Nrxn3 Gene Detail

Summary

• Symbol
  Nrxn3
• Name
  neurexin III
• Synonyms
  4933401A11Rik, 9330112C09Rik, D12Bwg0831e, neurexin III alpha, neurexin III alpha, neurexin III beta, neurexin III beta

• Feature Type
  protein coding gene
• IDs
  MGI:1096389
  NCBI Gene: 18191
• Alliance
  genome feature page
• Transcription Start Sites
  46 TSS

Location &
Maps

• Sequence Map
  Chr12:88689646-90301709 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 12, 42.94 cM
• Mapping Data
  4 experiments

Strain
Comparison

• SNPs within 2kb
  41293 from dbSNP Build 142
• Strain Annotations
  19

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1096389	protein coding gene	Chr12:88689454-90301709 (+)
129S1/SvImJ	ENSMUSG00200046998	protein coding gene	Chr12:80455580-82092625 (+)
A/J	ENSMUSG00195031792	protein coding gene	Chr12:83115011-84728159 (+)
AKR/J	ENSMUSG00220046995	protein coding gene	Chr12:80772011-82389473 (+)
BALB/cJ	ENSMUSG00180015381	protein coding gene	Chr12:82261058-83772443 (+)
C3H/HeJ	ENSMUSG00175036314	protein coding gene	Chr12:84882867-86495849 (+)
C57BL/6NJ	ENSMUSG00215014972	protein coding gene	Chr12:81458336-83071322 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017999	protein coding gene	Chr12:83929560-85533959 (+)
CAST/EiJ	ENSTCUG00005026320	protein coding gene	Chr12:81325132-82938224 (+)
CBA/J	ENSMUSG00210018754	protein coding gene	Chr12:81858476-83499514 (+)
DBA/2J	ENSMUSG00185002376	protein coding gene	Chr12:83710337-85323279 (+)
FVB/NJ	ENSMUSG00205000488	protein coding gene	Chr12:81073379-82712534 (+)
JF1/MsJ	ENSUMUG00000027832	protein coding gene	Chr12:88381557-90001002 (+)
LP/J	ENSMUSG00230042587	protein coding gene	Chr12:90772400-92409350 (+)
NOD/ShiLtJ	ENSMUSG00190024539	protein coding gene	Chr12:102656780-104272915 (-)
NZO/HlLtJ	ENSMUSG00225051767	protein coding gene	Chr12:92553927-94177524 (+)
PWK/PhJ	ENSLUMG00010003136	protein coding gene	Chr12:81871519-83476979 (+)
SPRET/EiJ	ENSMSPG00010001116	protein coding gene	Chr12:84285491-85828917 (+)
WSB/EiJ	ENSIUOG00005037122	protein coding gene	Chr12:81083604-82700075 (+)

Homology

• Human Ortholog
  NRXN3, neurexin 3

• Vertebrate Orthologs
  4

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  NRXN3, neurexin 3
  
• Synonyms
  C14orf60
• Links
  HGNC:8010

  NCBI Gene ID: 9369

  UniProt: Q9HDB5, Q9Y4C0

  
  
• Chr Location
  14q24.3-q31.1; chr14:78170373-79868291 (+)  GRCh38

---

• MGI Vertebrate Homology
  Nrxn3 stringent orthology
  1 human;1 mouse;1 rat;2 zebrafish
  
• HCOP
  vertebrate homology predictions: NRXN3
• Gene Tree
  Nrxn3
  

Human Diseases

• Diseases
  2 with human NRXN3 associations

				Human Disease	Mouse Models
				alcohol dependence IDs alcohol dependence       DOID:0050741 KEGG:05034 OMIM:103780
				nicotine dependence IDs nicotine dependence       DOID:0050742 EFO:0003768 ICD10CM:F17 MESH:D014029 NCI:C54203 UMLS_CUI:C0028043

Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  10 phenotypes from 6 alleles in 6 genetic backgrounds
  16 phenotypes from multigenic genotypes
  46 phenotype references
  

• All Mutations and Alleles
  17
• Chemically induced (other)
  1
• Endonuclease-mediated
  3
• Gene trapped
  3
• Spontaneous
  1
• Targeted
  7
• Transposon induced
  2
• Genomic Mutations
  1 involving Nrxn3
• Incidental Mutations
  Mutagenetix , APF
• Find Mice (IMSR)
  81 strains or lines available

Twenty percent of mice homozygous for a knock-out allele die postnatally prior to 20 days of age. Homozygosity for the 129S1-strain-specific p.R498W mutation or Sst+ neuron-specific conditional KO leads to enhanced empathy fear (observational fear).

