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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.

Additional gene information for NICN1 Gene

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

GeneHancer (GH) Regulatory Elements for NICN1 Gene

Promoters and enhancers for NICN1 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
GH03J049428 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 -0.2 -162 1.8 PKNOX1 SMAD1 MLX ARID4B SIN3A DMAP1 YBX1 ZNF2 YY1 POLR2B ENSG00000283189 NICN1 AMT QRICH1 USP19 TMEM115 WDR6 QARS ATRIP IP6K2
GH03J049429 Enhancer 0.6 ENCODE 650.7 +1.0 983 0.2 KLF1 PKNOX1 GLIS2 EBF1 ZNF600 PRDM10 DPF2 KLF14 ENSG00000283189 NICN1 GC03P049421 AMT
GH03J049016 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 50.2 +409.1 409065 6.8 CLOCK ZFP64 FEZF1 IRF4 YY1 E2F8 ZNF143 SP3 NFYC ZFP41 DALRD3 GC03M049024 MIR191 MIR425 NDUFAF3 WDR6 ENSG00000235236 NICN1 FCF1P2 QRICH1
GH03J049939 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 26.2 -511.1 -511118 2 HDGF PKNOX1 CLOCK SMAD1 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 RBM6 NICN1 ENSG00000235236 RBM5 QRICH1 ENSG00000223343 P4HTM NAA80 WDR6 GC03P049762
GH03J049338 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 15.7 +83.3 83276 14.7 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A USP4 AMT QRICH1 RBM6 RBM5 IP6K2 ATRIP USP19 WDR6 BSN-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around NICN1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the NICN1 gene promoter:

Genomic Locations for NICN1 Gene

Genomic Locations for NICN1 Gene
chr3:49,422,333-49,429,326
(GRCh38/hg38)
Size:
6,994 bases
Orientation:
Minus strand
chr3:49,459,766-49,466,759
(GRCh37/hg19)

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

Gene Families for NICN1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

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 UniProtKB/Swiss-Prot for NICN1 Gene

Function for NICN1 Gene

Phenotypes From GWAS Catalog for NICN1 Gene

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

Animal Model Products

Clone Products

  • Addgene plasmids for NICN1

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

Subcellular locations from the

Human Protein Atlas (HPA)

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: Q9BSH3-NICN1_HUMAN ENSP00000273598 for NICN1 Gene via IID STRING

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

mRNA/cDNA for NICN1 Gene

Unigene Clusters for NICN1 Gene

Nicolin 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for NICN1

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

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 33
  • 99.68 (n)
OneToOne
dog
(Canis familiaris)
Mammalia NICN1 34 33
  • 91.86 (n)
OneToOne
cow
(Bos Taurus)
Mammalia NICN1 34 33
  • 90.3 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Nicn1 33
  • 86.7 (n)
mouse
(Mus musculus)
Mammalia Nicn1 16 34 33
  • 86.54 (n)
oppossum
(Monodelphis domestica)
Mammalia NICN1 34
  • 76 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia NICN1 34
  • 64 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia NICN1 34
  • 61 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia mst1r 33
  • 61.35 (n)
zebrafish
(Danio rerio)
Actinopterygii nicn1 34 33
  • 55.5 (n)
OneToOne
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)
Aminode:
Evolutionary constrained regions (ECRs) for NICN1: view image

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 Variation AA Info Type
rs121964982 likely-pathogenic, pathogenic, Non-ketotic hyperglycinemia 49,422,223(-) C/A/T downstream_transcript_variant
rs121964983 pathogenic, Non-ketotic hyperglycinemia 49,422,237(-) T/C downstream_transcript_variant
rs145243292 uncertain-significance, Non-ketotic hyperglycinemia 49,422,167(-) G/A downstream_transcript_variant
rs34812788 uncertain-significance, Non-ketotic hyperglycinemia 49,422,210(-) G/A downstream_transcript_variant
rs386833677 likely-pathogenic, Non-ketotic hyperglycinemia 49,422,505(-) G/A 3_prime_UTR_variant

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)

Additional Variant Information for NICN1 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for NICN1 Gene

Additional Disease Information for NICN1

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

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 (European journal of biochemistry 2002) 2 3 4 22 58
  2. Genetic susceptibility to distinct bladder cancer subphenotypes. (PMID: 19692168) Guey LT … EPICURO/Spanish Bladder Cancer Study investigators (European urology 2010) 3 44 58
  3. Association analysis of 3p21 with Crohn's disease in a New Zealand population. (PMID: 20307617) Morgan AR … Ferguson LR (Human immunology 2010) 3 44 58
  4. 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
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for NICN1 Gene

Sources for NICN1 Gene

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