Human Gene NKX2-3 (ENST00000344586.9) from GENCODE V44
  Description: Homo sapiens NK2 homeobox 3 (NKX2-3), mRNA. (from RefSeq NM_145285)
RefSeq Summary (NM_145285): This gene encodes a homeodomain-containing transcription factor. The encoded protein is a member of the NKX family of homeodomain transcription factors. Studies of similar proteins in mouse and rat have indicated a potential role in cellular differentiation.[provided by RefSeq, Mar 2010]. Sequence Note: This RefSeq record was created from transcript and genomic sequence data because no single transcript was available for the full length of the gene. The extent of this transcript is supported by orthologous data and transcript alignments.
Gencode Transcript: ENST00000344586.9
Gencode Gene: ENSG00000119919.12
Transcript (Including UTRs)
   Position: hg38 chr10:99,532,942-99,536,524 Size: 3,583 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg38 chr10:99,533,132-99,535,721 Size: 2,590 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr10:99,532,942-99,536,524)mRNA (may differ from genome)Protein (364 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGencode
GeneCardsHGNCHPRDLynxMalacardsMGI
neXtProtOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NKX23_HUMAN
DESCRIPTION: RecName: Full=Homeobox protein Nkx-2.3; AltName: Full=Homeobox protein NK-2 homolog C;
FUNCTION: Transcription factor (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Belongs to the NK-2 homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAH25788.1; Type=Frameshift; Positions=273; Note=This frameshift is potential, but if it is real then the sequence of residues 274-302 are lacking from the translated cDNA while this region does not seem to correspond to an exon;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: NKX2-3
Diseases sorted by gene-association score: crohn's disease (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 28.68 RPKM in Colon - Sigmoid
Total median expression: 95.10 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 -81.10190-0.427 Picture PostScript Text
3' UTR -314.90803-0.392 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
  InterPro Domains: Graphical view of domain structure
IPR017970 - Homeobox_CS
IPR020479 - Homeobox_metazoa
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain

ModBase Predicted Comparative 3D Structure on Q8TAU0
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003674 molecular_function
GO:0003677 DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0001776 leukocyte homeostasis
GO:0002317 plasma cell differentiation
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006641 triglyceride metabolic process
GO:0006955 immune response
GO:0008150 biological_process
GO:0009791 post-embryonic development
GO:0022612 gland morphogenesis
GO:0030183 B cell differentiation
GO:0030225 macrophage differentiation
GO:0042127 regulation of cell proliferation
GO:0042475 odontogenesis of dentin-containing tooth
GO:0043367 CD4-positive, alpha-beta T cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0048535 lymph node development
GO:0048536 spleen development
GO:0048537 mucosal-associated lymphoid tissue development
GO:0048541 Peyer's patch development
GO:0048565 digestive tract development
GO:0048621 post-embryonic digestive tract morphogenesis
GO:0050900 leukocyte migration

Cellular Component:
GO:0005575 cellular_component
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  LF213448 - JP 2014500723-A/20951: Polycomb-Associated Non-Coding RNAs.
MA449025 - JP 2018138019-A/20951: Polycomb-Associated Non-Coding RNAs.
LF212790 - JP 2014500723-A/20293: Polycomb-Associated Non-Coding RNAs.
MA448367 - JP 2018138019-A/20293: Polycomb-Associated Non-Coding RNAs.
BC025788 - Homo sapiens NK2 transcription factor related, locus 3 (Drosophila), mRNA (cDNA clone MGC:34784 IMAGE:5229146), complete cds.
AK313485 - Homo sapiens cDNA, FLJ94036.
AK300856 - Homo sapiens cDNA FLJ60168 complete cds, highly similar to Homeobox protein Nkx-2.3.
JD281234 - Sequence 262258 from Patent EP1572962.
JD370506 - Sequence 351530 from Patent EP1572962.
JD200416 - Sequence 181440 from Patent EP1572962.
JD363524 - Sequence 344548 from Patent EP1572962.
KJ903917 - Synthetic construct Homo sapiens clone ccsbBroadEn_13311 NKX2-3 gene, encodes complete protein.
JD106329 - Sequence 87353 from Patent EP1572962.
JD431506 - Sequence 412530 from Patent EP1572962.
JD483512 - Sequence 464536 from Patent EP1572962.
JD461615 - Sequence 442639 from Patent EP1572962.
JD059128 - Sequence 40152 from Patent EP1572962.
JD522850 - Sequence 503874 from Patent EP1572962.
JD366999 - Sequence 348023 from Patent EP1572962.
JD174066 - Sequence 155090 from Patent EP1572962.
JD226906 - Sequence 207930 from Patent EP1572962.
JD474803 - Sequence 455827 from Patent EP1572962.
JD178082 - Sequence 159106 from Patent EP1572962.
JD180106 - Sequence 161130 from Patent EP1572962.
JD440640 - Sequence 421664 from Patent EP1572962.
JD045561 - Sequence 26585 from Patent EP1572962.
JD525585 - Sequence 506609 from Patent EP1572962.
JD423032 - Sequence 404056 from Patent EP1572962.
JD309837 - Sequence 290861 from Patent EP1572962.
JD289126 - Sequence 270150 from Patent EP1572962.
JD083787 - Sequence 64811 from Patent EP1572962.
JD383661 - Sequence 364685 from Patent EP1572962.
JD168562 - Sequence 149586 from Patent EP1572962.
JD203444 - Sequence 184468 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DUZ4, ENST00000344586.1, ENST00000344586.2, ENST00000344586.3, ENST00000344586.4, ENST00000344586.5, ENST00000344586.6, ENST00000344586.7, ENST00000344586.8, NKX23, NKX23_HUMAN, NKX2C, NM_145285, Q8TAU0, Q9NYS6, uc009xwj.1, uc009xwj.2, uc009xwj.3, uc009xwj.4, uc009xwj.5
UCSC ID: ENST00000344586.9
RefSeq Accession: NM_145285
Protein: Q8TAU0 (aka NKX23_HUMAN)
CCDS: CCDS41558.1

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