Human Gene SUPT20H (uc001uwg.3) Description and Page Index
  Description: Homo sapiens suppressor of Ty 20 homolog (S. cerevisiae) (SUPT20H), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr13:37,583,451-37,633,850 Size: 50,400 Total Exon Count: 26 Strand: -
Coding Region
   Position: hg19 chr13:37,583,809-37,625,627 Size: 41,819 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:37,583,451-37,633,850)mRNA (may differ from genome)Protein (779 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: FA48A_HUMAN
DESCRIPTION: RecName: Full=Protein FAM48A; AltName: Full=p38-interacting protein; Short=p38IP;
FUNCTION: Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down- regulation of E-cadherin during gastrulation by regulating E- cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by FGF signaling and Snail (By similarity). Required for starvation- induced ATG9A trafficking during autophagy.
SUBUNIT: Interacts with MAPK14. Interacts with ATG9A.
INTERACTION: Q16539:MAPK14; NbExp=5; IntAct=EBI-946984, EBI-73946;
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Highly expressed in testis, moderately in brain and pituitary gland. Expressed in several fetal tissues, including lung, brain, thymus and kidney. Expression is down- regulated in malignant prostate tissues.
SIMILARITY: Belongs to the FAM48 family.
SEQUENCE CAUTION: Sequence=AAQ15220.1; Type=Frameshift; Positions=562;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C479799 (E)-4-((2-N-(4-methoxybenzenesulfonyl)amino)stilbazole)1-oxide
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D004642 Emodin
  • C044887 beta-methylcholine

+  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: 24.17 RPKM in Testis
Total median expression: 494.38 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 -93.60248-0.377 Picture PostScript Text
3' UTR -64.90358-0.181 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
IPR021950 - Spt20

Pfam Domains:
PF12090 - Spt20 family

ModBase Predicted Comparative 3D Structure on Q8NEM7
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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:0003712 transcription cofactor activity
GO:0005515 protein binding

Biological Process:
GO:0006914 autophagy
GO:0007275 multicellular organism development
GO:0007369 gastrulation

Cellular Component:
GO:0000124 SAGA complex
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0070461 SAGA-type complex


-  Descriptions from all associated GenBank mRNAs
  AF093250 - Homo sapiens P38IP (P38IP) mRNA, complete cds.
AK225376 - Homo sapiens mRNA for family with sequence similarity 48, member A isoform b variant, clone: HRC01478.
AJ130894 - Homo sapiens mRNA for transcription factor.
BC001145 - Homo sapiens family with sequence similarity 48, member A, mRNA (cDNA clone MGC:1172 IMAGE:3533877), complete cds.
BC030686 - Homo sapiens family with sequence similarity 48, member A, mRNA (cDNA clone MGC:26084 IMAGE:4826077), complete cds.
AK292376 - Homo sapiens cDNA FLJ77238 complete cds.
KJ899153 - Synthetic construct Homo sapiens clone ccsbBroadEn_08547 FAM48A gene, encodes complete protein.
DQ891621 - Synthetic construct clone IMAGE:100004251; FLH178709.01X; RZPDo839G03128D family with sequence similarity 48, member A (FAM48A) gene, encodes complete protein.
DQ896826 - Synthetic construct Homo sapiens clone IMAGE:100011286; FLH178706.01L; RZPDo839G03127D family with sequence similarity 48, member A (FAM48A) gene, encodes complete protein.
AB590311 - Synthetic construct DNA, clone: pFN21AB6273, Homo sapiens FAM48A gene for family with sequence similarity 48, member A, without stop codon, in Flexi system.
AK304227 - Homo sapiens cDNA FLJ54575 complete cds, highly similar to Protein FAM48A.
AK027554 - Homo sapiens cDNA FLJ14648 fis, clone NT2RP2002046, highly similar to Protein FAM48A.
CU688982 - Synthetic construct Homo sapiens gateway clone IMAGE:100020077 5' read FAM48A mRNA.
AF445026 - Homo sapiens clone 111 tumor rejection antigen mRNA, complete cds.
AF370384 - Homo sapiens FP757 mRNA, complete cds.
AK056121 - Homo sapiens cDNA FLJ31559 fis, clone NT2RI2001385, highly similar to Homo sapiens P38IP mRNA.
AK026091 - Homo sapiens cDNA: FLJ22438 fis, clone HRC09232, highly similar to AF093250 Homo sapiens P38IP (P38IP) mRNA.
AK093723 - Homo sapiens cDNA FLJ36404 fis, clone THYMU2010030.
AK127995 - Homo sapiens cDNA FLJ46113 fis, clone TESTI2036285.
JD305128 - Sequence 286152 from Patent EP1572962.
JD459275 - Sequence 440299 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8NEM7 (Reactome details) participates in the following event(s):

R-HSA-3301237 KAT2 complexes acetylate histone H3
R-HSA-3214847 HATs acetylate histones
R-HSA-3247509 Chromatin modifying enzymes
R-HSA-4839726 Chromatin organization

-  Other Names for This Gene
  Alternate Gene Symbols: C13orf19, FA48A_HUMAN, FAM48A, FP757, NM_001014286, NP_001014308, Q71RF3, Q8NEM7, Q9Y6A6
UCSC ID: uc001uwg.3
RefSeq Accession: NM_001014286
Protein: Q8NEM7 (aka FA48A_HUMAN)
CCDS: CCDS31959.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001014286.2
exon count: 26CDS single in 3' UTR: no RNA size: 3003
ORF size: 2340CDS single in intron: no Alignment % ID: 99.97
txCdsPredict score: 4647.50frame shift in genome: no % Coverage: 98.10
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.