTOM5 Ensembl ENCODE dbSUPER 14.7 -838.2 -838176 19.3 CREB3L1 AGO1 DMAP1 FEZF1 YY1 ZNF416 ZNF143 SP3 MEF2D SSRP1 HYAL3 CYB561D2 NICN1 IFRD2 GNAI2 SEMA3F-AS1 HEMK1 AMT HYAL1 AMIGO3
GH03G049898 1.9 FANTOM5 Ensembl ENCODE dbSUPER 14.8 -473.4 -473375 9.2 HNRNPUL1 HDGF PKNOX1 CREB3L1 AGO1 ARID4B SIN3A DMAP1 ZNF2 YY1 RBM6 QRICH1 NICN1 TMEM115 CCDC71 SEMA3F-AS1 IMPDH2 ENSG00000235236 MST1R RHOA-IT1
GH03G049464 1.4 Ensembl ENCODE dbSUPER 16 -36.6 -36560 2.5 HDAC1 TBL1XR1 ARID4B TCF12 ZNF766 GATA2 EGR1 CREM THAP11 CEBPB WDR6 NICN1 ENSG00000223343 QRICH1 RNA5SP130 GC03M049467
GH03G048742 1.8 FANTOM5 Ensembl ENCODE dbSUPER 11.9 +687.0 686958 1.1 HDGF PKNOX1 ATF1 ARNT ZFP64 TCF12 NCOA1 ZNF623 ZNF518A ZNF592 WDR6 AMT ENSG00000235236 NICN1 ENSG00000223343 QRICH1 CCDC71 TREX1 DALRD3 ARIH2
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around NICN1 on UCSC Golden Path with GeneCards custom track

Promoters for NICN1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000152223 26 1401 PKNOX1 MLX CREB3L1 SIN3A ARID4B DMAP1 YBX1 ZNF2 YY1 ZNF766

Genomic Location for NICN1 Gene

Chromosome:
3
Start:
49,422,333 bp from pter
End:
49,429,326 bp from pter
Size:
6,994 bases
Orientation:
Minus strand

Genomic View for NICN1 Gene

Genes around NICN1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
NICN1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for NICN1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for NICN1 Gene

Proteins for NICN1 Gene

  • Protein details for NICN1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BSH3-NICN1_HUMAN
    Recommended name:
    Nicolin-1
    Protein Accession:
    Q9BSH3
    Secondary Accessions:
    • Q8IZQ2

    Protein attributes for NICN1 Gene

    Size:
    213 amino acids
    Molecular mass:
    24202 Da
    Quaternary structure:
    • Part of the neuronal tubulin polyglutamylase complex which contains TPGS1, TPGS2, TTLL1, LRRC49 and NICN1.

    Alternative splice isoforms for NICN1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for NICN1 Gene

Post-translational modifications for NICN1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for NICN1 Gene

No data available for DME Specific Peptides for NICN1 Gene

Domains & Families for NICN1 Gene

Protein Domains for NICN1 Gene

ProtoNet:

Suggested Antigen Peptide Sequences for NICN1 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with NICN1: view

No data available for Gene Families and UniProtKB/Swiss-Prot for NICN1 Gene

Function for NICN1 Gene

Phenotypes for NICN1 Gene

GenomeRNAi human phenotypes for NICN1:
genes like me logo Genes that share phenotypes with NICN1: 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 NICN1 Gene

Localization for NICN1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for NICN1 Gene

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 NICN1 gene
Compartment Confidence
nucleus 5
cytoskeleton 3
mitochondrion 2
extracellular 1
peroxisome 1
cytosol 1

Gene Ontology (GO) - Cellular Components for NICN1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005874 microtubule IEA --
genes like me logo Genes that share ontologies with NICN1: view

Pathways & Interactions for NICN1 Gene

SuperPathways for NICN1 Gene

No Data Available

Interacting Proteins for NICN1 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
http://version10.5.string-db.org/api/image/networkList?limit=0&targetmode=proteins&caller_identity=gene_cards&network_flavor=evidence&identifiers=9606.ENSP00000273598%0d%0a9606.ENSP00000367878%0d%0a
Selected Interacting proteins: ENSP00000273598 Q9BSH3-NICN1_HUMAN for NICN1 Gene via STRING IID

Gene Ontology (GO) - Biological Process for NICN1 Gene

None

No data available for Pathways by source and SIGNOR curated interactions for NICN1 Gene

