Sdc1 MGI Mouse Gene Detail - MGI:1349162

Symbol

Sdc1
Name

syndecan 1
Synonyms

CD138, syn-1, Synd, Synd1

Feature Type

protein coding gene
IDs

MGI:1349162
NCBI Gene: 20969
Alliance

gene page
Transcription Start Sites

13 TSS

Sequence Map

Chr12:8821396-8843716 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 12, 3.94 cM
Mapping Data

14 experiments

SNPs within 2kb

547 from dbSNP Build 142
Strain Annotations

18
RFLP

2

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1349162	protein coding gene	Chr12:8821323-8843716 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0019588	protein coding gene	Chr12:5840952-5863718 (+)
A/J	MGP_AJ_G0019555	protein coding gene	Chr12:5678830-5701588 (+)
AKR/J	MGP_AKRJ_G0019525	protein coding gene	Chr12:6059828-6082837 (+)
BALB/cJ	MGP_BALBcJ_G0019530	protein coding gene	Chr12:5804509-5827773 (+)
C3H/HeJ	MGP_C3HHeJ_G0019336	protein coding gene	Chr12:5889125-5912988 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0019979	protein coding gene	Chr12:6021992-6046481 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0017604	protein coding gene	Chr12:5489050-5511933 (+)
CAST/EiJ	MGP_CASTEiJ_G0018891	protein coding gene	Chr12:5882347-5903196 (+)
CBA/J	MGP_CBAJ_G0019307	protein coding gene	Chr12:6554006-6576389 (+)
DBA/2J	MGP_DBA2J_G0019420	protein coding gene	Chr12:5633869-5655998 (+)
FVB/NJ	MGP_FVBNJ_G0019411	protein coding gene	Chr12:5604177-5626083 (+)
LP/J	MGP_LPJ_G0019491	protein coding gene	Chr12:5888696-5912875 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0019444	protein coding gene	Chr12:6366603-6391578 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0020018	protein coding gene	Chr12:5796722-5817574 (+)
PWK/PhJ	MGP_PWKPhJ_G0018657	protein coding gene	Chr12:5699294-5720088 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0018448	protein coding gene	Chr12:5811739-5835461 (+)
WSB/EiJ	MGP_WSBEiJ_G0018942	protein coding gene	Chr12:5862002-5882786 (+)

Human Ortholog

SDC1, syndecan 1

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SDC1, syndecan 1
Synonyms

CD138, SDC, SYND1, syndecan
Links

HGNC:10658

NCBI Gene ID: 6382

neXtProt AC: NX_P18827

UniProt: P18827
Chr Location

2p24.1; chr2:20200797-20225475 (-) GRCh38

MGI Vertebrate Homology

Sdc1 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: SDC1
Gene Tree

Sdc1

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Phenotype Summary

17 phenotypes from 2 alleles in 6 genetic backgrounds
2 phenotypes from multigenic genotypes
79 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

10
Endonuclease-mediated

7
Targeted

3
Incidental Mutations

APF , CvDC
Find Mice (IMSR)

23 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Targeted mutant mice are overtly normal but resist mammary tumor development in response to Wnt1, and show delayed cutaneous and corneal wound healing, defective leukocyte adhesion to endothelia, increased angiogenesis, as well as reduced susceptibility to P. aeruginosa lung infection.

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All GO Annotations

28
GO References

11

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

1028
Tissues

203
cDNA Data

311
Literature Summary

57

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

GEISHA SDC1

Xenbase sdc1

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All Sequences

59
RefSeq

6
UniProt

4
CCDS

CCDS25803.1

Ensembl

ENSMUSG00000020592 (Evidence)
NCBI Gene

20969

			Length	Strain/Species	Flank
genomic	20969	NCBI Gene Model \| MGI Sequence Detail	22321	C57BL/6J	± kb
transcript	NM_011519	RefSeq \| MGI Sequence Detail	3057	ZRU/MplStud
polypeptide	P18828	UniProt \| EBI \| MGI Sequence Detail	311	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000001935 syndecan-1

(term hierarchy)
InterPro Domains

IPR003585 Neurexin/syndecan/glycophorin C

IPR001050 Syndecan

IPR030479 Syndecan, conserved site

IPR027789 Syndecan/Neurexin domain
GlyGen

P18828 6 sites

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All nucleic 325

Genomic 6

cDNA 313

Primer pair 3

Other 3

Microarray probesets 7

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MGD-MRK-14682, MGD-MRK-14686, MGI:2144723, MGI:2144725, MGI:98464

Summaries

All 218

Developmental Gene Expression 57

Gene Ontology 11

Phenotypes 79
Earliest

J:9669 Saunders S, et al., Molecular cloning of syndecan, an integral membrane proteoglycan. J Cell Biol. 1989 Apr;108(4):1547-56
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Sdc1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr112738	Chr12:8821040-8821062 (+)	-345 bp
Tssr112739	Chr12:8821317-8821328 (+)	-73 bp
Tssr112740	Chr12:8821345-8821361 (+)	-43 bp
Tssr112741	Chr12:8821378-8821394 (+)	-10 bp
Tssr112742	Chr12:8821405-8821425 (+)	19 bp
Tssr3790	Chr12:8821430-8821444 (+)	41 bp
Tssr112743	Chr12:8821448-8821464 (+)	60 bp
Tssr112744	Chr12:8824569-8824573 (+)	3,175 bp
Tssr112745	Chr12:8840700-8840740 (+)	19,324 bp
Tssr112746	Chr12:8841786-8841831 (+)	20,413 bp
Tssr112747	Chr12:8841887-8841936 (+)	20,516 bp
Tssr112748	Chr12:8842178-8842192 (+)	20,789 bp
Tssr112749	Chr12:8842427-8842446 (+)	21,041 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