Human Gene MSC (ENST00000325509.5_8) from GENCODE V47lift37
  Description: musculin (from RefSeq NM_005098.4)
Gencode Transcript: ENST00000325509.5_8
Gencode Gene: ENSG00000178860.9_9
Transcript (Including UTRs)
   Position: hg19 chr8:72,753,795-72,756,647 Size: 2,853 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr8:72,754,896-72,756,413 Size: 1,518 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:72,753,795-72,756,647)mRNA (may differ from genome)Protein (206 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MUSC_HUMAN
DESCRIPTION: RecName: Full=Musculin; AltName: Full=Activated B-cell factor 1; Short=ABF-1; AltName: Full=Class A basic helix-loop-helix protein 22; Short=bHLHa22;
FUNCTION: Transcription repressor capable of inhibiting the transactivation capability of TCF3/E47. May play a role in regulating antigen-dependent B-cell differentiation.
SUBUNIT: Efficient DNA binding requires dimerization with another bHLH protein. Binds DNA as a homodimer or a heterodimer. Forms a heterodimer with TCF3.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in lymphoid tissues, B-cell lines and activated B-cells.
SIMILARITY: Contains 1 bHLH (basic helix-loop-helix) domain.
SEQUENCE CAUTION: Sequence=AAC15071.1; Type=Frameshift; Positions=189;

-  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

+  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: 68.79 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 319.62 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 -106.50234-0.455 Picture PostScript Text
3' UTR -411.001101-0.373 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

SCOP Domains:
47459 - HLH, helix-loop-helix DNA-binding domain

ModBase Predicted Comparative 3D Structure on O60682
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:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001206 transcriptional repressor activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003714 transcription corepressor activity
GO:0046983 protein dimerization activity

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0014707 branchiomeric skeletal muscle development
GO:0060021 palate development
GO:0060539 diaphragm development
GO:1990830 cellular response to leukemia inhibitory factor

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC067827 - Homo sapiens musculin (activated B-cell factor-1), mRNA (cDNA clone MGC:87363 IMAGE:30336424), complete cds.
AF087036 - Homo sapiens musculin mRNA, partial cds.
BC006313 - Homo sapiens musculin (activated B-cell factor-1), mRNA (cDNA clone MGC:12624 IMAGE:4123825), complete cds.
AF060154 - Homo sapiens activated B-cell factor-1 (ABF-1) mRNA, complete cds.
JD431630 - Sequence 412654 from Patent EP1572962.
JD423636 - Sequence 404660 from Patent EP1572962.
JD160666 - Sequence 141690 from Patent EP1572962.
JD396628 - Sequence 377652 from Patent EP1572962.
JD408550 - Sequence 389574 from Patent EP1572962.
JD460928 - Sequence 441952 from Patent EP1572962.
JD500116 - Sequence 481140 from Patent EP1572962.
JD230866 - Sequence 211890 from Patent EP1572962.
JD104637 - Sequence 85661 from Patent EP1572962.
JD138046 - Sequence 119070 from Patent EP1572962.
JD250747 - Sequence 231771 from Patent EP1572962.
JD300773 - Sequence 281797 from Patent EP1572962.
JD101130 - Sequence 82154 from Patent EP1572962.
JD211979 - Sequence 193003 from Patent EP1572962.
JD411247 - Sequence 392271 from Patent EP1572962.
JD521664 - Sequence 502688 from Patent EP1572962.
AK313102 - Homo sapiens cDNA, FLJ93587.
JF432718 - Synthetic construct Homo sapiens clone IMAGE:100073960 musculin (activated B-cell factor-1) (MSC) gene, encodes complete protein.
KJ892725 - Synthetic construct Homo sapiens clone ccsbBroadEn_02119 MSC gene, encodes complete protein.
BT007169 - Homo sapiens musculin (activated B-cell factor-1) mRNA, complete cds.
AB463900 - Synthetic construct DNA, clone: pF1KB7559, Homo sapiens MSC gene for musculin, without stop codon, in Flexi system.
JD215972 - Sequence 196996 from Patent EP1572962.
JD462189 - Sequence 443213 from Patent EP1572962.
JD152646 - Sequence 133670 from Patent EP1572962.
JD336634 - Sequence 317658 from Patent EP1572962.
JD200879 - Sequence 181903 from Patent EP1572962.
JD219472 - Sequence 200496 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ABF1, BHLHA22, ENST00000325509.1, ENST00000325509.2, ENST00000325509.3, ENST00000325509.4, MUSC_HUMAN, NM_005098, O60682, O75946, Q53XZ2, Q9BRE7, uc317rws.1, uc317rws.2
UCSC ID: ENST00000325509.5_8
RefSeq Accession: NM_005098.4
Protein: O60682 (aka MUSC_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.