Human Gene HMGN2 (uc001bmp.4) Description and Page Index
  Description: Homo sapiens high mobility group nucleosomal binding domain 2 (HMGN2), mRNA.
RefSeq Summary (NM_005517): The protein encoded by this gene binds nucleosomal DNA and is associated with transcriptionally active chromatin. Along with a similar protein, HMGN1, the encoded protein may help maintain an open chromatin configuration around transcribable genes. The protein has also been found to have antimicrobial activity against bacteria, viruses and fungi. [provided by RefSeq, Oct 2014]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR3476690.264967.1, SRR1803617.180791.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000361427.6/ ENSP00000355228.5 Protein has antimicrobial activity :: PMID: 16204630 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:26,798,902-26,803,133 Size: 4,232 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr1:26,799,104-26,801,639 Size: 2,536 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:26,798,902-26,803,133)mRNA (may differ from genome)Protein (90 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: HMGN2_HUMAN
DESCRIPTION: RecName: Full=Non-histone chromosomal protein HMG-17; AltName: Full=High mobility group nucleosome-binding domain-containing protein 2;
FUNCTION: Binds to the inner side of the nucleosomal DNA thus altering the interaction between the DNA and the histone octamer. May be involved in the process which maintains transcribable genes in an unique chromatin conformation (By similarity).
INTERACTION: P62993:GRB2; NbExp=1; IntAct=EBI-1758689, EBI-401755;
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Cytoplasmic enrichment upon phosphorylation.
PTM: Phosphorylation favors cytoplasmic localization.
MASS SPECTROMETRY: Mass=9261.5; Method=Electrospray; Range=2-90; Source=PubMed:10739259;
MASS SPECTROMETRY: Mass=9341.3; Mass_error=1.9; Method=Electrospray; Range=2-90; Source=PubMed:10739259;
MASS SPECTROMETRY: Mass=9421.5; Method=Electrospray; Range=2-90; Source=PubMed:10739259;
SIMILARITY: Belongs to the HMGN family.

-  MalaCards Disease Associations
  MalaCards Gene Search: HMGN2
Diseases sorted by gene-association score: limited scleroderma (1)

-  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: 126.19 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2815.78 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -77.80202-0.385 Picture PostScript Text
3' UTR -451.751494-0.302 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
IPR000079 - HMGN_fam

Pfam Domains:
PF01101 - HMG14 and HMG17

ModBase Predicted Comparative 3D Structure on P05204
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    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0031492 nucleosomal DNA binding

Biological Process:
GO:0031640 killing of cells of other organism

Cellular Component:
GO:0000785 chromatin
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  EU446509 - Synthetic construct Homo sapiens clone IMAGE:100069931; IMAGE:100011718; FLH257113.01L high-mobility group nucleosomal binding domain 2 (HMGN2) gene, encodes complete protein.
BC075837 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:88719 IMAGE:6272425), complete cds.
BC070297 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:88292 IMAGE:4282630), complete cds.
BC110390 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:102817 IMAGE:5190365), complete cds.
BC000378 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:8383 IMAGE:2820349), complete cds.
BC071707 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:87991 IMAGE:3849426), complete cds.
BC003050 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:750 IMAGE:3543809), complete cds.
BC032140 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:29711 IMAGE:5021546), complete cds.
BC072010 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:88720 IMAGE:6273507), complete cds.
BC081567 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:88718 IMAGE:4131303), complete cds.
BC014644 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:15731 IMAGE:3355317), complete cds.
BC072011 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone MGC:88721 IMAGE:6647282), complete cds.
M12623 - Human non-histone chromosomal protein HMG-17 mRNA, complete cds.
BC003689 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone IMAGE:3455121).
AK026562 - Homo sapiens cDNA: FLJ22909 fis, clone KAT05694, highly similar to HUMHMG17 Human non-histone chromosomal protein HMG-17 mRNA.
JD200386 - Sequence 181410 from Patent EP1572962.
AB464439 - Synthetic construct DNA, clone: pF1KB3387, Homo sapiens HMGN2 gene for Non-histone chromosomal protein HMG-17, without stop codon, in Flexi system.
KJ891360 - Synthetic construct Homo sapiens clone ccsbBroadEn_00754 HMGN2 gene, encodes complete protein.
CR542122 - Homo sapiens full open reading frame cDNA clone RZPDo834C0523D for gene HMGN2, high-mobility group nucleosomal binding domain 2; complete cds, incl. stopcodon.
JD490033 - Sequence 471057 from Patent EP1572962.
JD464671 - Sequence 445695 from Patent EP1572962.
BC007124 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone IMAGE:3463052).
BC064347 - Homo sapiens cDNA clone IMAGE:4516246.
JD170503 - Sequence 151527 from Patent EP1572962.
JD170504 - Sequence 151528 from Patent EP1572962.
JD440656 - Sequence 421680 from Patent EP1572962.
BC061898 - Homo sapiens high-mobility group nucleosomal binding domain 2, mRNA (cDNA clone IMAGE:3452912).
JD182782 - Sequence 163806 from Patent EP1572962.
JD019116 - Sequence 140 from Patent EP1572962.
JD465840 - Sequence 446864 from Patent EP1572962.
DQ581351 - Homo sapiens piRNA piR-49463, complete sequence.
JD181789 - Sequence 162813 from Patent EP1572962.
BC020307 - Homo sapiens cDNA clone IMAGE:4993977.
JD172065 - Sequence 153089 from Patent EP1572962.
JD442108 - Sequence 423132 from Patent EP1572962.
JD207837 - Sequence 188861 from Patent EP1572962.
JD439938 - Sequence 420962 from Patent EP1572962.
JD050698 - Sequence 31722 from Patent EP1572962.
JD209199 - Sequence 190223 from Patent EP1572962.
JD549664 - Sequence 530688 from Patent EP1572962.
JD409743 - Sequence 390767 from Patent EP1572962.
JD489347 - Sequence 470371 from Patent EP1572962.
L32131 - Homo sapiens (clone XP2E8B) mRNA, partial cds.
JD088890 - Sequence 69914 from Patent EP1572962.
JD229261 - Sequence 210285 from Patent EP1572962.
JD082361 - Sequence 63385 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: HMG17, HMGN2_HUMAN, NM_005517, NP_005508, P05204, Q0VGD5, Q6FGI5, Q96C64
UCSC ID: uc001bmp.4
RefSeq Accession: NM_005517
Protein: P05204 (aka HMGN2_HUMAN)
CCDS: CCDS283.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005517.3
exon count: 6CDS single in 3' UTR: no RNA size: 1989
ORF size: 273CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 735.50frame shift in genome: no % Coverage: 98.99
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.