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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

NICN1 Gene

protein-coding GIFtS: 45
GCID: GC03M049435

nicolin 1

Explore 2 diseases affiliated with
NICN1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
Nicolin 1¹ ²
Tubulin Polyglutamylase Complex Subunit 5² ³
NPCEDRG² ³
PGs5² ³
MGC12936¹
Nicolin-1¹

External Ids:	HGNC: 18317¹	Entrez Gene: 84276²	Ensembl: ENSG00000145029⁷	OMIM: 611516⁵	UniProtKB: Q9BSH3³

Export aliases for NICN1 gene to outside databases

Previous GC identifers: GC03P048862 GC03M049314 GC03M049419

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for NICN1:

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)

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000003.11 NC_018914.1 NT_022517.18

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the NICN1 gene promoter:
SRF GR SRF (504 AA) ATF-2 GR-beta c-Jun GR-alpha
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: NICN1 promoter sequence

Search SABiosciences Chromatin IP Primers for NICN1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NICN1

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3p21.31 Ensembl cytogenetic band: 3p21.31 HGNC cytogenetic band: 3p21.31

NICN1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NICN1 gene location

GeneLoc information about chromosome 3 GeneLoc Exon Structure

GeneLoc location for GC03M049435: view genomic region (about GC identifiers)

Start:	49,459,766 bp from pter	End:	49,466,759 bp from pter
Size:	6,994 bases	Orientation:	minus strand

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: NICN1_HUMAN, Q9BSH3 (See protein sequence)

Recommended Name: Nicolin-1

Size: 213 amino acids; 24202 Da

Subunit: Part of the neuronal tubulin polyglutamylase complex which contains TPGS1, TPGS2, TTLL1, LRRC49 and NICN1 (By

similarity)

Subcellular location: Nucleus

Secondary accessions: Q8IZQ2

Alternative splicing: 2 isoforms: Q9BSH3-1 Q9BSH3-2

Explore the universe of human proteins at neXtProt for NICN1: NX_Q9BSH3

Post-translational modifications:

View modification sites using PhosphoSitePlus²

View neXtProt modification sites for NX_Q9BSH3

NICN1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_115692.1

ENSEMBL proteins:

ENSP00000273598 ENSP00000413115 ENSP00000402335

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Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	IEA	--
GO:0005874	microtubule	IEA	--

NICN1 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

ProtoNet protein and cluster: Q9BSH3

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

miRNA Products:		OriGene 3'-UTR Clone: NICN1 Browse MicroRNA Expression Plasmids
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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for NICN1

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

1 Interacting protein for NICN1 (ENSP00000273598⁴) via UniProtKB, MINT, STRING, and/or I2D

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
TPGS1	ENSP00000352265⁴	STRING: ENSP00000352265

About this table

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for NICN1
Search CenterWatch for drugs/clinical trials and news about NICN1

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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About This Section

REFSEQ mRNAs for NICN1 gene:

NM_032316.3

Unigene Cluster for NICN1:

Nicolin 1

Hs.191460 [show with all ESTs]

Unigene Representative Sequence: NM_032316

7 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000273598(uc003cwz.1 uc011bcr.2) ENST00000423832 ENST00000497742

ENST00000436744 ENST00000422593 ENST00000494057 ENST00000461015

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Additional cDNA sequence:

AJ299740.1 AK094248.1 AK301846.1 AK313073.1 BC005050.1 BC050653.1

13 DOTS entries:

DT.92010435 DT.92418890 DT.91955712 DT.100804815 DT.100027200 DT.120904077 DT.92418892 DT.95293059

DT.441687 DT.114158 DT.120904286 DT.120904696 DT.91941373

24/246 AceView cDNA sequences (see all 246):

CR613547 AI348172 BX358759 AI128880 BX471822 BE677482 AU098698 BP374048

AI057053 AU076448 BM843383 BM874253 BQ062172 AW591508 BX365555 AK096062

AI912969 BU846233 D13811 BM874694 BQ084371 N59532 AU103014 AI421971

GeneLoc Exon Structure

5/6 Alternative Splicing Database (ASD) splice patterns (SP) for NICN1 (see all 6) About this scheme

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

ECgene alternative splicing isoforms for NICN1

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

NICN1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

About this image

NICN1 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

1 LifeMap In Vivo Development Anatomical Compartment/Cell

Tissue

Anatomical Compartment

Cell

Category (developmental path)

Head Mesenchyme

Branchial Arch 1

Paraxial Mesoderm Cells

Bone, Skeletal Muscle

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See NICN1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for NICN1

SOURCE GeneReport for Unigene cluster: Hs.191460

UniProtKB/Swiss-Prot: NICN1_HUMAN, Q9BSH3

Tissue specificity: High expression level is found in brain, testis, liver and kidney. Weak expression in spleen,

leukocytes, small intestine and colon

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for NICN1 gene from 3/11 species (see all 11) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Nicn1^{1 , 5}	nicolin 1^{1, 5}	86.54(n)¹ 89.2(a)¹		9 (59.18 cM)⁵ 66257¹ NM_025449.3¹ NP_079725.1¹ 108290457⁵
lizard (Anolis carolinensis)	Reptilia	NICN1⁶	--	62(a)	1 ↔ 1	2(147135909-147140831)
zebrafish (Danio rerio)	Actinopterygii	nicn1¹	nicolin 1	55.34(n) 51.2(a)		445216 NM_001003610.1 NP_001003610.1

