Human Gene NRXN1 (ENST00000401710.5) from GENCODE V38
  Description: Homo sapiens neurexin 1 (NRXN1), transcript variant beta3, mRNA. (from RefSeq NM_001330092)
RefSeq Summary (NM_001330092): This gene encodes a single-pass type I membrane protein that belongs to the neurexin family. Neurexins are cell-surface receptors that bind neuroligins to form Ca(2+)-dependent neurexin/neuroligin complexes at synapses in the central nervous system. This complex is required for efficient neurotransmission and is involved in the formation of synaptic contacts. Three members of this gene family have been studied in detail and are estimated to generate over 3,000 variants through the use of two alternative promoters (alpha and beta) and extensive alternative splicing in each family member. Recently, a third promoter (gamma) was identified for this gene in the 3' region. Mutations in this gene are associated with Pitt-Hopkins-like syndrome-2 and may contribute to susceptibility to schizophrenia. [provided by RefSeq, Aug 2016]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Gencode Transcript: ENST00000401710.5
Gencode Gene: ENSG00000179915.24
Transcript (Including UTRs)
   Position: hg38 chr2:49,921,307-50,347,766 Size: 426,460 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg38 chr2:49,921,944-50,346,949 Size: 425,006 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2021-09-27 09:51:20

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr2:49,921,307-50,347,766)mRNA (may differ from genome)Protein (472 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Neurexin-1-beta; AltName: Full=Neurexin I-beta; Flags: Precursor;
FUNCTION: Neuronal cell surface protein that may be involved in cell recognition and cell adhesion by forming intracellular junctions through binding to neuroligins. May play a role in formation or maintenance of synaptic junctions. May mediate intracellular signaling. May play a role in angiogenesis (By similarity).
SUBUNIT: The cytoplasmic C-terminal region binds to CASK. Isoforms Beta 4b bind neuroligins NLGN1, NLGN2 and NLGN3, alpha- dystroglycan and alpha-latrotoxin. Binding to neuroligins is calcium-dependent, and the binding preference ranks as follow: NLGN1 > NLGN4 >> NLGN3 > NLGN2 (By similarity).
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein. Cell junction, synapse. Note=Localized on the pre- synaptic membrane (By similarity).
PTM: Highly O-glycosylated and minor N-glycosylated (By similarity).
SIMILARITY: Belongs to the neurexin family.
SIMILARITY: Contains 1 laminin G-like domain.
SEQUENCE CAUTION: Sequence=AF064842; Type=Frameshift; Positions=54;

-  MalaCards Disease Associations
  MalaCards Gene Search: NRXN1
Diseases sorted by gene-association score: pitt-hopkins-like syndrome 2* (1019), schizophrenia 17* (575), pitt-hopkins-like syndrome* (369), pitt-hopkins syndrome (14), astigmatism (7), autism spectrum disorder (6), schizophrenia (4), pervasive developmental disorder (2), autistic disorder (1), nicotine dependence, protection against (1), disease of mental health (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: 15.14 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 116.91 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 -351.60817-0.430 Picture PostScript Text
3' UTR -136.30637-0.214 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
IPR008985 - ConA-like_lec_gl_sf
IPR013320 - ConA-like_subgrp
IPR001791 - Laminin_G
IPR003585 - Neurexin-like

Pfam Domains:
PF02210 - Laminin G domain

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

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on P58400
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGI Ensembl   
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004888 transmembrane signaling receptor activity
GO:0005102 receptor binding
GO:0005105 type 1 fibroblast growth factor receptor binding
GO:0005515 protein binding
GO:0046872 metal ion binding
GO:0048306 calcium-dependent protein binding
GO:0050839 cell adhesion molecule binding
GO:0097109 neuroligin family protein binding

Biological Process:
GO:0001525 angiogenesis
GO:0007155 cell adhesion
GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0007158 neuron cell-cell adhesion
GO:0007165 signal transduction
GO:0007416 synapse assembly
GO:0007612 learning
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0010739 positive regulation of protein kinase A signaling
GO:0016339 calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules
GO:0021707 cerebellar granule cell differentiation
GO:0023041 neuronal signal transduction
GO:0030534 adult behavior
GO:0031175 neuron projection development
GO:0033138 positive regulation of peptidyl-serine phosphorylation
GO:0035176 social behavior
GO:0035418 protein localization to synapse
GO:0045184 establishment of protein localization
GO:0045743 positive regulation of fibroblast growth factor receptor signaling pathway
GO:0051490 negative regulation of filopodium assembly
GO:0051897 positive regulation of protein kinase B signaling
GO:0051965 positive regulation of synapse assembly
GO:0051968 positive regulation of synaptic transmission, glutamatergic
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071277 cellular response to calcium ion
GO:0071625 vocalization behavior
GO:0090126 protein complex assembly involved in synapse maturation
GO:0097091 synaptic vesicle clustering
GO:0097104 postsynaptic membrane assembly
GO:0097105 presynaptic membrane assembly
GO:0097112 gamma-aminobutyric acid receptor clustering
GO:0097114 NMDA glutamate receptor clustering
GO:0097116 gephyrin clustering involved in postsynaptic density assembly
GO:0097117 guanylate kinase-associated protein clustering
GO:0097118 neuroligin clustering involved in postsynaptic membrane assembly
GO:0097119 postsynaptic density protein 95 clustering
GO:0097120 receptor localization to synapse
GO:1900020 positive regulation of protein kinase C activity
GO:1903078 positive regulation of protein localization to plasma membrane
GO:1905520 positive regulation of presynaptic active zone assembly
GO:2000310 regulation of N-methyl-D-aspartate selective glutamate receptor activity
GO:2000311 regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity
GO:2000463 positive regulation of excitatory postsynaptic potential