Gene Ontology
(GO)
Classifications

• All GO Annotations
  72
• GO References
  14

Expression

• Assay Results
  826
• Tissues
  50
• cDNA Data
  17
• Literature Summary
  17

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas
• Other Vertebrate Links
  Xenbase nrxn3
  ZFIN nrxn3a, nrxn3b

Sequences &
Gene Models

• All Sequences
  150
• RefSeq
  75
• UniProt
  10
• CCDS
  CCDS49134.1, CCDS56856.1, CCDS79143.1

• Ensembl
  ENSMUSG00000066392 (Evidence)
• NCBI Gene
  18191

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000066392	Ensembl Gene Model | MGI Sequence Detail	1612064	C57BL/6J
transcript	ENSMUST00000163134	Ensembl | MGI Sequence Detail	7922	Not Applicable
polypeptide	ENSMUSP00000129678	Ensembl | MGI Sequence Detail	1571	Not Applicable

Protein
Information

• UniProt
  10 Sequences
• Protein Ontology
  PR:000040087 neurexin-3
  (term hierarchy)
• PDB
  3MW4
• InterPro Domains
  IPR013320 Concanavalin A-like lectin/glucanase domain superfamily
  IPR000742 EGF-like domain
  IPR000152 EGF-type aspartate/asparagine hydroxylation site
  IPR001791 Laminin G domain
  IPR050372 Neurexin-related cell adhesion and synaptic protein
  IPR003585 Neurexin/syndecan/glycophorin C
  IPR027789 Syndecan/Neurexin domain
• GlyGen
  Q6P9K9 8 sites, 6 N-linked glycans (4 sites), 1 O-linked glycan (1 site)

Molecular
Reagents

• All nucleic 26

  cDNA 18

  Primer pair 5

  Other 3

  
  

  Microarray probesets 5

Other
Accession IDs

MGD-MRK-34038, MGI:106346, MGI:1921683, MGI:1924757

References

• Summaries
  All 105

  Developmental Gene Expression 17

  Gene Ontology 14

  Phenotypes 46
• Earliest
  J:24533 Puschel AW, et al., Neurexins are differentially expressed in the embryonic nervous system of mice. J Neurosci. 1995 Apr;15(4):2849-56
• Latest
  J:386324 Ducrot C, et al., Neurexins contribute to inhibitory connectivity and dopamine neuron resilience in culture. Neuroscience. 2026 May 19;

TSS for Nrxn3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr114534	Chr12:88689636-88689663 (+)	4 bp
Tssr114535	Chr12:88691704-88691732 (+)	2,072 bp
Tssr114536	Chr12:88691740-88691769 (+)	2,109 bp
Tssr114537	Chr12:88691770-88691798 (+)	2,138 bp
Tssr114538	Chr12:88692365-88692377 (+)	2,725 bp
Tssr114539	Chr12:88692427-88692456 (+)	2,796 bp
Tssr114540	Chr12:88761576-88761590 (+)	71,937 bp
Tssr114541	Chr12:88761765-88761777 (+)	72,125 bp
Tssr114542	Chr12:88761781-88761804 (+)	72,147 bp
Tssr114543	Chr12:88829816-88829824 (+)	140,174 bp
Tssr114544	Chr12:88884041-88884046 (+)	194,398 bp
Tssr114545	Chr12:88920186-88920204 (+)	230,549 bp
Tssr114546	Chr12:88920208-88920231 (+)	230,574 bp
Tssr114547	Chr12:88924191-88924200 (+)	234,550 bp
Tssr114548	Chr12:88956919-88956922 (+)	267,275 bp
Tssr114549	Chr12:88979925-88979938 (+)	290,286 bp
Tssr114550	Chr12:88980018-88980065 (+)	290,396 bp
Tssr114551	Chr12:89012690-89012695 (+)	323,047 bp
Tssr114552	Chr12:89030686-89030728 (+)	341,061 bp
Tssr114553	Chr12:89048150-89048153 (+)	358,506 bp
Tssr114554	Chr12:89056224-89056226 (+)	366,579 bp
Tssr114555	Chr12:89257361-89257362 (+)	567,716 bp
Tssr3909	Chr12:89364762-89364766 (+)	675,118 bp
Tssr114556	Chr12:89370506-89370512 (+)	680,863 bp
Tssr114557	Chr12:89416956-89416961 (+)	727,313 bp
Tssr114558	Chr12:89420787-89420790 (+)	731,143 bp
Tssr114559	Chr12:89526554-89526558 (+)	836,910 bp
Tssr114560	Chr12:89558257-89558266 (+)	868,616 bp
Tssr114561	Chr12:89568761-89568765 (+)	879,117 bp
Tssr114562	Chr12:89609151-89609164 (+)	919,512 bp
Tssr114563	Chr12:89732156-89732160 (+)	1,042,512 bp
Tssr114564	Chr12:89738822-89738829 (+)	1,049,180 bp
Tssr114565	Chr12:89779118-89779121 (+)	1,089,474 bp
Tssr114566	Chr12:89779211-89779235 (+)	1,089,577 bp
Tssr114567	Chr12:89779237-89779258 (+)	1,089,602 bp
Tssr114568	Chr12:89779392-89779403 (+)	1,089,752 bp
Tssr114569	Chr12:89779579-89779588 (+)	1,089,938 bp
Tssr114570	Chr12:89779695-89779700 (+)	1,090,052 bp
Tssr114571	Chr12:89780001-89780014 (+)	1,090,362 bp
Tssr114572	Chr12:89780071-89780074 (+)	1,090,427 bp
Tssr114573	Chr12:89780346-89780387 (+)	1,090,721 bp
Tssr114574	Chr12:89801605-89801606 (+)	1,111,960 bp
Tssr3911	Chr12:89819111-89819113 (+)	1,129,466 bp
Tssr114575	Chr12:89837481-89837490 (+)	1,147,840 bp
Tssr114576	Chr12:90135809-90135814 (+)	1,446,166 bp
Tssr114577	Chr12:90206037-90206041 (+)	1,516,393 bp