Human Gene PICALM (ENST00000393346.8_10) from GENCODE V47lift37
  Description: phosphatidylinositol binding clathrin assembly protein, transcript variant 1 (from RefSeq NM_007166.4)
Gencode Transcript: ENST00000393346.8_10
Gencode Gene: ENSG00000073921.18_18
Transcript (Including UTRs)
   Position: hg19 chr11:85,668,218-85,780,126 Size: 111,909 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr11:85,670,089-85,779,822 Size: 109,734 Coding Exon Count: 20 

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 (chr11:85,668,218-85,780,126)mRNA (may differ from genome)Protein (652 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PICAL_HUMAN
DESCRIPTION: RecName: Full=Phosphatidylinositol-binding clathrin assembly protein; AltName: Full=Clathrin assembly lymphoid myeloid leukemia protein;
FUNCTION: Assembly protein recruiting clathrin and adaptor protein complex 2 (AP2) to cell membranes at sites of coated-pit formation and clathrin-vesicle assembly. May be required to determine the amount of membrane to be recycled, possibly by regulating the size of the clathrin cage. Involved in AP2-dependent clathrin-mediated endocytosis at the neuromuscular junction.
SUBUNIT: Binds clathrin; involves primarily the C-terminal sequences, but the full-length protein is required for full binding capacity. Binds phosphatidylinositol 4,5- bisphosphate.
SUBCELLULAR LOCATION: Membrane, clathrin-coated pit. Golgi apparatus. Cytoplasmic vesicle, clathrin-coated vesicle. Note=Colocalized with clathrin in the Golgi area.
TISSUE SPECIFICITY: Expressed in all tissues examined.
DISEASE: Note=A chromosomal aberration involving PICALM is found in diffuse histiocytic lymphomas. Translocation t(10;11)(p13;q14) with MLLT10.
SIMILARITY: Contains 1 ENTH (epsin N-terminal homology) domain.
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/CALM.html";

-  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: PICALM
Diseases sorted by gene-association score: leukemia, acute myeloid* (180), precursor t-cell acute lymphoblastic leukemia* (143), subvalvular aortic stenosis (11), chronic tic disorder (9), thyroid lymphoma (9), myeloid leukemia (9), leukemia, acute lymphoblastic (8), auditory neuropathy (5), alzheimer disease (3), hematologic cancer (1)
* = Manually curated disease association

-  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: 87.78 RPKM in Artery - Tibial
Total median expression: 2181.43 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 -175.10304-0.576 Picture PostScript Text
3' UTR -411.301871-0.220 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
IPR011417 - ANTH
IPR014712 - Clathrin_Pinositid-bd_GAT-like
IPR008942 - ENTH_VHS
IPR013809 - Epsin-like_N

Pfam Domains:
PF01417 - ENTH domain
PF07651 - ANTH domain

SCOP Domains:
48464 - ENTH/VHS domain
89009 - GAT-like domain

ModBase Predicted Comparative 3D Structure on Q13492
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
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0005543 phospholipid binding
GO:0005545 1-phosphatidylinositol binding
GO:0005546 phosphatidylinositol-4,5-bisphosphate binding
GO:0017137 Rab GTPase binding
GO:0030276 clathrin binding
GO:0032050 clathrin heavy chain binding
GO:0035615 clathrin adaptor activity
GO:0045296 cadherin binding
GO:0050750 low-density lipoprotein particle receptor binding

Biological Process:
GO:0006897 endocytosis
GO:0006898 receptor-mediated endocytosis
GO:0007409 axonogenesis
GO:0007611 learning or memory
GO:0008283 cell proliferation
GO:0010629 negative regulation of gene expression
GO:0016050 vesicle organization
GO:0016188 synaptic vesicle maturation
GO:0016192 vesicle-mediated transport
GO:0016197 endosomal transport
GO:0030097 hemopoiesis
GO:0030100 regulation of endocytosis
GO:0031623 receptor internalization
GO:0032880 regulation of protein localization
GO:0035459 cargo loading into vesicle
GO:0043547 positive regulation of GTPase activity
GO:0045056 transcytosis
GO:0045893 positive regulation of transcription, DNA-templated
GO:0048261 negative regulation of receptor-mediated endocytosis
GO:0048268 clathrin coat assembly
GO:0048813 dendrite morphogenesis
GO:0055072 iron ion homeostasis
GO:0061024 membrane organization
GO:0065003 macromolecular complex assembly
GO:0072583 clathrin-dependent endocytosis
GO:0090647 modulation of age-related behavioral decline
GO:0097494 regulation of vesicle size
GO:0098711 iron ion import across plasma membrane
GO:1900223 positive regulation of beta-amyloid clearance
GO:1901216 positive regulation of neuron death
GO:1902004 positive regulation of beta-amyloid formation
GO:1902959 regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process
GO:1902961 positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process
GO:1902963 negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process
GO:1903077 negative regulation of protein localization to plasma membrane
GO:2000009 negative regulation of protein localization to cell surface
GO:2000370 positive regulation of clathrin-dependent endocytosis
GO:1902003 regulation of beta-amyloid formation

