Human Gene ALCAM (ENST00000306107.9_10) from GENCODE V47lift37
  Description: activated leukocyte cell adhesion molecule, transcript variant 1 (from RefSeq NM_001627.4)
Gencode Transcript: ENST00000306107.9_10
Gencode Gene: ENSG00000170017.12_12
Transcript (Including UTRs)
   Position: hg19 chr3:105,085,753-105,295,744 Size: 209,992 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr3:105,086,253-105,290,783 Size: 204,531 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:105,085,753-105,295,744)mRNA (may differ from genome)Protein (583 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CD166_HUMAN
DESCRIPTION: RecName: Full=CD166 antigen; AltName: Full=Activated leukocyte cell adhesion molecule; AltName: CD_antigen=CD166; Flags: Precursor;
FUNCTION: Cell adhesion molecule that binds to CD6. Involved in neurite extension by neurons via heterophilic and homophilic interactions. May play a role in the binding of T- and B-cells to activated leukocytes, as well as in interactions between cells of the nervous system.
SUBCELLULAR LOCATION: Membrane; Single-pass type I membrane protein.
TISSUE SPECIFICITY: Spleen, placenta, liver, and weakly in liver. Expressed by activated T-cells, B-cells, monocytes and thymic epithelial cells. Expressed by neurons in the brain. Restricted expression in tumor cell lines. Preferentially expressed in highly metastasizing melanoma cell lines.
DOMAIN: The CD6 binding site is located in the N-terminal Ig-like domain.
SIMILARITY: Contains 3 Ig-like C2-type (immunoglobulin-like) domains.
SIMILARITY: Contains 2 Ig-like V-type (immunoglobulin-like) domains.

-  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: ALCAM
Diseases sorted by gene-association score: small intestinal adenocarcinoma (7), appendix adenocarcinoma (7), melanoma (3)

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

+  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: 55.27 RPKM in Artery - Aorta
Total median expression: 726.19 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 -202.20500-0.404 Picture PostScript Text
3' UTR -542.002449-0.221 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
IPR013162 - CD80_C2-set
IPR007110 - Ig-like
IPR013783 - Ig-like_fold
IPR003599 - Ig_sub
IPR013106 - Ig_V-set

Pfam Domains:
PF08205 - CD80-like C2-set immunoglobulin domain
PF13927 - Immunoglobulin domain

SCOP Domains:
48726 - Immunoglobulin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1KJC - Model


ModBase Predicted Comparative 3D Structure on Q13740
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005515 protein binding
GO:0042802 identical protein binding

Biological Process:
GO:0002250 adaptive immune response
GO:0002376 immune system process
GO:0007155 cell adhesion
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0007165 signal transduction
GO:0007411 axon guidance
GO:0008045 motor neuron axon guidance
GO:0031290 retinal ganglion cell axon guidance
GO:0048846 axon extension involved in axon guidance
GO:1990138 neuron projection extension

Cellular Component:
GO:0001772 immunological synapse
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0005925 focal adhesion
GO:0009897 external side of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030424 axon
GO:0030425 dendrite
GO:0031226 intrinsic component of plasma membrane
GO:0042995 cell projection
GO:0043025 neuronal cell body
GO:0070062 extracellular exosome
GO:0042101 T cell receptor complex


-  Descriptions from all associated GenBank mRNAs
  AK054632 - Homo sapiens cDNA FLJ30070 fis, clone ASTRO2000046, highly similar to CD166 ANTIGEN PRECURSOR.
BC017840 - Homo sapiens cDNA clone IMAGE:4689305, **** WARNING: chimeric clone ****.
BC057809 - Homo sapiens activated leukocyte cell adhesion molecule, mRNA (cDNA clone IMAGE:4814389), complete cds.
AK316113 - Homo sapiens cDNA, FLJ79012 complete cds, highly similar to CD166 antigen precursor.
BC041127 - Homo sapiens activated leukocyte cell adhesion molecule, mRNA (cDNA clone IMAGE:5730490), with apparent retained intron.
AL833702 - Homo sapiens mRNA; cDNA DKFZp667I089 (from clone DKFZp667I089).
AY644765 - Homo sapiens activated leukocyte cell adhesion molecule soluble isoform (ALCAM) mRNA, complete cds.
BC137096 - Homo sapiens activated leukocyte cell adhesion molecule, mRNA (cDNA clone MGC:168716 IMAGE:9021093), complete cds.
BC137097 - Homo sapiens activated leukocyte cell adhesion molecule, mRNA (cDNA clone MGC:168717 IMAGE:9021094), complete cds.
BC029639 - Homo sapiens cDNA clone IMAGE:4931979, containing frame-shift errors.
AK300362 - Homo sapiens cDNA FLJ59249 complete cds, highly similar to CD166 antigen precursor.
L38608 - Homo sapiens CD6 ligand (ALCAM) mRNA, complete cds.
DQ486140 - Homo sapiens activated leukocyte cell adhesion molecule variant 2 mRNA, complete cds, alternatively spliced.
DQ486139 - Homo sapiens activated leukocyte cell adhesion molecule variant 1 mRNA, complete cds, alternatively spliced.
AB590953 - Synthetic construct DNA, clone: pFN21AE2008, Homo sapiens ALCAM gene for activated leukocyte cell adhesion molecule, without stop codon, in Flexi system.
KJ896406 - Synthetic construct Homo sapiens clone ccsbBroadEn_05800 ALCAM gene, encodes complete protein.
Y10183 - H.sapiens mRNA for MEMD protein.
AK301804 - Homo sapiens cDNA FLJ52980 complete cds, highly similar to CD166 antigen precursor.
JD177802 - Sequence 158826 from Patent EP1572962.
AK127617 - Homo sapiens cDNA FLJ45715 fis, clone FELNG2000720, highly similar to CD166 antigen precursor.
AK095833 - Homo sapiens cDNA FLJ38514 fis, clone HCHON2000673, highly similar to CD166 ANTIGEN PRECURSOR.
AB074167 - Homo sapiens primary neuroblastoma cDNA, clone:Nbla04099, full insert sequence.
JD288536 - Sequence 269560 from Patent EP1572962.
JD396375 - Sequence 377399 from Patent EP1572962.
JD260565 - Sequence 241589 from Patent EP1572962.
JD084544 - Sequence 65568 from Patent EP1572962.
JD460526 - Sequence 441550 from Patent EP1572962.
JD369499 - Sequence 350523 from Patent EP1572962.
JD449357 - Sequence 430381 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q13740 (Reactome details) participates in the following event(s):

R-HSA-443780 Cis-heterodimerization of L1 and DM-GRASP/ALCAM/BEN
R-HSA-373760 L1CAM interactions
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: B2RNS3, B4DTU0, CD166_HUMAN, ENST00000306107.1, ENST00000306107.2, ENST00000306107.3, ENST00000306107.4, ENST00000306107.5, ENST00000306107.6, ENST00000306107.7, ENST00000306107.8, MEMD , NM_001627, O60892, Q13740, Q1HGM8, Q1HGM9, Q6PEY4, Q6ZS95, uc317nts.1, uc317nts.2
UCSC ID: ENST00000306107.9_10
RefSeq Accession: NM_001627.4
Protein: Q13740 (aka CD166_HUMAN or C166_HUMAN)

-  Gene Model Information
  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.