Human Gene NECAP1 (ENST00000339754.11_12) from GENCODE V47lift37
  Description: NECAP endocytosis associated 1, transcript variant 1 (from RefSeq NM_015509.4)
Gencode Transcript: ENST00000339754.11_12
Gencode Gene: ENSG00000089818.18_18
Transcript (Including UTRs)
   Position: hg19 chr12:8,234,870-8,250,477 Size: 15,608 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr12:8,234,885-8,248,686 Size: 13,802 Coding Exon Count: 8 

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 (chr12:8,234,870-8,250,477)mRNA (may differ from genome)Protein (275 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NECP1_HUMAN
DESCRIPTION: RecName: Full=Adaptin ear-binding coat-associated protein 1; AltName: Full=NECAP endocytosis-associated protein 1; Short=NECAP-1;
FUNCTION: Involved in endocytosis (By similarity).
SUBUNIT: Interacts with AP1G1 and AP2A1 components of the adapter protein complexes AP-1 and AP-2. Interacts with the GAE domain proteins GGA1, GGA2 and GGA3 (By similarity).
SUBCELLULAR LOCATION: Cytoplasmic vesicle, clathrin-coated vesicle membrane (By similarity). Cell membrane (By similarity). Note=Colocalizes with AP-2 at the plasma membrane (By similarity).
DOMAIN: The WXXF motifs mediate binding of accessory proteins to the ear-domain of AP-1, GGAs and AP-2 through hydrophobic interactions. Selective binding to the GAE domains of AP-1 or to the alpha-ear domain of AP-2 is tuned by the acidic context surrounding the motif and the properties of the second residue of the motif itself. The WXXF motif 1, which is preceded by an acidic residue and has a glycine in second position mediates specific interaction with AP-1. The WXXF motif 2, which is followed by the C-terminal carboxyl group negative charge, allows specific interaction with AP-2 (By similarity).
SIMILARITY: Belongs to the NECAP family.
SEQUENCE CAUTION: Sequence=AAH02888.1; Type=Erroneous initiation;

-  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: NECAP1
Diseases sorted by gene-association score: epileptic encephalopathy, early infantile, 21* (669), undetermined early-onset epileptic encephalopathy* (247), infantile epileptic encephalopathy (14), cataract 8, multiple types (12), hypertonia (10)
* = 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: 71.79 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 1007.45 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
3' UTR -476.601791-0.266 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
IPR012466 - NECAP-1

Pfam Domains:
PF07933 - Protein of unknown function (DUF1681)

SCOP Domains:
50729 - PH domain-like

ModBase Predicted Comparative 3D Structure on Q8NC96
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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    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0006897 endocytosis
GO:0015031 protein transport
GO:0061024 membrane organization

Cellular Component:
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0005905 clathrin-coated pit
GO:0016020 membrane
GO:0030125 clathrin vesicle coat
GO:0030665 clathrin-coated vesicle membrane
GO:0031410 cytoplasmic vesicle


