Human Gene NICN1 (ENST00000273598.8_8) from GENCODE V47lift37
  Description: nicolin 1, tubulin polyglutamylase complex subunit (from RefSeq NM_032316.3)
Gencode Transcript: ENST00000273598.8_8
Gencode Gene: ENSG00000145029.15_10
Transcript (Including UTRs)
   Position: hg19 chr3:49,459,766-49,466,757 Size: 6,992 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr3:49,462,266-49,466,672 Size: 4,407 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:49,459,766-49,466,757)mRNA (may differ from genome)Protein (213 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NICN1_HUMAN
DESCRIPTION: RecName: Full=Nicolin-1; AltName: Full=NPCEDRG; AltName: Full=Tubulin polyglutamylase complex subunit 5; Short=PGs5;
SUBUNIT: Part of the neuronal tubulin polyglutamylase complex which contains TPGS1, TPGS2, TTLL1, LRRC49 and NICN1 (By similarity).
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: High expression level is found in brain, testis, liver and kidney. Weak expression in spleen, leukocytes, small intestine and colon.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 23.86 RPKM in Brain - Cerebellum
Total median expression: 605.37 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -36.4085-0.428 Picture PostScript Text
3' UTR -1214.802500-0.486 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  SCOP Domains:
49785 - Galactose-binding domain-like

ModBase Predicted Comparative 3D Structure on Q9BSH3
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005874 microtubule


