Human Gene HMGN3 (uc003pis.3)
  Description: Homo sapiens high mobility group nucleosomal binding domain 3 (HMGN3), transcript variant 2, mRNA.
RefSeq Summary (NM_138730): The protein encoded by this gene binds thyroid hormone receptor beta in the presence of thyroid hormone. The encoded protein, a member of the HMGN protein family, is thought to reduce the compactness of the chromatin fiber in nucleosomes, thereby enhancing transcription from chromatin templates. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. There is a related pseudogene on chromosome 1. [provided by RefSeq, Jan 2016].
Transcript (Including UTRs)
   Position: hg19 chr6:79,910,962-79,944,455 Size: 33,494 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr6:79,911,430-79,944,277 Size: 32,848 Coding Exon Count: 6 

Page IndexSequence and LinksPrimersCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:79,910,962-79,944,455)mRNA (may differ from genome)Protein (77 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIOMIM
PubMedTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  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: 131.18 RPKM in Pituitary
Total median expression: 3524.47 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 -76.60178-0.430 Picture PostScript Text
3' UTR -114.11468-0.244 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
  Pfam Domains:
PF01101 - HMG14 and HMG17

ModBase Predicted Comparative 3D Structure on Q15651-2
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AY043282 - Homo sapiens TRIP7-like protein mRNA, complete cds.
BX648085 - Homo sapiens mRNA; cDNA DKFZp686E20226 (from clone DKFZp686E20226).
AK124181 - Homo sapiens cDNA FLJ42187 fis, clone THYMU2032358.
AF401520 - Homo sapiens TRIP7 variant protein mRNA, complete cds, alternatively spliced.
BC009529 - Homo sapiens high mobility group nucleosomal binding domain 3, mRNA (cDNA clone MGC:10048 IMAGE:3890883), complete cds.
AF274949 - Homo sapiens PNAS-24 mRNA, complete cds.
JD546519 - Sequence 527543 from Patent EP1572962.
JD237960 - Sequence 218984 from Patent EP1572962.
JD093509 - Sequence 74533 from Patent EP1572962.
JD237272 - Sequence 218296 from Patent EP1572962.
L40357 - Homo sapiens thyroid receptor interactor (TRIP7) mRNA, 3' end of cds.
JD092955 - Sequence 73979 from Patent EP1572962.
JD316482 - Sequence 297506 from Patent EP1572962.
AK315391 - Homo sapiens cDNA, FLJ96439, Homo sapiens high mobility group nucleosomal binding domain 3(HMGN3), transcript variant 2, mRNA.
KJ892745 - Synthetic construct Homo sapiens clone ccsbBroadEn_02139 HMGN3 gene, encodes complete protein.
JD205487 - Sequence 186511 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: NM_138730, NP_620058, PNAS-24, Q15651-2, TRIP7
UCSC ID: uc003pis.3
RefSeq Accession: NM_138730
Protein: Q15651-2, splice isoform of Q15651 CCDS: CCDS4989.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138730.2
exon count: 6CDS single in 3' UTR: no RNA size: 894
ORF size: 234CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 668.00frame shift in genome: no % Coverage: 98.43
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.