Sema6d MGI Mouse Gene Detail - MGI:2387661 - sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D

Symbol

Sema6d
Name

sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D
Synonyms

1110067B02Rik, mKIAA1479, Sema6D-1, Sema6D-2, Sema6D-4, Sema6D-5, Sema6D-6

Feature Type

protein coding gene
IDs

MGI:2387661
NCBI Gene: 214968
Alliance

gene page
Transcription Start Sites

8 TSS

Sequence Map

Chr2:123931889-124509690 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 2, 60.69 cM
Mapping Data

4 experiments

SNPs within 2kb

14457 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_2387661	protein coding gene	Chr2:123931089-124509711 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0026422	protein coding gene	Chr2:127229841-127820640 (+)
A/J	MGP_AJ_G0026384	protein coding gene	Chr2:122038383-122624278 (+)
AKR/J	MGP_AKRJ_G0026360	protein coding gene	Chr2:125546227-126135216 (+)
BALB/cJ	MGP_BALBcJ_G0026396	protein coding gene	Chr2:122321829-122902710 (+)
C3H/HeJ	MGP_C3HHeJ_G0026140	protein coding gene	Chr2:126015279-126607143 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0026843	protein coding gene	Chr2:131311977-131914638 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024220	protein coding gene	Chr2:116860544-117428936 (+)
CAST/EiJ	MGP_CASTEiJ_G0025602	protein coding gene	Chr2:126267277-126860004 (+)
CBA/J	MGP_CBAJ_G0026120	protein coding gene	Chr2:136045763-136676857 (+)
DBA/2J	MGP_DBA2J_G0026254	protein coding gene	Chr2:121447944-122023144 (+)
FVB/NJ	MGP_FVBNJ_G0026218	protein coding gene	Chr2:120179999-120745071 (+)
LP/J	MGP_LPJ_G0026359	protein coding gene	Chr2:127466006-128059333 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026239	protein coding gene	Chr2:140230437-140851396 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0026897	protein coding gene	Chr2:125549665-126149298 (+)
PWK/PhJ	MGP_PWKPhJ_G0025338	protein coding gene	Chr2:121005867-121581329 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0025139	protein coding gene	Chr2:124652921-125263463 (+)
WSB/EiJ	MGP_WSBEiJ_G0025675	protein coding gene	Chr2:126470503-127064032 (+)

Human Ortholog

SEMA6D, semaphorin 6D

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SEMA6D, semaphorin 6D
Links

HGNC:16770

NCBI Gene ID: 80031

neXtProt AC: NX_Q8NFY4

UniProt: Q8NFY4
Chr Location

15q21.1; chr15:47184089-47774228 (+) GRCh38

MGI Vertebrate Homology

Sema6d stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SEMA6D
Gene Tree

Sema6d

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Phenotype Summary

3 phenotypes from 2 alleles in 2 genetic backgrounds
20 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

11
Chemically induced (other)

1
Endonuclease-mediated

2
Gene trapped

3
Radiation induced

1
Targeted

4
Genomic Mutations

2 involving Sema6d
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

62 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit normal dendritic cell trafficking and antigen-specific T cell priming.

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All GO Annotations

26
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

1060
Tissues

114
cDNA Data

14
Literature Summary

26

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

Xenbase sema6d

ZFIN sema6d

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All Sequences

158
RefSeq

96
UniProt

3
CCDS

CCDS16670.1, CCDS16671.1, CCDS16672.1, CCDS16673.1, CCDS38225.1, CCDS71132.1

Ensembl

ENSMUSG00000027200 (Evidence)
NCBI Gene

214968

			Length	Strain/Species	Flank
genomic	ENSMUSG00000027200	Ensembl Gene Model \| MGI Sequence Detail	577802	C57BL/6J	± kb
transcript	ENSMUST00000103239	Ensembl \| MGI Sequence Detail	6225	Not Applicable
polypeptide	ENSMUSP00000099529	Ensembl \| MGI Sequence Detail	1073	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000014632 semaphorin-6D

(term hierarchy)
InterPro Domains

IPR002165 Plexin repeat

IPR001627 Sema domain

IPR036352 Sema domain superfamily

IPR027231 Semaphorin

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

Q76KF0 7 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (2 sites)

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All nucleic 20

cDNA 15

Primer pair 2

Other 3

Microarray probesets 7

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MGI:1916098, MGI:2138763

Summaries

All 72

Developmental Gene Expression 26

Gene Ontology 9

Phenotypes 20
Earliest

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

J:353779 Nakanishi Y, et al., Semaphorin 6D tunes amygdalar circuits for emotional, metabolic, and inflammatory outputs. Neuron. 2024 Sep 4;112(17):2955-2972.e9

TSS for Sema6d:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr19870	Chr2:123931881-123931938 (+)	21 bp
Tssr630	Chr2:124016351-124016353 (+)	84,463 bp
Tssr19871	Chr2:124451801-124451824 (+)	519,924 bp
Tssr631	Chr2:124451988-124452051 (+)	520,131 bp
Tssr19872	Chr2:124452198-124452205 (+)	520,313 bp
Tssr19873	Chr2:124452342-124452356 (+)	520,460 bp
Tssr19874	Chr2:124452512-124452533 (+)	520,634 bp
Tssr19875	Chr2:124491262-124491268 (+)	559,376 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 11/12/2024 MGI 6.24