Syp MGI Mouse Gene Detail - MGI:98467

Symbol

Syp
Name

synaptophysin
Synonyms

A230093K24Rik, p38, Syn, Syp I

Feature Type

protein coding gene
IDs

MGI:98467
NCBI Gene: 20977
Alliance

gene page
Transcription Start Sites

12 TSS

Sequence Map

ChrX:7504819-7519495 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome X, 3.44 cM, cytoband A-D
Mapping Data

11 experiments

SNPs within 2kb

324 from dbSNP Build 142
Strain Annotations

18
PCR

1
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_98467	protein coding gene	ChrX:7504710-7519495 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0035515	protein coding gene	ChrX:2251412-2266725 (+)
A/J	MGP_AJ_G0035493	protein coding gene	ChrX:2211985-2228064 (+)
AKR/J	MGP_AKRJ_G0035426	protein coding gene	ChrX:2313321-2329987 (+)
BALB/cJ	MGP_BALBcJ_G0035489	protein coding gene	ChrX:2230983-2246302 (+)
C3H/HeJ	MGP_C3HHeJ_G0035197	protein coding gene	ChrX:2285371-2300049 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0036013	protein coding gene	ChrX:2328614-2343300 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0032888	protein coding gene	ChrX:1780007-1794574 (+)
CAST/EiJ	MGP_CASTEiJ_G0034497	protein coding gene	ChrX:2185319-2200904 (+)
CBA/J	MGP_CBAJ_G0035167	protein coding gene	ChrX:2441707-2460736 (+)
DBA/2J	MGP_DBA2J_G0035324	protein coding gene	ChrX:2232988-2247681 (+)
FVB/NJ	MGP_FVBNJ_G0035271	protein coding gene	ChrX:2196928-2211515 (+)
LP/J	MGP_LPJ_G0035401	protein coding gene	ChrX:2252795-2267495 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0035310	protein coding gene	ChrX:2406165-2423238 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0036031	protein coding gene	ChrX:2234384-2249063 (+)
PWK/PhJ	MGP_PWKPhJ_G0034199	protein coding gene	ChrX:2165518-2180740 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0034036	protein coding gene	ChrX:2204691-2219255 (+)
WSB/EiJ	MGP_WSBEiJ_G0034620	protein coding gene	ChrX:2237069-2254581 (+)

Human Ortholog

SYP, synaptophysin

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SYP, synaptophysin
Synonyms

MRX96, MRXSYP, XLID96
Links

HGNC:11506

NCBI Gene ID: 6855

neXtProt AC: NX_P08247

UniProt: P08247
Chr Location

Xp11.23; chrX:49187815-49200218 (-) GRCh38

MGI Vertebrate Homology

Syp stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: SYP
Gene Tree

Syp

Diseases

1 with human SYP associations

				Human Disease	Mouse Models
				non-syndromic X-linked intellectual disability 96 IDs non-syndromic X-linked intellectual disability 96 DOID:0112035 OMIM:300802

Click on a disease name to see all genes associated with that disease.

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Phenotype Summary

2 phenotypes from 4 alleles in 4 genetic backgrounds
5 phenotypes 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

28
Endonuclease-mediated

3
Gene trapped

20
Targeted

4
Transgenic

1
Incidental Mutations

APF
Find Mice (IMSR)

22 strains or lines available

Mice homozygous for either one of two independently generated knock-out mutations are viable and fertile and display normal central nervous system morphology and synaptic transmission with no detectable changes in synaptic plasticity or neurotransmitter release.

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All GO Annotations

57
GO References

44

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	non-membrane-bounded 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

1083
Tissues

148
cDNA Data

110
Literature Summary

309

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase syp

ZFIN sypb

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All Sequences

46
RefSeq

2
UniProt

3
CCDS

CCDS29967.2

Ensembl

ENSMUSG00000031144 (Evidence)
NCBI Gene

20977

			Length	Strain/Species	Flank
genomic	20977	NCBI Gene Model \| MGI Sequence Detail	14677	C57BL/6J	± kb
transcript	NM_009305	RefSeq \| MGI Sequence Detail	2482	ZRU/MplStud
polypeptide	Q62277	UniProt \| EBI \| MGI Sequence Detail	314	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000015890 synaptophysin

(term hierarchy)
InterPro Domains

IPR008253 Marvel domain

IPR001285 Synaptophysin/synaptoporin
GlyGen

Q62277 2 sites, 1 N-linked glycan (1 site), 1 O-linked glycan (1 site)

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All nucleic 128

Genomic 12

cDNA 113

Primer pair 3

Microarray probesets 4

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MGD-MRK-14690, MGI:2147923, MGI:2441790

Summaries

All 419

Developmental Gene Expression 309

Gene Ontology 44

Phenotypes 26
Earliest

J:10700 Ozcelik T, et al., Synaptophysin: structure of the human gene and assignment to the X chromosome in man and mouse. Am J Hum Genet. 1990 Sep;47(3):551-61
Latest

J:348363 Matsumoto Y, et al., Slitrk4 is required for the development of inhibitory neurons in the fear memory circuit of the lateral amygdala. Front Mol Neurosci. 2024;17:1386924

TSS for Syp:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr160397	ChrX:7504913-7504936 (+)	106 bp
Tssr160398	ChrX:7507332-7507348 (+)	2,521 bp
Tssr160399	ChrX:7510378-7510392 (+)	5,566 bp
Tssr160400	ChrX:7510471-7510483 (+)	5,658 bp
Tssr160401	ChrX:7511059-7511075 (+)	6,248 bp
Tssr160402	ChrX:7514957-7514968 (+)	10,144 bp
Tssr160403	ChrX:7518121-7518140 (+)	13,312 bp
Tssr160404	ChrX:7518221-7518235 (+)	13,409 bp
Tssr160405	ChrX:7518706-7518725 (+)	13,897 bp
Tssr160406	ChrX:7519054-7519068 (+)	14,242 bp
Tssr160407	ChrX:7519166-7519183 (+)	14,356 bp
Tssr160408	ChrX:7519204-7519220 (+)	14,393 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 09/17/2024 MGI 6.24