Human Gene SOX14 (ENST00000306087.3) from GENCODE V44
  Description: Homo sapiens SRY-box transcription factor 14 (SOX14), mRNA. (from RefSeq NM_004189)
RefSeq Summary (NM_004189): This intronless gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. Mutations in this gene are suggested to be responsible for the limb defects associated with blepharophimosis, ptosis, epicanthus inversus syndrome (BPES) and Mobius syndrome. [provided by RefSeq, Jul 2008]. Sequence Note: The RefSeq transcript was derived from the reference genome assembly. The genomic coordinates were determined from alignments.
Gencode Transcript: ENST00000306087.3
Gencode Gene: ENSG00000168875.3
Transcript (Including UTRs)
   Position: hg38 chr3:137,764,315-137,766,334 Size: 2,020 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg38 chr3:137,764,785-137,765,507 Size: 723 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 (chr3:137,764,315-137,766,334)mRNA (may differ from genome)Protein (240 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SOX14_HUMAN
DESCRIPTION: RecName: Full=Transcription factor SOX-14; AltName: Full=Protein SOX-28;
FUNCTION: Acts as a negative regulator of transcription (By similarity).
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 HMG box DNA-binding 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: 0.32 RPKM in Brain - Hypothalamus
Total median expression: 0.66 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 -198.30470-0.422 Picture PostScript Text
3' UTR -227.10827-0.275 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
IPR009071 - HMG_superfamily
IPR022097 - TF_SOX

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF12336 - SOX transcription factor

ModBase Predicted Comparative 3D Structure on O95416
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 orthologGenome BrowserNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl WormBase 
Protein SequenceProtein SequenceProtein Sequence Protein Sequence 
AlignmentAlignmentAlignment Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding
GO:0046982 protein heterodimerization 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:0007399 nervous system development
GO:0007601 visual perception
GO:0009649 entrainment of circadian clock
GO:0045892 negative regulation of transcription, DNA-templated
GO:2001222 regulation of neuron migration

Cellular Component:
GO:0005575 cellular_component
GO:0005634 nucleus
GO:0044798 nuclear transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  AK314127 - Homo sapiens cDNA, FLJ94824, Homo sapiens SRY (sex determining region Y)-box 14 (SOX14), mRNA.
BC106729 - Homo sapiens SRY (sex determining region Y)-box 14, mRNA (cDNA clone MGC:119898 IMAGE:40015392), complete cds.
BC106730 - Homo sapiens SRY (sex determining region Y)-box 14, mRNA (cDNA clone MGC:119899 IMAGE:40015393), complete cds.
JD395324 - Sequence 376348 from Patent EP1572962.
KJ892527 - Synthetic construct Homo sapiens clone ccsbBroadEn_01921 SOX14 gene, encodes complete protein.
KJ897840 - Synthetic construct Homo sapiens clone ccsbBroadEn_07234 SOX14 gene, encodes complete protein.
AB464714 - Synthetic construct DNA, clone: pF1KB9651, Homo sapiens SOX14 gene for SRY (sex determining region Y)-box 14, without stop codon, in Flexi system.
JD116552 - Sequence 97576 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2RAC0, ENST00000306087.1, ENST00000306087.2, NM_004189, O95416, Q3KPH7, SOX14_HUMAN, SOX28, uc003erm.1, uc003erm.2, uc003erm.3, uc003erm.4
UCSC ID: ENST00000306087.3
RefSeq Accession: NM_004189
Protein: O95416 (aka SOX14_HUMAN or SX14_HUMAN)
CCDS: CCDS3094.1

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