Human Gene HMGN1 (ENST00000380749.10) from GENCODE V44
  Description: Homo sapiens high mobility group nucleosome binding domain 1 (HMGN1), mRNA. (from RefSeq NM_004965)
RefSeq Summary (NM_004965): The protein encoded by this gene binds nucleosomal DNA and is associated with transcriptionally active chromatin. Along with a similar protein, HMG17, the encoded protein may help maintain an open chromatin configuration around transcribable genes. [provided by RefSeq, Aug 2011].
Gencode Transcript: ENST00000380749.10
Gencode Gene: ENSG00000205581.11
Transcript (Including UTRs)
   Position: hg38 chr21:39,342,315-39,349,088 Size: 6,774 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg38 chr21:39,343,112-39,348,917 Size: 5,806 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr21:39,342,315-39,349,088)mRNA (may differ from genome)Protein (100 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGImyGene2
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HMGN1_HUMAN
DESCRIPTION: RecName: Full=Non-histone chromosomal protein HMG-14; AltName: Full=High mobility group nucleosome-binding domain-containing protein 1;
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. Inhibits the phosphorylation of nucleosomal histones H3 and H2A by RPS6KA5/MSK1 and RPS6KA3/RSK2 (By similarity).
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Cytoplasmic enrichment upon phosphorylation. The RNA edited version localizes to the nucleus.
PTM: Phosphorylation on Ser-21 and Ser-25 weakens binding to nucleosomes and increases the rate of H3 phosphorylation (By similarity). Phosphorylation favors cytoplasmic localization.
RNA EDITING: Modified_positions=Not_applicable; Note=Partially edited. A new initiator methionine may be created by a single uridine insertion in the 5'-UTR, causing an N-terminal extension of 45 amino acids. The existence of the RNA edited version is supported by direct protein sequencing by MS/MS of the following peptides specific to that version: 23-31 and 40-48. The RNA edited version is called ET-HMGN1.
MASS SPECTROMETRY: Mass=10527.8; Mass_error=0.7; Method=Electrospray; Range=2-100; Source=PubMed:10739259;
MASS SPECTROMETRY: Mass=10608; Method=Electrospray; Range=2-100; Source=PubMed:10739259;
MASS SPECTROMETRY: Mass=10688; Mass_error=1.3; Method=Electrospray; Range=2-100; Source=PubMed:10739259;
MASS SPECTROMETRY: Mass=10768; Method=Electrospray; Range=2-100; Source=PubMed:10739259;
SIMILARITY: Belongs to the HMGN family.

-  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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 76.69 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1494.29 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 -91.50171-0.535 Picture PostScript Text
3' UTR -176.10797-0.221 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 P05114
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     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0031492 nucleosomal DNA binding

Biological Process:
GO:0000720 pyrimidine dimer repair by nucleotide-excision repair
GO:0006283 transcription-coupled nucleotide-excision repair
GO:0006325 chromatin organization
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0010224 response to UV-B
GO:0010225 response to UV-C
GO:0032786 positive regulation of DNA-templated transcription, elongation
GO:0040034 regulation of development, heterochronic
GO:0048597 post-embryonic camera-type eye morphogenesis
GO:0050678 regulation of epithelial cell proliferation
GO:1901666 positive regulation of NAD+ ADP-ribosyltransferase activity