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

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

Paralogs for NICN1 gene

NICN1 for paralogs About GeneDecksing

1 Pseudogenes.org Pseudogene for NICN1
PGOHUM00000241270

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 3 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs139254977^1,2		--	49462123(+)	`GAGAAG/TCCTGA`	1	--	ut3¹		0	--	--	--	--
rs181793435^1,2		--	49462138(+)	`GTGAAG/TGTGGC`	1	--	ut3¹		0	--	--	--	--
rs186097465^1,2		--	49462154(+)	`CAGAAC/TAGGCA`	1	--	ut3¹		0	--	--	--	--
rs143705175^1,2		--	49462214(+)	`CCCAAA/GCCAAG`	1	--	ut3¹		0	--	--	--	--
rs146812560^1,2		--	49462215(+)	`CCAAAC/TCAAGT`	1	--	ut3¹		0	--	--	--	--
rs200380201^1,2		--	49462243(+)	`GGCCAA/CCATCT`	1	--	ut3¹		0	--	--	--	--
rs199800701^1,2		--	49462251(+)	`TCTTGC/GCTAGG`	1	--	ut3¹		0	--	--	--	--
rs189963854^1,2	C,	--	49462293(+)	`AGGTCA/GTAACA`	2	Y	syn¹		0	--	--	--	--
rs201058670^1,2		--	49462395(+)	`GGCCGA/GTCCTT`	2	T I	mis¹		0	--	--	--	--
rs200643542^1,2		--	49462403(+)	`CTTGCA/GGAGGT`	2	S	syn¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for NICN1 (49459766 - 49466759 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for NICN1: --

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

NICN1 for disorders           About GeneDecksing

OMIM gene information: 611516    OMIM disorders: --

2 diseases for NICN1:    About MalaCards

crohn's disease neuronitis

1 disease from the University of Copenhagen DISEASES database for NICN1:

Glycine encephalopathy

Human Genome Epidemiology (HuGE) Navigator: NICN1 (2 documents)

Export disorders for NICN1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for NICN1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with NICN1)

Utopia: connect your pdf to the dynamic
world of online information

Cloning and characterization of the mammalian-specific nicolin 1 gene (NICN1) encoding a nuclear 24 kDa protein. (PubMed id 12392556)^{1, 2, 3, 9} Backofen B.... Leeb T. (2002)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{1, 2} Gerhard D.S....Malek J. (2004)
Cloning and characterization of the NPCEDRG gene prom oter. (PubMed id 20821255)¹ Hou D....Chen Z. (2011)
Association analysis of 3p21 with Crohn's disease in a New Zealand population. (PubMed id 20307617)¹ Morgan A.R....Ferguson L.R. (2010)
Genetic susceptibility to distinct bladder cancer sub phenotypes. (PubMed id 19692168)¹ Guey L.T....Malats N. (2010)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)¹ Ota T.... Sugano S. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)
Genomic organization of the murine aminomethyltransferase gene (Amt). (PubMed id 12487019)¹ Backofen B. and Leeb T. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 84276	HGNC: 18317	AceView: AMTandNICN1	Ensembl:ENSG00000145029	euGenes: HUgn84276
ECgene: NICN1	H-InvDB: NICN1

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for NICN1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for NICN1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for NICN1 gene:
Search GeneIP for patents involving NICN1

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
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About This Section


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	Browse OriGene basic RS shRNAs		Browse OriGene validated miRNA SYBR primer pairs
	Browse OriGene full length recombinant human proteins expressed in human HEK293 cells		OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
	OriGene Custom Antibody Services for NICN1		OriGene Custom Protein Services for NICN1
	OriGene Custom Immunoassay Development

	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat NICN1
	QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing NICN1
	QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat NICN1
	QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat NICN1
	QIAGEN QuantiFast Probe-based Assays in human, mouse, rat NICN1
	QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat NICN1

	GenScript Custom Purified and Recombinant Proteins Services for NICN1		GenScript cDNA clones with any tag delivered in your preferred vector for NICN1
	GenScript Custom Assay Services for NICN1		GenScript Custom Superior Antibodies Services for NICN1
	GenScript Custom overexpressing Cell Line Services for NICN1		CloneReady with Over 120,000 Genes
	Gene Synthesis: Any Gene in Any Vector		Vector-based siRNA and miRNA, Ready for Transfection
	Gene Mutant Library, Variants up to 10^11		Plasmid Preparation
	Custom Peptide Services

Search for Antibodies & Assays

	Regulatory tfbs in NICN1 promoter
	Search Chromatin IP Primers for NICN1
	RT² qPCR Primer Assay in human, mouse, rat NICN1
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	Browse Sino Biological Proteins and Antibodies
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Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

	Novus Tissue Slides
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	Search for Antibodies for NICN1 at Abcam
	See all of Abcam's Antibodies, Kits and Proteins for NICN1
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Search LifeMap BioReagents cell lines for NICN1

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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NICN1

	SwitchGear 3'UTR luciferase reporter plasmids for NICN1
	SwitchGear Promoter luciferase reporter plasmids for NICN1

ThermoFisher Antibodies for NICN1

Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat NICN1

GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
GIFtS Group

The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

The GeneCards Human Gene Database

Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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NICN1 Gene

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