Human Gene MSGN1 (ENST00000281047.4) from GENCODE V44
  Description: Homo sapiens mesogenin 1 (MSGN1), mRNA. (from RefSeq NM_001105569)
Gencode Transcript: ENST00000281047.4
Gencode Gene: ENSG00000151379.4
Transcript (Including UTRs)
   Position: hg38 chr2:17,816,460-17,817,798 Size: 1,339 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg38 chr2:17,816,519-17,817,100 Size: 582 Coding Exon Count: 1 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:17,816,460-17,817,798)mRNA (may differ from genome)Protein (193 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MSGN1_HUMAN
DESCRIPTION: RecName: Full=Mesogenin-1; AltName: Full=Paraxial mesoderm-specific mesogenin1; AltName: Full=pMesogenin1; Short=pMsgn1;
FUNCTION: Involved in specifying the paraxial, but not dorsal, mesoderm. May regulate the expression of T-box transcription factors required for mesoderm formation and differentiation (By similarity).
SUBCELLULAR LOCATION: Nucleus (Potential).
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) 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


-  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: 0.12 RPKM in Esophagus - Mucosa
Total median expression: 0.35 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 -13.6059-0.231 Picture PostScript Text
3' UTR -190.70698-0.273 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
IPR011598 - HLH_dom

Pfam Domains:
PF00010 - Helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on A6NI15
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 BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0046983 protein dimerization activity

Biological Process:
GO:0001707 mesoderm formation
GO:0001756 somitogenesis
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0007379 segment specification
GO:0009880 embryonic pattern specification
GO:0030154 cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  BC172301 - Synthetic construct Homo sapiens clone IMAGE:100068995, MGC:199006 mesogenin 1 (MSGN1) mRNA, encodes complete protein.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NI15, ENST00000281047.1, ENST00000281047.2, ENST00000281047.3, MSGN1_HUMAN, NM_001105569, uc010yjt.1, uc010yjt.2, uc010yjt.3, uc010yjt.4
UCSC ID: ENST00000281047.4
RefSeq Accession: NM_001105569
Protein: A6NI15 (aka MSGN1_HUMAN)
CCDS: CCDS42657.1

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