Sema3d MGI Mouse Gene Detail - MGI:1860118 - sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D

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

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

SNPs within 2kb

6703 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
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 (+)

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

HGNC:10726

NCBI Gene ID: 223117

neXtProt AC: NX_O95025

UniProt: O95025
Chr Location

7q21.11

MGI Vertebrate Homology

Sema3d stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SEMA3D
Gene Tree

Sema3d

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Phenotype Summary

8 phenotypes from 3 alleles in 2 genetic backgrounds
14 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

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.

All Mutations and Alleles

7
Endonuclease-mediated

2
Targeted

5
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

53 strains or lines available
Comparison Matrix

Gene Expression + Phenotype
Recombinase Activity

Comparison Matrix Gene Expression + Recombinase Activity

Mice homozygous for a knock-out allele exhibit pulmonary vein connection to the right atrium and atrial septal defect.

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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.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

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

950
Tissues

80
cDNA Data

37
Literature Summary

40

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA SEMA3D

Xenbase sema3d

ZFIN sema3d

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All Sequences

51
RefSeq

4
UniProt

5
CCDS

CCDS39013.1

Ensembl

ENSMUSG00000040254 (Evidence)
NCBI Gene

108151

			Length	Strain/Species	Flank
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

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UniProt

5 Sequences
Protein Ontology

PR:000014618 semaphorin-3D

(term hierarchy)
InterPro Domains

IPR041416 IL-1Ra-like, immunoglobulin domain

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR016201 PSI domain

IPR001627 Sema domain

IPR036352 Sema domain superfamily

IPR027231 Semaphorin

IPR042582 Semaphorin-3D, Sema domain

IPR015943 WD40/YVTN repeat-like-containing domain superfamily
GlyGen

Q8BH34 3 sites

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All nucleic 49

cDNA 39

Primer pair 5

Other 5

Microarray probesets 4

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MGI:1921595

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

TSS for Sema3d:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr45166	Chr5:12433123-12433144 (+)	-218 bp
Tssr45167	Chr5:12433267-12433289 (+)	-74 bp
Tssr45168	Chr5:12433292-12433303 (+)	-54 bp
Tssr45169	Chr5:12433308-12433318 (+)	-39 bp
Tssr45170	Chr5:12433344-12433362 (+)	1 bp
Tssr45171	Chr5:12433450-12433510 (+)	128 bp
Tssr45172	Chr5:12516841-12516846 (+)	83,492 bp

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 Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 12/10/2024 MGI 6.24