Human Gene HMGXB4 (ENST00000216106.6_4) from GENCODE V47lift37
  Description: HMG-box containing 4, transcript variant 3 (from RefSeq NM_001362972.2)
Gencode Transcript: ENST00000216106.6_4
Gencode Gene: ENSG00000100281.14_8
Transcript (Including UTRs)
   Position: hg19 chr22:35,653,486-35,691,800 Size: 38,315 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr22:35,658,384-35,689,644 Size: 31,261 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:35,653,486-35,691,800)mRNA (may differ from genome)Protein (601 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HMGX4_HUMAN
DESCRIPTION: RecName: Full=HMG domain-containing protein 4; AltName: Full=HMG box-containing protein 4; AltName: Full=High mobility group protein 2-like 1; AltName: Full=Protein HMGBCG;
FUNCTION: Negatively regulates Wnt/beta-catenin signaling during development (By similarity).
SUBCELLULAR LOCATION: Nucleus (Potential).
SIMILARITY: Contains 1 HMG box DNA-binding domain.

-  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: HMGXB4
Diseases sorted by gene-association score: spherocytosis, type 4 (2)

-  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: 8.80 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 233.01 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 -42.20133-0.317 Picture PostScript Text
3' UTR -563.002156-0.261 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
IPR025228 - DUF4171
IPR009071 - HMG_superfamily

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF09011 - HMG-box domain
PF13775 - Domain of unknown function (DUF4171)

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on Q9UGU5
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 Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

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

Biological Process:
GO:0008333 endosome to lysosome transport
GO:0016055 Wnt signaling pathway
GO:0030178 negative regulation of Wnt signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0016589 NURF complex


-  Descriptions from all associated GenBank mRNAs
  LF384401 - JP 2014500723-A/191904: Polycomb-Associated Non-Coding RNAs.
AK299833 - Homo sapiens cDNA FLJ60863 complete cds, highly similar to High mobility group protein 2-like 1.
BC080611 - Homo sapiens high-mobility group protein 2-like 1, mRNA (cDNA clone IMAGE:5802064).
BC052624 - Homo sapiens HMG box domain containing 4, mRNA (cDNA clone IMAGE:6574134), partial cds.
AJ010070 - Homo sapiens mRNA encompasing THC211630.
AL079310 - Novel human gene mapping to chomosome 22.
BC062413 - Homo sapiens HMG box domain containing 4, mRNA (cDNA clone IMAGE:6202719), partial cds.
BC011723 - Homo sapiens high-mobility group protein 2-like 1, mRNA (cDNA clone IMAGE:4299753), partial cds.
BC017326 - Homo sapiens HMG box domain containing 4, mRNA (cDNA clone IMAGE:4549441), partial cds.
BC033783 - Homo sapiens high-mobility group protein 2-like 1, mRNA (cDNA clone IMAGE:4478964), partial cds.
BC025303 - Homo sapiens HMG box domain containing 4, mRNA (cDNA clone IMAGE:3949218), partial cds.
BC111373 - Homo sapiens HMG box domain containing 4, mRNA (cDNA clone IMAGE:7475493), partial cds.
CR456504 - Homo sapiens HMG2L1 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.HMG2L1.V4).
CU013390 - Homo sapiens HMG2L1, mRNA (cDNA clone IMAGE:100000265), complete cds, without stop codon, in Gateway system.
CU013102 - Homo sapiens HMG2L1, mRNA (cDNA clone IMAGE:100000361), complete cds, with stop codon, in Gateway system.
AB463067 - Synthetic construct DNA, clone: pF1KB9544, Homo sapiens HMG2L1 gene for high-mobility group protein 2-like 1, without stop codon, in Flexi system.
LF372994 - JP 2014500723-A/180497: Polycomb-Associated Non-Coding RNAs.
JD436362 - Sequence 417386 from Patent EP1572962.
BC004194 - Homo sapiens HMG box domain containing 4, mRNA (cDNA clone IMAGE:3528436), partial cds.
BC104754 - Homo sapiens HMG box domain containing 4, mRNA (cDNA clone MGC:132414 IMAGE:8143757), complete cds.
BC104756 - Homo sapiens HMG box domain containing 4, mRNA (cDNA clone MGC:132416 IMAGE:8143759), complete cds.
LF372997 - JP 2014500723-A/180500: Polycomb-Associated Non-Coding RNAs.
LF372998 - JP 2014500723-A/180501: Polycomb-Associated Non-Coding RNAs.
LF373000 - JP 2014500723-A/180503: Polycomb-Associated Non-Coding RNAs.
LF373001 - JP 2014500723-A/180504: Polycomb-Associated Non-Coding RNAs.
BC040447 - Homo sapiens cDNA clone IMAGE:4399221, containing frame-shift errors.
LF373002 - JP 2014500723-A/180505: Polycomb-Associated Non-Coding RNAs.
AJ010069 - Homo sapiens mRNA for HMGBCG protein.
JD174811 - Sequence 155835 from Patent EP1572962.
JD255653 - Sequence 236677 from Patent EP1572962.
JD234508 - Sequence 215532 from Patent EP1572962.
JD264477 - Sequence 245501 from Patent EP1572962.
JD488697 - Sequence 469721 from Patent EP1572962.
JD160681 - Sequence 141705 from Patent EP1572962.
JD087680 - Sequence 68704 from Patent EP1572962.
JD387278 - Sequence 368302 from Patent EP1572962.
JD314414 - Sequence 295438 from Patent EP1572962.
JD402391 - Sequence 383415 from Patent EP1572962.
JD393825 - Sequence 374849 from Patent EP1572962.
JD402345 - Sequence 383369 from Patent EP1572962.
JD163752 - Sequence 144776 from Patent EP1572962.
JD519573 - Sequence 500597 from Patent EP1572962.
JD392367 - Sequence 373391 from Patent EP1572962.
JD262755 - Sequence 243779 from Patent EP1572962.
JD151227 - Sequence 132251 from Patent EP1572962.
JD228056 - Sequence 209080 from Patent EP1572962.
JD565826 - Sequence 546850 from Patent EP1572962.
JD303920 - Sequence 284944 from Patent EP1572962.
JD093382 - Sequence 74406 from Patent EP1572962.
JD225800 - Sequence 206824 from Patent EP1572962.
JD558159 - Sequence 539183 from Patent EP1572962.
MA619978 - JP 2018138019-A/191904: Polycomb-Associated Non-Coding RNAs.
MA608571 - JP 2018138019-A/180497: Polycomb-Associated Non-Coding RNAs.
MA608574 - JP 2018138019-A/180500: Polycomb-Associated Non-Coding RNAs.
MA608575 - JP 2018138019-A/180501: Polycomb-Associated Non-Coding RNAs.
MA608577 - JP 2018138019-A/180503: Polycomb-Associated Non-Coding RNAs.
MA608578 - JP 2018138019-A/180504: Polycomb-Associated Non-Coding RNAs.
MA608579 - JP 2018138019-A/180505: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000216106.1, ENST00000216106.2, ENST00000216106.3, ENST00000216106.4, ENST00000216106.5, HMG2L1, HMGBCG, HMGX4_HUMAN, NM_001362972, O75672, O75673, Q9UGU5, Q9UMT5, uc317coj.1, uc317coj.2
UCSC ID: ENST00000216106.6_4
RefSeq Accession: NM_001003681.3
Protein: Q9UGU5 (aka HMGX4_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.