Cellular Component:
GO:0005622 intracellular
GO:0005634 nucleus
GO:0005769 early endosome
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0005905 clathrin-coated pit
GO:0009986 cell surface
GO:0016020 membrane
GO:0030136 clathrin-coated vesicle
GO:0031224 intrinsic component of membrane
GO:0031410 cytoplasmic vesicle
GO:0031982 vesicle
GO:0042734 presynaptic membrane
GO:0043025 neuronal cell body
GO:0043231 intracellular membrane-bounded organelle
GO:0045211 postsynaptic membrane
GO:0045334 clathrin-coated endocytic vesicle
GO:0048471 perinuclear region of cytoplasm
GO:0070381 endosome to plasma membrane transport vesicle
GO:0097418 neurofibrillary tangle
GO:0030122 AP-2 adaptor complex
GO:0030132 clathrin coat of coated pit


-  Descriptions from all associated GenBank mRNAs
  BC048259 - Homo sapiens phosphatidylinositol binding clathrin assembly protein, mRNA (cDNA clone MGC:51891 IMAGE:5537605), complete cds.
FW339997 - Screening.
BC073961 - Homo sapiens phosphatidylinositol binding clathrin assembly protein, mRNA (cDNA clone MGC:87981 IMAGE:6183858), complete cds.
BC064357 - Homo sapiens phosphatidylinositol binding clathrin assembly protein, mRNA (cDNA clone MGC:70760 IMAGE:5112878), complete cds.
AB210017 - Homo sapiens mRNA for PICALM variant protein, clone: fj13355.
AK291414 - Homo sapiens cDNA FLJ75056 complete cds, highly similar to Homo sapiens phosphatidylinositol binding clathrin assembly protein (PICALM), mRNA.
U45976 - Human clathrin assembly protein lymphoid myeloid leukemia (CALM) mRNA, complete cds.
AK300275 - Homo sapiens cDNA FLJ54310 complete cds, highly similar to Phosphatidylinositol-binding clathrin assembly protein.
AB451308 - Homo sapiens PICALM mRNA for phosphatidylinositol-binding clathrin assembly protein isoform 2, complete cds, clone: FLJ08165AAAN.
AB384373 - Synthetic construct DNA, clone: pF1KSDB0036, Homo sapiens PICALM gene for phosphatidylinositol binding clathrin assembly protein, complete cds, without stop codon, in Flexi system.
KJ892490 - Synthetic construct Homo sapiens clone ccsbBroadEn_01884 PICALM gene, encodes complete protein.
CR749664 - Homo sapiens mRNA; cDNA DKFZp686K06131 (from clone DKFZp686K06131).
AK128786 - Homo sapiens cDNA FLJ45466 fis, clone BRSTN2013931.
AY326466 - Homo sapiens putative protein STRF11 (STRF11) mRNA, complete cds.
AK297062 - Homo sapiens cDNA FLJ52661 complete cds, highly similar to Homo sapiens phosphatidylinositol binding clathrin assembly protein, transcript variant 2, mRNA.
JD197649 - Sequence 178673 from Patent EP1572962.
AF060928 - Homo sapiens type II AF10/CALM fusion protein (AF10/CALM) mRNA, partial cds.
AF060931 - Homo sapiens type V AF10/CALM fusion protein (AF10/CALM) mRNA, partial cds.
AF060929 - Homo sapiens type III AF10/CALM fusion protein (AF10/CALM) mRNA, partial cds.
AF060930 - Homo sapiens type IV AF10/CALM fusion protein (AF10/CALM) mRNA, partial cds.
AF060939 - Homo sapiens type I CALM protein (CALM) mRNA, partial cds.
AF060940 - Homo sapiens type II CALM protein (CALM) mRNA, partial cds.
JD331524 - Sequence 312548 from Patent EP1572962.
EF051633 - Homo sapiens CALM/AF10 fusion protein (CALM/AF10 fusion) mRNA, partial cds.
AF477006 - Homo sapiens myeloid/lymphoid or mixed-lineage leukemia/clathrin assembly protein fusion protein (MLL/CALM fusion) mRNA, partial cds.
AF060933 - Homo sapiens type III CALM/AF10 fusion protein (CALM/AF10) mRNA, partial cds.
JD540778 - Sequence 521802 from Patent EP1572962.
JD409230 - Sequence 390254 from Patent EP1572962.
JD396324 - Sequence 377348 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_ndkDynaminPathway - Endocytotic role of NDK, Phosphins and Dynamin

Reactome (by CSHL, EBI, and GO)

Protein Q13492 (Reactome details) participates in the following event(s):

R-HSA-421836 trans-Golgi Network Derived Vesicle Uncoating
R-HSA-421833 Vamp And trans-Golgi Network AP-1 Binding Coupled With Cargo Capture
R-HSA-8867613 PICALM binds R-SNAREs
R-HSA-421835 trans-Golgi Network Vesicle Scission
R-HSA-421831 trans-Golgi Network Coat Assembly
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8871194 RAB5 and GAPVD1 bind AP-2
R-HSA-8868658 HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
R-HSA-8868659 Clathrin recruits auxilins to the clathrin-coated vesicle
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: B4DTM3, CALM, E9PN05, ENST00000393346.1, ENST00000393346.2, ENST00000393346.3, ENST00000393346.4, ENST00000393346.5, ENST00000393346.6, ENST00000393346.7, F8VPG7, NM_007166, O60700, PICAL_HUMAN, Q13492, Q4LE54, Q6GMQ6, Q86XZ9, uc318vua.1, uc318vua.2
UCSC ID: ENST00000393346.8_10
RefSeq Accession: NM_007166.4
Protein: Q13492 (aka PICAL_HUMAN or PICA_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.