Human Gene HAL (uc010sux.2) Description and Page Index
  Description: Homo sapiens histidine ammonia-lyase (HAL), transcript variant 3, mRNA.
RefSeq Summary (NM_001258334): Histidine ammonia-lyase is a cytosolic enzyme catalyzing the first reaction in histidine catabolism, the nonoxidative deamination of L-histidine to trans-urocanic acid. Histidine ammonia-lyase defects cause histidinemia which is characterized by increased histidine and histamine and decreased urocanic acid in body fluids. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012].
Transcript (Including UTRs)
   Position: hg19 chr12:96,366,440-96,390,143 Size: 23,704 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr12:96,368,138-96,389,688 Size: 21,551 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr12:96,366,440-96,390,143)mRNA (may differ from genome)Protein (591 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Histidine ammonia-lyase; EC=;
CATALYTIC ACTIVITY: L-histidine = urocanate + NH(3).
PATHWAY: Amino-acid degradation; L-histidine degradation into L- glutamate; N-formimidoyl-L-glutamate from L-histidine: step 1/3.
SIMILARITY: Belongs to the PAL/histidase family.
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): HAL
CDC HuGE Published Literature: HAL

-  MalaCards Disease Associations
  MalaCards Gene Search: HAL
Diseases sorted by gene-association score: histidinemia* (820), histidine metabolism disease (19)
* = Manually curated disease association

-  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: 52.87 RPKM in Liver
Total median expression: 106.47 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 -129.10369-0.350 Picture PostScript Text
3' UTR -485.261698-0.286 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
IPR001106 - Aromatic_Lyase
IPR005921 - HutH
IPR008948 - L-Aspartase-like
IPR024083 - L-Aspartase-like_N
IPR022313 - Phe/His_NH3-lyase_AS

Pfam Domains:
PF00221 - Aromatic amino acid lyase
PF12053 - N-terminal of Par3 and HAL proteins

SCOP Domains:
48557 - L-aspartase-like

ModBase Predicted Comparative 3D Structure on F5GXF2
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Descriptions from all associated GenBank mRNAs
  D16626 - Homo sapiens mRNA for histidase, complete cds.
JD287247 - Sequence 268271 from Patent EP1572962.
JD091117 - Sequence 72141 from Patent EP1572962.
JD446643 - Sequence 427667 from Patent EP1572962.
AK303544 - Homo sapiens cDNA FLJ61019 complete cds, highly similar to Histidine ammonia-lyase (EC
JD243058 - Sequence 224082 from Patent EP1572962.
AK297004 - Homo sapiens cDNA FLJ57123 complete cds, highly similar to Histidine ammonia-lyase (EC
AK298736 - Homo sapiens cDNA FLJ59235 complete cds, highly similar to Histidine ammonia-lyase (EC
JD367330 - Sequence 348354 from Patent EP1572962.
JD287755 - Sequence 268779 from Patent EP1572962.
BC096096 - Homo sapiens histidine ammonia-lyase, mRNA (cDNA clone IMAGE:40001284), complete cds.
BC096097 - Homo sapiens histidine ammonia-lyase, mRNA (cDNA clone MGC:116739 IMAGE:40001285), complete cds.
BC096098 - Homo sapiens histidine ammonia-lyase, mRNA (cDNA clone MGC:116740 IMAGE:40001286), complete cds.
BC096099 - Homo sapiens histidine ammonia-lyase, mRNA (cDNA clone MGC:116741 IMAGE:40001287), complete cds.
JD450669 - Sequence 431693 from Patent EP1572962.
JD086070 - Sequence 67094 from Patent EP1572962.
KJ896956 - Synthetic construct Homo sapiens clone ccsbBroadEn_06350 HAL gene, encodes complete protein.
KR711754 - Synthetic construct Homo sapiens clone CCSBHm_00030757 HAL (HAL) mRNA, encodes complete protein.
KR711755 - Synthetic construct Homo sapiens clone CCSBHm_00030758 HAL (HAL) mRNA, encodes complete protein.
KR711756 - Synthetic construct Homo sapiens clone CCSBHm_00030759 HAL (HAL) mRNA, encodes complete protein.
JD495390 - Sequence 476414 from Patent EP1572962.
JD136650 - Sequence 117674 from Patent EP1572962.
JD536288 - Sequence 517312 from Patent EP1572962.
JD189695 - Sequence 170719 from Patent EP1572962.
JD454650 - Sequence 435674 from Patent EP1572962.
JD158378 - Sequence 139402 from Patent EP1572962.
JD485527 - Sequence 466551 from Patent EP1572962.
JD215135 - Sequence 196159 from Patent EP1572962.
JD483829 - Sequence 464853 from Patent EP1572962.
JD440254 - Sequence 421278 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00340 - Histidine metabolism
hsa00910 - Nitrogen metabolism
hsa01100 - Metabolic pathways

-  Other Names for This Gene
  Alternate Gene Symbols: F5GXF2, F5GXF2_HUMAN, NM_001258334, NP_001245263, uc010sux.1
UCSC ID: uc010sux.2
RefSeq Accession: NM_001258334
Protein: F5GXF2 CCDS: CCDS58265.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001258334.1
exon count: 20CDS single in 3' UTR: no RNA size: 3857
ORF size: 1776CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3576.00frame shift in genome: no % Coverage: 99.64
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.