Human Gene HDGFL2 (ENST00000616600.5_8) from GENCODE V47lift37
  Description: HDGF like 2, transcript variant 3 (from RefSeq NM_001348169.2)
Gencode Transcript: ENST00000616600.5_8
Gencode Gene: ENSG00000167674.15_20
Transcript (Including UTRs)
   Position: hg19 chr19:4,472,294-4,502,219 Size: 29,926 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg19 chr19:4,472,348-4,502,022 Size: 29,675 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:4,472,294-4,502,219)mRNA (may differ from genome)Protein (671 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: HDGR2_HUMAN
DESCRIPTION: RecName: Full=Hepatoma-derived growth factor-related protein 2; Short=HRP-2; AltName: Full=Hepatoma-derived growth factor 2; Short=HDGF-2;
SUBUNIT: May interact with trimethylated histone H3 (H3K79me3).
INTERACTION: P49407:ARRB1; NbExp=3; IntAct=EBI-1049136, EBI-743313;
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the HDGF family.
SIMILARITY: Contains 1 PWWP 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


+  Common Gene Haplotype Alleles
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+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -18.1054-0.335 Picture PostScript Text
3' UTR -64.50197-0.327 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
IPR021567 - LEDGF
IPR000313 - PWWP
IPR017923 - TFIIS_N

Pfam Domains:
PF00855 - PWWP domain
PF11467 - Lens epithelium-derived growth factor (LEDGF)

SCOP Domains:
47676 - Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
140576 - HIV integrase-binding domain
63748 - Tudor/PWWP/MBT

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3EAE - X-ray 3QBY - X-ray 3QJ6 - X-ray


ModBase Predicted Comparative 3D Structure on Q7Z4V5
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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0005515 protein binding

Biological Process:
GO:0030307 positive regulation of cell growth

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AY358600 - Homo sapiens clone DNA71286 HGDF-related pro 2 (UNQ785) mRNA, complete cds.
AF294267 - Homo sapiens hepatoma-derived growth factor 2 (HDGF2) mRNA, complete cds.
BC000755 - Homo sapiens hepatoma-derived growth factor-related protein 2, mRNA (cDNA clone MGC:2641 IMAGE:3507276), complete cds.
JD156182 - Sequence 137206 from Patent EP1572962.
CU674386 - Synthetic construct Homo sapiens gateway clone IMAGE:100023430 5' read HDGF2 mRNA.
KJ899827 - Synthetic construct Homo sapiens clone ccsbBroadEn_09221 HDGFRP2 gene, encodes complete protein.
DQ892175 - Synthetic construct clone IMAGE:100004805; FLH183699.01X; RZPDo839F07142D hepatoma-derived growth factor-related protein 2 (HDGF2) gene, encodes complete protein.
DQ895370 - Synthetic construct Homo sapiens clone IMAGE:100009830; FLH183695.01L; RZPDo839F07141D hepatoma-derived growth factor-related protein 2 (HDGF2) gene, encodes complete protein.
AB208892 - Homo sapiens mRNA for hepatoma-derived growth factor-related protein 2 isoform 1 variant protein.
BC009449 - Homo sapiens hepatoma-derived growth factor-related protein 2, mRNA (cDNA clone IMAGE:3530894), partial cds.
DQ570346 - Homo sapiens piRNA piR-30458, complete sequence.
DQ570347 - Homo sapiens piRNA piR-30459, complete sequence.
LF210885 - JP 2014500723-A/18388: Polycomb-Associated Non-Coding RNAs.
LF341709 - JP 2014500723-A/149212: Polycomb-Associated Non-Coding RNAs.
LF341712 - JP 2014500723-A/149215: Polycomb-Associated Non-Coding RNAs.
AK027353 - Homo sapiens cDNA FLJ14447 fis, clone HEMBB1001331, weakly similar to Mus musculus mRNA for hepatoma-derived growth factor.
LF210887 - JP 2014500723-A/18390: Polycomb-Associated Non-Coding RNAs.
LF341714 - JP 2014500723-A/149217: Polycomb-Associated Non-Coding RNAs.
JD141703 - Sequence 122727 from Patent EP1572962.
JD466112 - Sequence 447136 from Patent EP1572962.
JD107906 - Sequence 88930 from Patent EP1572962.
JD157359 - Sequence 138383 from Patent EP1572962.
JD163642 - Sequence 144666 from Patent EP1572962.
JD064830 - Sequence 45854 from Patent EP1572962.
JD103586 - Sequence 84610 from Patent EP1572962.
JD268565 - Sequence 249589 from Patent EP1572962.
JD297359 - Sequence 278383 from Patent EP1572962.
MA577286 - JP 2018138019-A/149212: Polycomb-Associated Non-Coding RNAs.
MA577289 - JP 2018138019-A/149215: Polycomb-Associated Non-Coding RNAs.
MA577291 - JP 2018138019-A/149217: Polycomb-Associated Non-Coding RNAs.
MA446462 - JP 2018138019-A/18388: Polycomb-Associated Non-Coding RNAs.
MA446464 - JP 2018138019-A/18390: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000616600.1, ENST00000616600.2, ENST00000616600.3, ENST00000616600.4, HDGF2 , HDGFL2 , HDGFRP2, HDGR2_HUMAN, HRP2, I3L080, K7EQZ6, NM_001348169, Q7Z4V5, Q96GI5, Q9BW08, uc327qpb.1, uc327qpb.2, UNQ785/PRO1604
UCSC ID: ENST00000616600.5_8
RefSeq Accession: NM_001001520.3
Protein: Q7Z4V5 (aka HDGR2_HUMAN)

-  Gene Model Information
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-  Methods, Credits, and Use Restrictions
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