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Sema3d Gene Detail
Summary
  • Symbol
    Sema3d
  • Name
    sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D
  • Synonyms
    4631426B19Rik
  • Feature Type
    protein coding gene
  • IDs
    MGI:1860118
    NCBI Gene: 108151
  • Alliance
    gene page
  • Transcription Start Sites
    7 TSS
Location &
Maps
more
  • Sequence Map
    Chr5:12433352-12638915 bp, + strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 5, 3.97 cM, cytoband A2
  • Mapping Data
    4 experiments
Strain
Comparison
more
  • SNPs within 2kb
    6703 from dbSNP Build 142
  • Strain Annotations
    18
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_1860118
 protein coding gene Chr5:12433133-12638920 (+)
129S1/SvImJ MGP_129S1SvImJ_G0029294
 protein coding gene Chr5:9523575-9741834 (+)
A/J MGP_AJ_G0029257
 protein coding gene Chr5:9231537-9436877 (+)
AKR/J MGP_AKRJ_G0029206
 protein coding gene Chr5:9821367-10026825 (+)
BALB/cJ MGP_BALBcJ_G0029274
 protein coding gene Chr5:9652329-9853864 (+)
C3H/HeJ MGP_C3HHeJ_G0028994
 protein coding gene Chr5:9695235-9922194 (+)
C57BL/6NJ MGP_C57BL6NJ_G0029724
 protein coding gene Chr5:10557789-10812055 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0026967
 protein coding gene Chr5:7806078-7996084 (+)
CAST/EiJ MGP_CASTEiJ_G0028407
 protein coding gene Chr5:9383408-9593495 (+)
CBA/J MGP_CBAJ_G0028955
 protein coding gene Chr5:10413846-10632591 (+)
DBA/2J MGP_DBA2J_G0029109
 protein coding gene Chr5:9561428-9774225 (+)
FVB/NJ MGP_FVBNJ_G0029071
 protein coding gene Chr5:9092794-9295986 (+)
LP/J MGP_LPJ_G0029198
 protein coding gene Chr5:9867238-10080769 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0029100
 protein coding gene Chr5:10880328-11203765 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0029755
 protein coding gene Chr5:9382618-9593531 (+)
PWK/PhJ MGP_PWKPhJ_G0028129
 protein coding gene Chr5:9082249-9275555 (+)
SPRET/EiJ MGP_SPRETEiJ_G0027962
 protein coding gene Chr5:9218304-9427305 (+)
WSB/EiJ MGP_WSBEiJ_G0028487
 protein coding gene Chr5:9348983-9557247 (+)



Homology
more
  • Human Ortholog
    SEMA3D, semaphorin 3D
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SEMA3D, semaphorin 3D
  • Synonyms
    coll-2, Sema-Z2
  • Links
    NCBI Gene ID: 223117
    neXtProt AC: NX_O95025
    UniProt: O95025

  • Chr Location
    7q21.11
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    8 phenotypes from 3 alleles in 2 genetic backgrounds
    14 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.
Mice homozygous for a knock-out allele exhibit pulmonary vein connection to the right atrium and atrial septal defect.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    14
  • GO References
    4
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
    948
  • Tissues
    78
  • cDNA Data
    37
  • Literature Summary
    40
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000040254 Ensembl Gene Model | MGI Sequence Detail 205564 C57BL/6J ±  kb
    transcript ENSMUST00000030868 Ensembl | MGI Sequence Detail 6307 Not Applicable  
    polypeptide ENSMUSP00000030868 Ensembl | MGI Sequence Detail 777 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    Molecular
    Reagents
    less
    • All nucleic 49
      cDNA 39
      Primer pair 5
      Other 5

      Microarray probesets 4
    Other
    Accession IDs
    less
    MGI:1921595
    References
    more
    • Summaries
      All 77
      Developmental Gene Expression 40
      Gene Ontology 4
      Phenotypes 14
    • Earliest
      J:62530 Tarantino LM, et al., A high-resolution radiation hybrid map of the proximal portion of mouse chromosome 5. Genomics. 2000 May 15;66(1):55-64
    • Latest
      J:345835 Qiu C, et al., A single-cell time-lapse of mouse prenatal development from gastrula to birth. Nature. 2024 Feb;626(8001):1084-1093
    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)
    Citing These Resources
    Funding Information
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    Send questions and comments to User Support.     		last database update
    11/19/2024
    MGI 6.24     		The Jackson Laboratory