Human Gene FERD3L (ENST00000275461.3) from GENCODE V44
  Description: Homo sapiens Fer3 like bHLH transcription factor (FERD3L), mRNA. (from RefSeq NM_152898)
Gencode Transcript: ENST00000275461.3
Gencode Gene: ENSG00000146618.3
Transcript (Including UTRs)
   Position: hg38 chr7:19,144,782-19,145,421 Size: 640 Total Exon Count: 1 Strand: -
Coding Region
   Position: hg38 chr7:19,144,862-19,145,362 Size: 501 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 (chr7:19,144,782-19,145,421)mRNA (may differ from genome)Protein (166 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FER3L_HUMAN
DESCRIPTION: RecName: Full=Fer3-like protein; AltName: Full=Basic helix-loop-helix protein N-twist; AltName: Full=Class A basic helix-loop-helix protein 31; Short=bHLHa31; AltName: Full=Nephew of atonal 3; AltName: Full=Neuronal twist;
FUNCTION: Transcription factor that binds to the E-box and functions as inhibitor of transcription. DNA binding requires dimerization with an E protein. Inhibits transcription activation by ASCL1/MASH1 by sequestering E proteins (By similarity).
SUBUNIT: Heterodimer with TCF3/E12. Interacts with the bHLH domain of TCF3/E12 (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.09 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 0.60 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 -15.2059-0.258 Picture PostScript Text
3' UTR -27.2080-0.340 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 Q96RJ6
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 BrowserGenome BrowserNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsemblEnsembl  
Protein SequenceProtein SequenceProtein SequenceProtein Sequence  
AlignmentAlignmentAlignmentAlignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0005515 protein binding
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:0033504 floor plate development
GO:0045892 negative regulation of transcription, DNA-templated
GO:0048468 cell development
GO:0050767 regulation of neurogenesis

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AF517122 - Homo sapiens N-TWIST basic helix-loop-helix protein (NTWIST) mRNA, complete cds.
BC101135 - Homo sapiens Fer3-like (Drosophila), mRNA (cDNA clone MGC:119858 IMAGE:40014737), complete cds.
BC101136 - Homo sapiens Fer3-like (Drosophila), mRNA (cDNA clone MGC:119859 IMAGE:40014740), complete cds.
BC101137 - Homo sapiens Fer3-like (Drosophila), mRNA (cDNA clone MGC:119860 IMAGE:40014741), complete cds.
BC101138 - Homo sapiens Fer3-like (Drosophila), mRNA (cDNA clone MGC:119861 IMAGE:40014747), complete cds.
JD257569 - Sequence 238593 from Patent EP1572962.
JD467213 - Sequence 448237 from Patent EP1572962.
BC069147 - Homo sapiens Fer3-like (Drosophila), mRNA (cDNA clone MGC:95432 IMAGE:7217007), complete cds.
KJ904045 - Synthetic construct Homo sapiens clone ccsbBroadEn_13439 FERD3L gene, encodes complete protein.
AB528954 - Synthetic construct DNA, clone: pF1KB6831, Homo sapiens FERD3L gene for Fer3-like, without stop codon, in Flexi system.

-  Other Names for This Gene
  Alternate Gene Symbols: BHLHA31, ENST00000275461.1, ENST00000275461.2, FER3L_HUMAN, NATO3, NM_152898, NTWIST, Q495K0, Q96RJ6, uc003suo.1
UCSC ID: ENST00000275461.3
RefSeq Accession: NM_152898
Protein: Q96RJ6 (aka FER3L_HUMAN)
CCDS: CCDS5368.1

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