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030139 endocytic vesicle
GO:0031965 nuclear membrane
GO:0031982 vesicle
GO:0042734 presynaptic membrane
GO:0043025 neuronal cell body
GO:0044295 axonal growth cone
GO:0045202 synapse
GO:0098793 presynapse
GO:0099056 integral component of presynaptic membrane

-  Descriptions from all associated GenBank mRNAs
  AB011150 - Homo sapiens mRNA for KIAA0578 protein, partial cds.
AB035356 - Homo sapiens mRNA for neurexin I-alpha protein, complete cds.
EF539882 - Homo sapiens NRXN1-alpha mRNA, complete cds, alternatively spliced.
AF064842 - Homo sapiens map 2q30-p32; 202.6 cR from top repeat region, complete sequence.
BC125179 - Homo sapiens neurexin 1, mRNA (cDNA clone IMAGE:40121982), partial cds.
BC125180 - Homo sapiens neurexin 1, mRNA (cDNA clone IMAGE:40121989), complete cds.
AB383911 - Synthetic construct DNA, clone: pF1KSDA0578, Homo sapiens NRXN1 gene for neurexin-1-alpha precursor, complete cds, without stop codon, in Flexi system.
AK093260 - Homo sapiens cDNA FLJ35941 fis, clone TESTI2011680, highly similar to Homo sapiens mRNA for neurexin I-alpha protein.
BX647616 - Homo sapiens mRNA; cDNA DKFZp313P2036 (from clone DKFZp313P2036).
AK295773 - Homo sapiens cDNA FLJ57994 complete cds, highly similar to Neurexin-1-alpha precursor.
AF087975 - Homo sapiens full length insert cDNA clone YW18F07.
JD472056 - Sequence 453080 from Patent EP1572962.
JD526426 - Sequence 507450 from Patent EP1572962.
JD052326 - Sequence 33350 from Patent EP1572962.
JD087600 - Sequence 68624 from Patent EP1572962.
LF210956 - JP 2014500723-A/18459: Polycomb-Associated Non-Coding RNAs.
MA446533 - JP 2018138019-A/18459: Polycomb-Associated Non-Coding RNAs.
JD479751 - Sequence 460775 from Patent EP1572962.
JD120423 - Sequence 101447 from Patent EP1572962.
JD124936 - Sequence 105960 from Patent EP1572962.
JD392117 - Sequence 373141 from Patent EP1572962.
JD464389 - Sequence 445413 from Patent EP1572962.
JD406038 - Sequence 387062 from Patent EP1572962.
JD126775 - Sequence 107799 from Patent EP1572962.
JD330354 - Sequence 311378 from Patent EP1572962.
JD392091 - Sequence 373115 from Patent EP1572962.
JD157985 - Sequence 139009 from Patent EP1572962.
JD180385 - Sequence 161409 from Patent EP1572962.
JD224888 - Sequence 205912 from Patent EP1572962.
JD496867 - Sequence 477891 from Patent EP1572962.
JD523496 - Sequence 504520 from Patent EP1572962.
JD527814 - Sequence 508838 from Patent EP1572962.
JD274317 - Sequence 255341 from Patent EP1572962.
JD408487 - Sequence 389511 from Patent EP1572962.
JD476343 - Sequence 457367 from Patent EP1572962.
JD395990 - Sequence 377014 from Patent EP1572962.
JD143594 - Sequence 124618 from Patent EP1572962.
JD289383 - Sequence 270407 from Patent EP1572962.
JD521573 - Sequence 502597 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04514 - Cell adhesion molecules (CAMs)

Reactome (by CSHL, EBI, and GO)

Protein P58400 (Reactome details) participates in the following event(s):

R-HSA-6794346 NRXNs bind NLGNs
R-HSA-6794348 NRXNs bind SYTs
R-HSA-6794352 NRXNs binds CASK tripartite complex
R-HSA-6794353 NRXNs binds MUNC18
R-HSA-6797974 LRRTMs bind NRXNs
R-HSA-6794345 NLGNs binds PSD-95 subfamily members
R-HSA-6797568 NRXNs bind CASK:Protein 4.1
R-HSA-6794338 GKAPs bind PSD-95 members
R-HSA-6794357 SHANK proteins bind GKAPs
R-HSA-6794344 HOMER binds SHANK proteins
R-HSA-6797554 ABP1 binds SHANK proteins
R-HSA-6794361 Neurexins and neuroligins
R-HSA-6794362 Protein-protein interactions at synapses
R-HSA-112316 Neuronal System

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000401710.1, ENST00000401710.2, ENST00000401710.3, ENST00000401710.4, NM_001330092, NRX1B_HUMAN, P58400, uc061jbd.1
UCSC ID: ENST00000401710.5
RefSeq Accession: NM_001330092
Protein: P58400 (aka NRX1B_HUMAN or NX1B_HUMAN)
CCDS: CCDS82446.1, CCDS82447.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.