Human Gene NETO1 (ENST00000327305.11_7) from GENCODE V47lift37
  Description: neuropilin and tolloid like 1, transcript variant 8 (from RefSeq NR_148695.2)
Gencode Transcript: ENST00000327305.11_7
Gencode Gene: ENSG00000166342.19_13
Transcript (Including UTRs)
   Position: hg19 chr18:70,410,991-70,535,222 Size: 124,232 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr18:70,416,263-70,534,526 Size: 118,264 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr18:70,410,991-70,535,222)mRNA (may differ from genome)Protein (533 aa)
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BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NETO1_HUMAN
DESCRIPTION: RecName: Full=Neuropilin and tolloid-like protein 1; AltName: Full=Brain-specific transmembrane protein containing 2 CUB and 1 LDL-receptor class A domains protein 1; Flags: Precursor;
FUNCTION: Involved in the development and/or maintenance of neuronal circuitry. Accessory subunit of the neuronal N-methyl-D- aspartate receptor (NMDAR) critical for maintaining the abundance of GRIN2A-containing NMDARs in the postsynaptic density. Regulates long-term NMDA receptor-dependent synaptic plasticity and cognition, at least in the context of spatial learning and memory (By similarity).
SUBUNIT: Interacts with PLZ domains of DLG2, DLG3 and DLG4 via its C-terminal TRV domain. Interacts with GRIN2A and GRIN2B via its CUB domains (By similarity).
SUBCELLULAR LOCATION: Isoform 2: Cell membrane; Single-pass type I membrane protein (Potential). Cell junction, synapse, postsynaptic cell membrane, postsynaptic density (By similarity). Note=Component of the postsynaptic density (PSD) of excitatory synapses (By similarity).
SUBCELLULAR LOCATION: Isoform 3: Cell membrane; Single-pass type I membrane protein (Potential).
SUBCELLULAR LOCATION: Isoform 1: Secreted (Potential).
TISSUE SPECIFICITY: Isoform 1 and isoform 2 are retina-specific. Isoform 3 is found in retina as well as at lower levels in adult and fetal brain.
SIMILARITY: Contains 2 CUB domains.
SIMILARITY: Contains 1 LDL-receptor class A domain.

-  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


-  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: 3.98 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 27.82 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -334.40696-0.480 Picture PostScript Text
3' UTR -922.404423-0.209 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
IPR000859 - CUB
IPR023415 - LDLR_class-A_CS
IPR002172 - LDrepeatLR_classA_rpt

Pfam Domains:
PF00057 - Low-density lipoprotein receptor domain class A
PF00431 - CUB domain

SCOP Domains:
49854 - Spermadhesin, CUB domain
57424 - LDL receptor-like module

ModBase Predicted Comparative 3D Structure on Q8TDF5
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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 Details  
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0035255 ionotropic glutamate receptor binding

Biological Process:
GO:0007613 memory
GO:0008542 visual learning
GO:0048168 regulation of neuronal synaptic plasticity
GO:0048169 regulation of long-term neuronal synaptic plasticity
GO:0097120 receptor localization to synapse
GO:2000312 regulation of kainate selective glutamate receptor activity
GO:2000463 positive regulation of excitatory postsynaptic potential

Cellular Component:
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0014069 postsynaptic density
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0045202 synapse
GO:0045211 postsynaptic membrane
GO:0060076 excitatory synapse
GO:0098839 postsynaptic density membrane


-  Descriptions from all associated GenBank mRNAs
  BC050329 - Homo sapiens neuropilin (NRP) and tolloid (TLL)-like 1, mRNA (cDNA clone MGC:48642 IMAGE:4821317), complete cds.
AL834354 - Homo sapiens mRNA; cDNA DKFZp547B197 (from clone DKFZp547B197).
AF448838 - Homo sapiens neuropilin and tolloid like-1 mRNA, complete cds.
AF448839 - Homo sapiens neuropilin and tolloid like-1 mRNA, complete cds, alternatively spliced.
AK123319 - Homo sapiens cDNA FLJ41325 fis, clone BRAMY2046871.
JD553225 - Sequence 534249 from Patent EP1572962.
JD488971 - Sequence 469995 from Patent EP1572962.
JD439314 - Sequence 420338 from Patent EP1572962.
JD263970 - Sequence 244994 from Patent EP1572962.
JD080642 - Sequence 61666 from Patent EP1572962.
LF211121 - JP 2014500723-A/18624: Polycomb-Associated Non-Coding RNAs.
LF344121 - JP 2014500723-A/151624: Polycomb-Associated Non-Coding RNAs.
MA579698 - JP 2018138019-A/151624: Polycomb-Associated Non-Coding RNAs.
MA446698 - JP 2018138019-A/18624: Polycomb-Associated Non-Coding RNAs.
JD136523 - Sequence 117547 from Patent EP1572962.
JD338021 - Sequence 319045 from Patent EP1572962.
JD444242 - Sequence 425266 from Patent EP1572962.
JD482320 - Sequence 463344 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: BTCL1, ENST00000327305.1, ENST00000327305.10, ENST00000327305.2, ENST00000327305.3, ENST00000327305.4, ENST00000327305.5, ENST00000327305.6, ENST00000327305.7, ENST00000327305.8, ENST00000327305.9, NETO1_HUMAN, NR_148695, Q86W85, Q8ND78, Q8TDF4, Q8TDF5, uc317sge.1, uc317sge.2
UCSC ID: ENST00000327305.11_7
RefSeq Accession: NM_138966.5
Protein: Q8TDF5 (aka NETO1_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.