Human Gene FOXD4L1 (ENST00000306507.7) from GENCODE V44
  Description: Homo sapiens forkhead box D4 like 1 (FOXD4L1), mRNA. (from RefSeq NM_012184)
RefSeq Summary (NM_012184): This gene is a member of the forkhead/winged-helix (FOX) family of transcription factors with highly conserved FOX DNA-binding domains. Members of the FOX family of transcription factors are regulators of embryogenesis and may play a role in human cancer. This gene lies in a region of chromosome 2 that surrounds the site where two ancestral chromosomes fused to form human chromosome 2. This region is duplicated elsewhere in the human genome, primarily in subtelomeric and pericentromeric locations, thus mutiple copies of this gene have been found. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000306507.7
Gencode Gene: ENSG00000184492.7
Transcript (Including UTRs)
   Position: hg38 chr2:113,498,665-113,501,150 Size: 2,486 Total Exon Count: 1 Strand: +
Coding Region
   Position: hg38 chr2:113,499,257-113,500,483 Size: 1,227 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 (chr2:113,498,665-113,501,150)mRNA (may differ from genome)Protein (408 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDMalacardsMGIneXtProtOMIMPubMed
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: FX4L1_HUMAN
DESCRIPTION: RecName: Full=Forkhead box protein D4-like 1; Short=FOXD4-like 1;
SUBCELLULAR LOCATION: Nucleus (By similarity).
SIMILARITY: Contains 1 fork-head 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: 1.06 RPKM in Testis
Total median expression: 5.40 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 -212.30592-0.359 Picture PostScript Text
3' UTR -207.74667-0.311 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
IPR001766 - TF_fork_head
IPR018122 - TF_fork_head_CS
IPR011991 - WHTH_trsnscrt_rep_DNA-bd

Pfam Domains:
PF00250 - Forkhead domain

ModBase Predicted Comparative 3D Structure on Q9NU39
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 BrowserNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI     
Protein Sequence     
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:0003700 transcription factor activity, sequence-specific DNA binding
GO:0043565 sequence-specific DNA binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0009653 anatomical structure morphogenesis
GO:0030154 cell differentiation

Cellular Component:
GO:0005634 nucleus


-  Descriptions from all associated GenBank mRNAs
  AK125398 - Homo sapiens cDNA FLJ43409 fis, clone OCBBF2020838, highly similar to Forkhead box protein D4-like 1.
AK122950 - Homo sapiens cDNA FLJ16666 fis, clone THYMU2032732, highly similar to Forkhead box protein D4-like 1.
BC136428 - Homo sapiens forkhead box D4-like 1, mRNA (cDNA clone MGC:168040 IMAGE:9020417), complete cds.
AY344639 - Homo sapiens FOXD4-like 1 (FOXD4L1) mRNA, complete cds.
JD174387 - Sequence 155411 from Patent EP1572962.
AF452723 - Homo sapiens forkhead box D4 like 1 protein (FOXD4L1) mRNA, complete cds.
BC153201 - Synthetic construct Homo sapiens clone IMAGE:100016545, MGC:184334 forkhead box D4-like 1 (FOXD4L1) mRNA, encodes complete protein.
BC148648 - Synthetic construct Homo sapiens clone IMAGE:100015584, MGC:183107 FOXD4L1 protein (FOXD4L1) mRNA, encodes complete protein.
JD164356 - Sequence 145380 from Patent EP1572962.
JD464007 - Sequence 445031 from Patent EP1572962.
JD255660 - Sequence 236684 from Patent EP1572962.
JD500375 - Sequence 481399 from Patent EP1572962.
JD064907 - Sequence 45931 from Patent EP1572962.
JD375311 - Sequence 356335 from Patent EP1572962.
JD248959 - Sequence 229983 from Patent EP1572962.
JD191848 - Sequence 172872 from Patent EP1572962.
JD060411 - Sequence 41435 from Patent EP1572962.
JD460160 - Sequence 441184 from Patent EP1572962.
JD387989 - Sequence 369013 from Patent EP1572962.
JD141861 - Sequence 122885 from Patent EP1572962.
JD219231 - Sequence 200255 from Patent EP1572962.
JD140249 - Sequence 121273 from Patent EP1572962.
JD195007 - Sequence 176031 from Patent EP1572962.
JD438570 - Sequence 419594 from Patent EP1572962.
JD157384 - Sequence 138408 from Patent EP1572962.
JD128820 - Sequence 109844 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KWN1, B9EGF3, ENST00000306507.1, ENST00000306507.2, ENST00000306507.3, ENST00000306507.4, ENST00000306507.5, ENST00000306507.6, FX4L1_HUMAN, NM_012184, Q9NU39, uc002tjw.1, uc002tjw.2, uc002tjw.3, uc002tjw.4, uc002tjw.5, uc002tjw.6
UCSC ID: ENST00000306507.7
RefSeq Accession: NM_012184
Protein: Q9NU39 (aka FX4L1_HUMAN)

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