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Sema3a Gene Detail
Summary
  • Symbol
    Sema3a
  • Name
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A
  • Synonyms
    collapsin-1, Semad, sema III, semaphorin III, SemD
  • Feature Type
    protein coding gene
  • IDs
    MGI:107558
    NCBI Gene: 20346
  • Alliance
    gene page
  • Transcription Start Sites
    14 TSS
Location &
Maps
more
  • Sequence Map
    Chr5:13175381-13652533 bp, + strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 5, 4.31 cM
  • Mapping Data
    2 experiments
Strain
Comparison
more
  • SNPs within 2kb
    15428 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_107558
 protein coding gene Chr5:13174789-13653453 (+)
129S1/SvImJ MGP_129S1SvImJ_G0029295
 protein coding gene Chr5:10313287-10840478 (+)
A/J MGP_AJ_G0029258
 protein coding gene Chr5:9962344-10451180 (+)
AKR/J MGP_AKRJ_G0029207
 protein coding gene Chr5:10575405-11085807 (+)
BALB/cJ MGP_BALBcJ_G0029275
 protein coding gene Chr5:10399027-10882239 (+)
C3H/HeJ MGP_C3HHeJ_G0028995
 protein coding gene Chr5:10500303-11013575 (+)
C57BL/6NJ MGP_C57BL6NJ_G0029725
 protein coding gene Chr5:11437095-11957959 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0026968
 protein coding gene Chr5:8480267-8956214 (+)
CAST/EiJ MGP_CASTEiJ_G0028408
 protein coding gene Chr5:10195034-10736247 (+)
CBA/J MGP_CBAJ_G0028956
 protein coding gene Chr5:11257965-11847046 (+)
DBA/2J MGP_DBA2J_G0029110
 protein coding gene Chr5:10317046-10808726 (+)
FVB/NJ MGP_FVBNJ_G0029072
 protein coding gene Chr5:9834914-10310635 (+)
LP/J MGP_LPJ_G0029199
 protein coding gene Chr5:10636622-11170940 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0029101
 protein coding gene Chr5:11977788-12659364 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0029756
 protein coding gene Chr5:10134740-10643658 (+)
PWK/PhJ MGP_PWKPhJ_G0028130
 protein coding gene Chr5:9813727-10302339 (+)
SPRET/EiJ MGP_SPRETEiJ_G0027963
 protein coding gene Chr5:10012648-10538569 (+)
WSB/EiJ MGP_WSBEiJ_G0028488
 protein coding gene Chr5:10110128-10617646 (+)



Homology
more
  • Human Ortholog
    SEMA3A, semaphorin 3A
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SEMA3A, semaphorin 3A
  • Synonyms
    coll-1, COLL1, HH16, Hsema-I, Hsema-III, SEMA1, SEMAD, SEMAIII, SEMAL, SemD
  • Links
    NCBI Gene ID: 10371
    neXtProt AC: NX_Q14563
    UniProt: Q14563

  • Chr Location
    7q21.11; chr7:83955777-84492725 (-)  GRCh38
Human Diseases
more
  • Diseases
    1 with human SEMA3A associations

Human Disease Mouse Models
      
IDs
Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    41 phenotypes from 3 alleles in 5 genetic backgrounds
    4 phenotypes from multigenic genotypes
    94 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
Homozygotes for targeted null mutations exhibit patterning abnormalities of sensory and sympathetic neurons, abnormal embryonic bones and cartilaginous structures, cardiac defects, and high postnatal mortality.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    81
  • GO References
    33
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    1276
  • Tissues
    448
  • cDNA Data
    30
  • Literature Summary
    139
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000028883 Ensembl Gene Model | MGI Sequence Detail 477153 C57BL/6J ±  kb
    transcript ENSMUST00000095012 Ensembl | MGI Sequence Detail 4085 Not Applicable  
    polypeptide ENSMUSP00000092621 Ensembl | MGI Sequence Detail 772 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 56
      Genomic 2
      cDNA 34
      Primer pair 7
      Other 13

      Microarray probesets 7
    Other
    Accession IDs
    less
    MGD-MRK-36129
    References
    more
    • Summaries
      All 279
      Developmental Gene Expression 139
      Gene Ontology 33
      Phenotypes 94
    • Earliest
      J:25500 Puschel AW, et al., Murine semaphorin D/collapsin is a member of a diverse gene family and creates domains inhibitory for axonal extension. Neuron. 1995 May;14(5):941-8
    • Latest
      J:353479 Erickson AG, et al., Motor innervation directs the correct development of the mouse sympathetic nervous system. Nat Commun. 2024 Aug 16;15(1):7065
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    11/12/2024
    MGI 6.24     		The Jackson Laboratory