Cellular Component:
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC107741 - Homo sapiens high-mobility group nucleosome binding domain 1, mRNA (cDNA clone MGC:104230 IMAGE:6495117), complete cds.
BC023984 - Homo sapiens high-mobility group nucleosome binding domain 1, mRNA (cDNA clone MGC:23740 IMAGE:4104558), complete cds.
BC070154 - Homo sapiens high-mobility group nucleosome binding domain 1, mRNA (cDNA clone MGC:88134 IMAGE:6495327), complete cds.
BC000075 - Homo sapiens high-mobility group nucleosome binding domain 1, mRNA (cDNA clone MGC:1997 IMAGE:3510312), complete cds.
AK130775 - Homo sapiens cDNA FLJ27265 fis, clone TMS00186.
AK056033 - Homo sapiens cDNA FLJ31471 fis, clone NT2NE2001435.
AB209245 - Homo sapiens mRNA for Hypothetical protein FLJ31471 variant protein.
BC071643 - Homo sapiens high-mobility group nucleosome binding domain 1, mRNA (cDNA clone MGC:87800 IMAGE:5549431), complete cds.
BC072672 - Homo sapiens high-mobility group nucleosome binding domain 1, mRNA (cDNA clone MGC:87801 IMAGE:6166317), complete cds.
BC106080 - Homo sapiens high-mobility group nucleosome binding domain 1, mRNA (cDNA clone MGC:117425 IMAGE:3855939), complete cds.
J02621 - Human non-histone chromosomal protein HMG-14 mRNA, complete cds.
JD326212 - Sequence 307236 from Patent EP1572962.
JD224900 - Sequence 205924 from Patent EP1572962.
JD552809 - Sequence 533833 from Patent EP1572962.
BC070153 - Homo sapiens high-mobility group nucleosome binding domain 1, mRNA (cDNA clone MGC:88133 IMAGE:6450636), complete cds.
JD481535 - Sequence 462559 from Patent EP1572962.
JD566363 - Sequence 547387 from Patent EP1572962.
JD545886 - Sequence 526910 from Patent EP1572962.
JD231743 - Sequence 212767 from Patent EP1572962.
AK315410 - Homo sapiens cDNA, FLJ96459.
BT007337 - Homo sapiens high-mobility group nucleosome binding domain 1 mRNA, complete cds.
KJ891359 - Synthetic construct Homo sapiens clone ccsbBroadEn_00753 HMGN1 gene, encodes complete protein.
DQ891741 - Synthetic construct clone IMAGE:100004371; FLH180249.01X; RZPDo839A02134D high-mobility group nucleosome binding domain 1 (HMGN1) gene, encodes complete protein.
DQ894919 - Synthetic construct Homo sapiens clone IMAGE:100009379; FLH180245.01L; RZPDo839A02133D high-mobility group nucleosome binding domain 1 (HMGN1) gene, encodes complete protein.
AB590110 - Synthetic construct DNA, clone: pFN21AE1455, Homo sapiens HMGN1 gene for high-mobility group nucleosome binding domain 1, without stop codon, in Flexi system.
JD436997 - Sequence 418021 from Patent EP1572962.
JD460539 - Sequence 441563 from Patent EP1572962.
JD142281 - Sequence 123305 from Patent EP1572962.
JD480659 - Sequence 461683 from Patent EP1572962.
JD122416 - Sequence 103440 from Patent EP1572962.
JD217673 - Sequence 198697 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_p38mapkPathway - p38 MAPK Signaling Pathway

Reactome (by CSHL, EBI, and GO)

Protein P05114 (Reactome details) participates in the following event(s):

R-HSA-6782004 Assembly of the pre-incision complex in TC-NER
R-HSA-6782069 UVSSA:USP7 deubiquitinates ERCC6
R-HSA-6782131 RNA Pol II backtracking in TC-NER
R-HSA-6782138 ERCC5 and RPA bind TC-NER site
R-HSA-6782211 DNA polymerases delta, epsilon or kappa bind the TC-NER site
R-HSA-6782204 5' incision of damaged DNA strand by ERCC1:ERCC4 in TC-NER
R-HSA-6782224 3' incision by ERCC5 (XPG) in TC-NER
R-HSA-6782227 Ligation of newly synthesized repair patch to incised DNA in TC-NER
R-HSA-6782208 Repair DNA synthesis of ~27-30 bases long patch by POLD, POLE or POLK in TC-NER
R-HSA-6782141 Binding of ERCC1:ERCC4 (ERCC1:XPF) to pre-incision complex in TC-NER
R-HSA-6781823 Formation of TC-NER Pre-Incision Complex
R-HSA-6781827 Transcription-Coupled Nucleotide Excision Repair (TC-NER)
R-HSA-6782135 Dual incision in TC-NER
R-HSA-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-HSA-5696398 Nucleotide Excision Repair
R-HSA-73894 DNA Repair

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000380749.1, ENST00000380749.2, ENST00000380749.3, ENST00000380749.4, ENST00000380749.5, ENST00000380749.6, ENST00000380749.7, ENST00000380749.8, ENST00000380749.9, HMG14, HMGN1_HUMAN, NM_004965, P05114, Q3KQR8, uc002yxo.1, uc002yxo.2, uc002yxo.3, uc002yxo.4, uc002yxo.5
UCSC ID: ENST00000380749.10
RefSeq Accession: NM_004965
Protein: P05114 (aka HMGN1_HUMAN)
CCDS: CCDS33559.1

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