Sema3c MGI Mouse Gene Detail - MGI:107557 - sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C

Symbol

Sema3c
Name

sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C
Synonyms

1110036B02Rik, Semae

Feature Type

protein coding gene
IDs

MGI:107557
NCBI Gene: 20348
Alliance

gene page
Transcription Start Sites

17 TSS

Sequence Map

Chr5:17779814-17935266 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 5, 7.99 cM
Mapping Data

3 experiments

SNPs within 2kb

5027 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_107557	protein coding gene	Chr5:17779279-17935266 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0029305	protein coding gene	Chr5:14965151-15118403 (+)
A/J	MGP_AJ_G0029270	protein coding gene	Chr5:14514752-14665811 (+)
AKR/J	MGP_AKRJ_G0029221	protein coding gene	Chr5:15134748-15279715 (+)
BALB/cJ	MGP_BALBcJ_G0029282	protein coding gene	Chr5:14933133-15086126 (+)
C3H/HeJ	MGP_C3HHeJ_G0029001	protein coding gene	Chr5:15119671-15282691 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0029735	protein coding gene	Chr5:16256625-16415451 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026974	protein coding gene	Chr5:12795632-12945928 (+)
CAST/EiJ	MGP_CASTEiJ_G0028413	protein coding gene	Chr5:14461327-14619435 (+)
CBA/J	MGP_CBAJ_G0028968	protein coding gene	Chr5:16282114-16451782 (+)
DBA/2J	MGP_DBA2J_G0029120	protein coding gene	Chr5:14796119-14964797 (+)
FVB/NJ	MGP_FVBNJ_G0029078	protein coding gene	Chr5:14229828-14384052 (+)
LP/J	MGP_LPJ_G0029204	protein coding gene	Chr5:15393185-15545425 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0029106	protein coding gene	Chr5:17367346-17541325 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0029768	protein coding gene	Chr5:14756474-14916284 (+)
PWK/PhJ	MGP_PWKPhJ_G0028135	protein coding gene	Chr5:13849705-13998362 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0027968	protein coding gene	Chr5:14115144-14269340 (+)
WSB/EiJ	MGP_WSBEiJ_G0028493	protein coding gene	Chr5:14759058-14917697 (+)

Human Ortholog

SEMA3C, semaphorin 3C

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SEMA3C, semaphorin 3C
Synonyms

SEMAE, SemE
Links

HGNC:10725

NCBI Gene ID: 10512

neXtProt AC: NX_Q99985

UniProt: Q99985
Chr Location

7q21.11; chr7:80742538-80922389 (-) GRCh38

MGI Vertebrate Homology

Sema3c stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SEMA3C
Gene Tree

Sema3c

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References

1 with disease annotations

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Phenotype Summary

17 phenotypes from 2 alleles in 3 genetic backgrounds
1 phenotype from multigenic genotypes
26 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

9
Chemically induced (ENU)

1
Chemically induced (other)

2
Endonuclease-mediated

1
Radiation induced

1
Spontaneous

1
Targeted

3
Genomic Mutations

4 involving Sema3c
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

46 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for an ENU mutation exhibit perinatal lethality, hypopigmentation and abnormal heart development. Mice homozygous for a knock-out allele exhibit prenatal lethality associated with heart defects.

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All GO Annotations

33
GO References

9

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

1192
Tissues

369
cDNA Data

24
Literature Summary

125

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

GEISHA SEMA3C

Xenbase sema3c

ZFIN sema3c

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All Sequences

44
RefSeq

2
UniProt

3
CCDS

CCDS19099.1

Ensembl

ENSMUSG00000028780 (Evidence)
NCBI Gene

20348

			Length	Strain/Species	Flank
genomic	20348	NCBI Gene Model \| MGI Sequence Detail	155453	C57BL/6J	± kb
transcript	NM_013657	RefSeq \| MGI Sequence Detail	4956	C57BL/6
polypeptide	Q62181	UniProt \| EBI \| MGI Sequence Detail	751	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000014617 semaphorin-3C

(term hierarchy)
InterPro Domains

IPR013098 Immunoglobulin I-set

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR003599 Immunoglobulin subtype

IPR003598 Immunoglobulin subtype 2

IPR016201 PSI domain

IPR001627 Sema domain

IPR036352 Sema domain superfamily

IPR027231 Semaphorin

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

Q62181 7 sites, 4 N-linked glycans (5 sites)

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All nucleic 58

Genomic 1

cDNA 27

Primer pair 11

Other 19

Microarray probesets 6

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MGD-MRK-36128, MGI:1915946

Summaries

All 171

Developmental Gene Expression 125

Diseases 1

Gene Ontology 9

Phenotypes 26
Earliest

J:109968 Roderick TH, et al., Nineteen paracentric chromosomal inversions in mice. Genetics. 1974 Jan;76(1):109-17
Latest

J:354184 Pineiro-Sabaris R, et al., Deficient GATA6-CXCR7 signaling leads to bicuspid aortic valve. Dis Model Mech. 2024 Sep 1;17(9)

TSS for Sema3c:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr45238	Chr5:17779218-17779238 (+)	-586 bp
Tssr45239	Chr5:17779266-17779291 (+)	-535 bp
Tssr45240	Chr5:17779421-17779437 (+)	-385 bp
Tssr45241	Chr5:17779452-17779463 (+)	-356 bp
Tssr45242	Chr5:17779468-17779484 (+)	-338 bp
Tssr45243	Chr5:17779515-17779526 (+)	-293 bp
Tssr45244	Chr5:17779538-17779547 (+)	-271 bp
Tssr45245	Chr5:17779569-17779576 (+)	-241 bp
Tssr45246	Chr5:17779583-17779603 (+)	-221 bp
Tssr45247	Chr5:17779606-17779629 (+)	-196 bp
Tssr45248	Chr5:17779636-17779664 (+)	-164 bp
Tssr45249	Chr5:17779665-17779684 (+)	-139 bp
Tssr45250	Chr5:17779693-17779712 (+)	-111 bp
Tssr45251	Chr5:17779724-17779778 (+)	-63 bp
Tssr45252	Chr5:17782036-17782044 (+)	2,226 bp
Tssr45253	Chr5:17782818-17782829 (+)	3,010 bp
Tssr45254	Chr5:17899653-17899655 (+)	119,840 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)
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