Human Gene SUPT20H (ENST00000360252.8) Description and Page Index
  Description: Homo sapiens SPT20 homolog, SAGA complex component (SUPT20H), transcript variant 2, mRNA. (from RefSeq NM_017569)
Gencode Transcript: ENST00000360252.8
Gencode Gene: ENSG00000102710.20
Transcript (Including UTRs)
   Position: hg38 chr13:37,009,316-37,059,713 Size: 50,398 Total Exon Count: 25 Strand: -
Coding Region
   Position: hg38 chr13:37,009,709-37,051,490 Size: 41,782 Coding Exon Count: 24 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr13:37,009,316-37,059,713)mRNA (may differ from genome)Protein (733 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
EnsemblEntrez GeneExonPrimerGeneCardsHGNCHPRD
LynxMGIneXtProtOMIMPubMedReactome
Stanford SOURCEUniProtKBWikipedia

-  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

-  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 -91.70248-0.370 Picture PostScript Text
3' UTR -68.90393-0.175 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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-  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: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
  AF370384 - Homo sapiens FP757 mRNA, complete cds.
AK056121 - Homo sapiens cDNA FLJ31559 fis, clone NT2RI2001385, highly similar to Homo sapiens P38IP mRNA.
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.
AK026091 - Homo sapiens cDNA: FLJ22438 fis, clone HRC09232, highly similar to AF093250 Homo sapiens P38IP (P38IP) mRNA.
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.
AK093723 - Homo sapiens cDNA FLJ36404 fis, clone THYMU2010030.
AK127995 - Homo sapiens cDNA FLJ46113 fis, clone TESTI2036285.
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.
JD305128 - Sequence 286152 from Patent EP1572962.
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.
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_017569, Q71RF3, Q8NEM7, Q9Y6A6, uc001uwj.1, uc001uwj.2, uc001uwj.3, uc001uwj.4
UCSC ID: uc001uwj.4
RefSeq Accession: NM_001278481
Protein: Q8NEM7 (aka FA48A_HUMAN)
CCDS: CCDS9362.1

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