Drugs & Compounds for NICN1 Gene

No Compound Related Data Available

Transcripts for NICN1 Gene

Unigene Clusters for NICN1 Gene

Nicolin 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for NICN1 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c
SP1: - -
SP2: - - - -
SP3: -
SP4:
SP5:
SP6: -

Relevant External Links for NICN1 Gene

GeneLoc Exon Structure for
NICN1
ECgene alternative splicing isoforms for
NICN1

Expression for NICN1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for NICN1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of NICN1 Gene:

NICN1

SOURCE GeneReport for Unigene cluster for NICN1 Gene:

Hs.191460

mRNA Expression by UniProt/SwissProt for NICN1 Gene:

Q9BSH3-NICN1_HUMAN
Tissue specificity: High expression level is found in brain, testis, liver and kidney. Weak expression in spleen, leukocytes, small intestine and colon.

Evidence on tissue expression from TISSUES for NICN1 Gene

  • Lung(4.2)
  • Nervous system(3.4)
genes like me logo Genes that share expression patterns with NICN1: view

Primer Products

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for NICN1 Gene

Orthologs for NICN1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for NICN1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia NICN1 34 35
  • 99.68 (n)
dog
(Canis familiaris)
Mammalia NICN1 34 35
  • 91.86 (n)
cow
(Bos Taurus)
Mammalia NICN1 34 35
  • 90.3 (n)
rat
(Rattus norvegicus)
Mammalia Nicn1 34
  • 86.7 (n)
mouse
(Mus musculus)
Mammalia Nicn1 34 16 35
  • 86.54 (n)
oppossum
(Monodelphis domestica)
Mammalia NICN1 35
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NICN1 35
  • 64 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NICN1 35
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia mst1r 34
  • 61.35 (n)
zebrafish
(Danio rerio)
Actinopterygii nicn1 34 35
  • 55.5 (n)
Species where no ortholog for NICN1 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)
  • chicken (Gallus gallus)
  • 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 NICN1 Gene

ENSEMBL:
Gene Tree for NICN1 (if available)
TreeFam:
Gene Tree for NICN1 (if available)

Paralogs for NICN1 Gene

Paralogs for NICN1 Gene

Pseudogenes.org Pseudogenes for NICN1 Gene

genes like me logo Genes that share paralogs with NICN1: view

Variants for NICN1 Gene

Sequence variations from dbSNP and Humsavar for NICN1 Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs121964982 Pathogenic 49,422,223(-) ACGGC(A/G/T)GGAAA intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs121964983 Pathogenic 49,422,237(-) CTTCC(A/G)CCTGG intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense
rs386833677 Likely pathogenic 49,422,505(-) CCCGG(C/T)GTGCC nc-transcript-variant, utr-variant-3-prime, utr-variant-5-prime
rs386833678 Likely pathogenic 49,422,214(-) AAATG(-/G)TGGCG intron-variant, nc-transcript-variant, downstream-variant-500B, reference, frameshift-variant
rs386833679 Likely pathogenic 49,422,145(-) ACACA(C/T)GCCAG intron-variant, nc-transcript-variant, downstream-variant-500B, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for NICN1 Gene

Variant ID Type Subtype PubMed ID
nsv834687 CNV loss 17160897

Variation tolerance for NICN1 Gene

Residual Variation Intolerance Score: 32% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.30; 25.92% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for NICN1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
NICN1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for NICN1 Gene

Disorders for NICN1 Gene

Relevant External Links for NICN1

Genetic Association Database (GAD)
NICN1
Human Genome Epidemiology (HuGE) Navigator
NICN1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
NICN1

No disorders were found for NICN1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for NICN1 Gene

Publications for NICN1 Gene

  1. Cloning and characterization of the mammalian-specific nicolin 1 gene (NICN1) encoding a nuclear 24 kDa protein. (PMID: 12392556) Backofen B. … Leeb T. (Eur. J. Biochem. 2002) 2 3 4 22 64
  2. Genetic susceptibility to distinct bladder cancer subphenotypes. (PMID: 19692168) Guey L.T. … Malats N. (Eur. Urol. 2010) 3 46 64
  3. Association analysis of 3p21 with Crohn's disease in a New Zealand population. (PMID: 20307617) Morgan A.R. … Ferguson L.R. (Hum. Immunol. 2010) 3 46 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64

Products for NICN1 Gene

Sources for NICN1 Gene

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