Human Gene CHL1 (uc003bov.2)
  Description: Homo sapiens cell adhesion molecule with homology to L1CAM (close homolog of L1) (CHL1), transcript variant 4, non-coding RNA.
RefSeq Summary (NR_045572): The protein encoded by this gene is a member of the L1 gene family of neural cell adhesion molecules. It is a neural recognition molecule that may be involved in signal transduction pathways. The deletion of one copy of this gene may be responsible for mental defects in patients with 3p- syndrome. This protein may also play a role in the growth of certain cancers. Alternate splicing results in both coding and non-coding variants. [provided by RefSeq, Nov 2011].
Transcript (Including UTRs)
   Position: hg19 chr3:239,326-290,282 Size: 50,957 Total Exon Count: 3 Strand: +


Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionOther SpeciesmRNA DescriptionsOther NamesModel Information
Methods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:239,326-290,282)mRNA (may differ from genome)No protein
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
EnsemblExonPrimerH-INVHGNCLynxMalacards
PubMedWikipedia

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CHL1
CDC HuGE Published Literature: CHL1
Positive Disease Associations: Death, Sudden, Cardiac , Hemoglobin A, Glycosylated , schizophrenia
Related Studies:
  1. Death, Sudden, Cardiac
    Bradley E Aouizerat et al. BMC cardiovascular disorders 2012, GWAS for discovery and replication of genetic loci associated with sudden cardiac arrest in patients with coronary artery disease., BMC cardiovascular disorders. [PubMed 21658281]
    We demonstrate 11 gene associations for sudden cardiac arrest due to ventricular tachycardia/ventricular fibrillation in patients with coronary artery disease. Validation studies in independent cohorts and functional studies are required to confirm these associations.
  2. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
  3. Hemoglobin A, Glycosylated
    Andrew D Paterson et al. Diabetes 2010, A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose., Diabetes. [PubMed 19875614]
    A major locus for A1C and glucose in individuals with diabetes is near SORCS1. This may influence the design and analysis of genetic studies attempting to identify risk factors for long-term diabetic complications.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: CHL1
Diseases sorted by gene-association score: 3p- syndrome* (40), large cell carcinoma with rhabdoid phenotype (15), myositis fibrosa (8), adult mesoblastic nephroma (8), null-cell leukemia (7), gastric small cell carcinoma (7), pulmonary large cell neuroendocrine carcinoma (7), gastric tubular adenocarcinoma (6), mixed ductal-endocrine carcinoma (5), nephrogenic adenofibroma (4), peptic ulcer perforation (4), schizophrenia (1), autonomic nervous system neoplasm (1), peripheral nervous system neoplasm (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.58 RPKM in Nerve - Tibial
Total median expression: 200.57 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.

-  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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AB209329 - Homo sapiens mRNA for Neural cell adhesion molecule variant protein.
AF002246 - Homo sapiens neural cell adhesion molecule (CALL) mRNA, complete cds.
AK126878 - Homo sapiens cDNA FLJ44930 fis, clone BRAMY3015549, highly similar to Neural cell adhesion molecule L1-like protein precursor.
AK055236 - Homo sapiens cDNA FLJ30674 fis, clone FCBBF1000748.
JD320164 - Sequence 301188 from Patent EP1572962.
AL359583 - Homo sapiens mRNA; cDNA DKFZp547L174 (from clone DKFZp547L174).
CR749682 - Homo sapiens mRNA; cDNA DKFZp547L174 (from clone DKFZp547L174).

-  Other Names for This Gene
  Alternate Gene Symbols: NR_045572
UCSC ID: uc003bov.2
RefSeq Accession: NR_045572

-  Gene Model Information
 
category: nearCoding nonsense-mediated-decay: no RNA accession: NR_045572.1
exon count: 3CDS single in 3' UTR: no RNA size: 2585
ORF size: 0CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 363.00frame shift in genome: no % Coverage: 99.11
has start codon: no stop codon in genome: no # of Alignments: 1
has end codon: no 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.