-  Descriptions from all associated GenBank mRNAs
  AK074880 - Homo sapiens cDNA FLJ90399 fis, clone NT2RP2005887.
AK074858 - Homo sapiens cDNA FLJ90377 fis, clone NT2RP2004837.
AK303675 - Homo sapiens cDNA FLJ52944 complete cds, highly similar to Adaptin ear-binding coat-associated protein 1.
AK074923 - Homo sapiens cDNA FLJ90442 fis, clone NT2RP3001044.
AK314424 - Homo sapiens cDNA, FLJ95211.
BC110876 - Homo sapiens NECAP endocytosis associated 1, mRNA (cDNA clone MGC:131900 IMAGE:5553942), complete cds.
AL050272 - Homo sapiens mRNA; cDNA DKFZp566B183 (from clone DKFZp566B183).
AK290537 - Homo sapiens cDNA FLJ78563 complete cds.
AK075013 - Homo sapiens cDNA FLJ90532 fis, clone NT2RP4002715.
BC002888 - Homo sapiens NECAP endocytosis associated 1, mRNA (cDNA clone IMAGE:3940703), complete cds.
JD019618 - Sequence 642 from Patent EP1572962.
BC067367 - Homo sapiens NECAP endocytosis associated 1, mRNA (cDNA clone IMAGE:5731908), partial cds.
JD032861 - Sequence 13885 from Patent EP1572962.
AK094805 - Homo sapiens cDNA FLJ37486 fis, clone BRAWH2014473.
BC084551 - Homo sapiens NECAP endocytosis associated 1, mRNA (cDNA clone IMAGE:5020141), partial cds.
KJ902401 - Synthetic construct Homo sapiens clone ccsbBroadEn_11795 NECAP1 gene, encodes complete protein.
JD025817 - Sequence 6841 from Patent EP1572962.
JD028293 - Sequence 9317 from Patent EP1572962.
JD455938 - Sequence 436962 from Patent EP1572962.
JD299867 - Sequence 280891 from Patent EP1572962.
JD551046 - Sequence 532070 from Patent EP1572962.
JD291698 - Sequence 272722 from Patent EP1572962.
JD262596 - Sequence 243620 from Patent EP1572962.
JD315540 - Sequence 296564 from Patent EP1572962.
JD431414 - Sequence 412438 from Patent EP1572962.
JD135288 - Sequence 116312 from Patent EP1572962.
JD259585 - Sequence 240609 from Patent EP1572962.
JD274820 - Sequence 255844 from Patent EP1572962.
JD377215 - Sequence 358239 from Patent EP1572962.
JD527413 - Sequence 508437 from Patent EP1572962.
JD295842 - Sequence 276866 from Patent EP1572962.
JD263943 - Sequence 244967 from Patent EP1572962.
JD362115 - Sequence 343139 from Patent EP1572962.
JD312824 - Sequence 293848 from Patent EP1572962.
JD252162 - Sequence 233186 from Patent EP1572962.
JD294730 - Sequence 275754 from Patent EP1572962.
JD563965 - Sequence 544989 from Patent EP1572962.
JD091596 - Sequence 72620 from Patent EP1572962.
JD284615 - Sequence 265639 from Patent EP1572962.

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

Protein Q8NC96 (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-8856808 Recruitment of AP-2 complex and clathrin
R-HSA-421835 trans-Golgi Network Vesicle Scission
R-HSA-421831 trans-Golgi Network Coat Assembly
R-HSA-8866283 ARBB recruits GPCRs into clathrin-coated pits
R-HSA-8867756 CLASP proteins and cargo are recruited to the nascent clathrin-coated pit
R-HSA-8856813 AAK1 phosphorylates AP-2 mu subunit at T156
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-8868661 Dynamin-mediated GTP hydrolysis promotes vesicle scission
R-HSA-8868660 Auxilin recruits HSPA8:ATP to the clathrin-coated vesicle
R-HSA-8868648 SYNJ hydrolyze PI(4,5)P2 to PI(4)P
R-HSA-8868071 Clathrin recruits PIK3C2A
R-HSA-8868230 SNX9 recruits components of the actin polymerizing machinery
R-HSA-8867754 F- and N- BAR domain proteins bind the clathrin-coated pit
R-HSA-8868236 BAR domain proteins recruit dynamin
R-HSA-8868072 Clathrin-associated PIK3C2A phosphorylates PI(4)P to PI(3,4)P2
R-HSA-8868651 Endophilins recruit synaptojanins to the clathrin-coated pit
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-8856828 Clathrin-mediated endocytosis
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-8856825 Cargo recognition for clathrin-mediated endocytosis
R-HSA-199991 Membrane Trafficking
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000339754.1, ENST00000339754.10, ENST00000339754.2, ENST00000339754.3, ENST00000339754.4, ENST00000339754.5, ENST00000339754.6, ENST00000339754.7, ENST00000339754.8, ENST00000339754.9, NECP1_HUMAN, NM_015509, Q2NL73, Q5XG95, Q6NWY6, Q8N153, Q8NC96, Q8NCB0, Q9BU52, Q9Y407, uc317vli.1, uc317vli.2
UCSC ID: ENST00000339754.11_12
RefSeq Accession: NM_015509.4
Protein: Q8NC96 (aka NECP1_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.