-  Descriptions from all associated GenBank mRNAs
  JD055140 - Sequence 36164 from Patent EP1572962.
JD306264 - Sequence 287288 from Patent EP1572962.
BC007546 - Homo sapiens aminomethyltransferase, mRNA (cDNA clone IMAGE:2959737), partial cds.
AK091738 - Homo sapiens cDNA FLJ34419 fis, clone HEART2008257, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AX747153 - Sequence 678 from Patent EP1308459.
AK296177 - Homo sapiens cDNA FLJ55081 complete cds, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK096062 - Homo sapiens cDNA FLJ38743 fis, clone KIDNE2012025, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
D13811 - Homo sapiens mRNA for glycine cleavage system T-protein, complete cds.
BC094771 - Homo sapiens cDNA clone IMAGE:5310714, containing frame-shift errors.
LF208627 - JP 2014500723-A/16130: Polycomb-Associated Non-Coding RNAs.
AK293481 - Homo sapiens cDNA FLJ59845 complete cds, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK293594 - Homo sapiens cDNA FLJ59850 complete cds, moderately similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK294592 - Homo sapiens cDNA FLJ59878 complete cds, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK290600 - Homo sapiens cDNA FLJ76259 complete cds, highly similar to Homo sapiens aminomethyltransferase (glycine cleavage system protein T) (AMT), mRNA.
AK301072 - Homo sapiens cDNA FLJ60001 complete cds, highly similar to Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10).
AK311636 - Homo sapiens cDNA, FLJ18678.
LF378532 - JP 2014500723-A/186035: Polycomb-Associated Non-Coding RNAs.
JD325503 - Sequence 306527 from Patent EP1572962.
JD525532 - Sequence 506556 from Patent EP1572962.
JD411362 - Sequence 392386 from Patent EP1572962.
JD116518 - Sequence 97542 from Patent EP1572962.
LF208626 - JP 2014500723-A/16129: Polycomb-Associated Non-Coding RNAs.
JD082717 - Sequence 63741 from Patent EP1572962.
JD313154 - Sequence 294178 from Patent EP1572962.
BC005050 - Homo sapiens nicolin 1, mRNA (cDNA clone MGC:12936 IMAGE:2820022), complete cds.
AF538150 - Homo sapiens NPCEDRGP (NPCEDRG) mRNA, NPCEDRG-s allele, complete cds.
BC050653 - Homo sapiens nicolin 1, mRNA (cDNA clone MGC:60162 IMAGE:6015080), complete cds.
AK094248 - Homo sapiens cDNA FLJ36929 fis, clone BRACE2005231, highly similar to Nicolin-1.
JD427707 - Sequence 408731 from Patent EP1572962.
JD311404 - Sequence 292428 from Patent EP1572962.
AK301846 - Homo sapiens cDNA FLJ52908 complete cds, highly similar to Nicolin-1.
JD214069 - Sequence 195093 from Patent EP1572962.
JD401404 - Sequence 382428 from Patent EP1572962.
JD235574 - Sequence 216598 from Patent EP1572962.
JD250262 - Sequence 231286 from Patent EP1572962.
JD459409 - Sequence 440433 from Patent EP1572962.
JD179851 - Sequence 160875 from Patent EP1572962.
JD362467 - Sequence 343491 from Patent EP1572962.
JD278913 - Sequence 259937 from Patent EP1572962.
JD342094 - Sequence 323118 from Patent EP1572962.
JD107997 - Sequence 89021 from Patent EP1572962.
JD262016 - Sequence 243040 from Patent EP1572962.
JD087009 - Sequence 68033 from Patent EP1572962.
LF378531 - JP 2014500723-A/186034: Polycomb-Associated Non-Coding RNAs.
JD229462 - Sequence 210486 from Patent EP1572962.
JD306263 - Sequence 287287 from Patent EP1572962.
JD169579 - Sequence 150603 from Patent EP1572962.
JD438895 - Sequence 419919 from Patent EP1572962.
JD264178 - Sequence 245202 from Patent EP1572962.
JD105343 - Sequence 86367 from Patent EP1572962.
JD036731 - Sequence 17755 from Patent EP1572962.
JD179618 - Sequence 160642 from Patent EP1572962.
JD481313 - Sequence 462337 from Patent EP1572962.
JD187305 - Sequence 168329 from Patent EP1572962.
JD272561 - Sequence 253585 from Patent EP1572962.
AJ299740 - Homo sapiens mRNA for nicolin 1 (NICN1 gene), clone IMAGE: 433564.
JD301817 - Sequence 282841 from Patent EP1572962.
JD052655 - Sequence 33679 from Patent EP1572962.
LF378530 - JP 2014500723-A/186033: Polycomb-Associated Non-Coding RNAs.
JD171582 - Sequence 152606 from Patent EP1572962.
JD059293 - Sequence 40317 from Patent EP1572962.
JD338152 - Sequence 319176 from Patent EP1572962.
JD455144 - Sequence 436168 from Patent EP1572962.
LF378529 - JP 2014500723-A/186032: Polycomb-Associated Non-Coding RNAs.
JD156603 - Sequence 137627 from Patent EP1572962.
JD256189 - Sequence 237213 from Patent EP1572962.
JD555948 - Sequence 536972 from Patent EP1572962.
JD115524 - Sequence 96548 from Patent EP1572962.
AK313073 - Homo sapiens cDNA, FLJ93554, Homo sapiens nicolin 1 (NICN1), mRNA.
JF432736 - Synthetic construct Homo sapiens clone IMAGE:100073979 nicolin 1 (NICN1) gene, encodes complete protein.
KJ894960 - Synthetic construct Homo sapiens clone ccsbBroadEn_04354 NICN1 gene, encodes complete protein.
MA444204 - JP 2018138019-A/16130: Polycomb-Associated Non-Coding RNAs.
MA614109 - JP 2018138019-A/186035: Polycomb-Associated Non-Coding RNAs.
MA444203 - JP 2018138019-A/16129: Polycomb-Associated Non-Coding RNAs.
MA614108 - JP 2018138019-A/186034: Polycomb-Associated Non-Coding RNAs.
MA614107 - JP 2018138019-A/186033: Polycomb-Associated Non-Coding RNAs.
MA614106 - JP 2018138019-A/186032: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BSH3 (Reactome details) participates in the following event(s):

R-HSA-8955869 Polyglutamylase complex (TTLL1) polyglutamylates alpha subunits of tubulin
R-HSA-8955332 Carboxyterminal post-translational modifications of tubulin
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000273598.1, ENST00000273598.2, ENST00000273598.3, ENST00000273598.4, ENST00000273598.5, ENST00000273598.6, ENST00000273598.7, NICN1_HUMAN, NM_032316, Q8IZQ2, Q9BSH3, uc317jcm.1, uc317jcm.2
UCSC ID: ENST00000273598.8_8
RefSeq Accession: NM_032316.3
Protein: Q9BSH3 (aka NICN1_HUMAN or NIL1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.