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Human Gene ALX1 (ENST00000316824.4) from GENCODE V50
  Description: ALX homeobox 1 (from RefSeq NM_006982.3)
Gencode Transcript: ENST00000316824.4
Gencode Gene: ENSG00000180318.5
Transcript (Including UTRs)
   Position: hg38 chr12:85,280,220-85,301,784 Size: 21,565 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr12:85,280,262-85,301,475 Size: 21,214 Coding Exon Count: 4 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2026-07-12 09:30:09

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: ALX1
Diseases sorted by gene-association score: frontonasal dysplasia 3* (1419), frontonasal dysplasia-severe microphthalmia-severe facial clefting syndrome* (400), craniofrontonasal dysplasia (8), neural tube defects (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 2.05 RPKM in Fallopian Tube
Total median expression: 9.35 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
 
Expression ratio colors:

GTEx Gene Expression

       
      
       
       
      
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GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -8.6042-0.205 Picture PostScript Text
3' UTR -45.17309-0.146 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.

-  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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Descriptions from all associated GenBank mRNAs
  U31986 - Human cartilage-specific homeodomain protein Cart-1 mRNA, complete cds.
BC010923 - Homo sapiens ALX homeobox 1, mRNA (cDNA clone MGC:13497 IMAGE:4278460), complete cds.
EU794597 - Homo sapiens epididymis luminal protein 23 (HEL23) mRNA, complete cds.
KJ897807 - Synthetic construct Homo sapiens clone ccsbBroadEn_07201 ALX1 gene, encodes complete protein.
JD456198 - Sequence 437222 from Patent EP1572962.
JD224281 - Sequence 205305 from Patent EP1572962.
JD083541 - Sequence 64565 from Patent EP1572962.
JD486911 - Sequence 467935 from Patent EP1572962.
JD515853 - Sequence 496877 from Patent EP1572962.
JD043307 - Sequence 24331 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CART1 , ENST00000316824.1, ENST00000316824.2, ENST00000316824.3, hCG_26534 , HEL23 , NM_006982, uc001tae.1, uc001tae.2, uc001tae.3, uc001tae.4, uc001tae.5, uc001tae.6, V9HWA7, V9HWA7_HUMAN
UCSC ID: ENST00000316824.4
RefSeq Accession: NM_006982.3
CCDS: CCDS9028.1

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