Syngr3 (synaptogyrin 3) - Rat Genome Database

Name: Syngr3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Syngr3 (synaptogyrin 3) Rattus norvegicus

Analyze

Symbol:

Syngr3

Name:

synaptogyrin 3

RGD ID:

1311801

Description:

Predicted to enable SH2 domain binding activity. Involved in regulation of neurotransmitter uptake. Predicted to be located in synapse. Predicted to be active in neuromuscular junction and synaptic vesicle membrane. Orthologous to human SYNGR3 (synaptogyrin 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; acrylamide.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC302975; synaptogyrin-3

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	SYNGR3 (synaptogyrin 3)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Syngr3 (synaptogyrin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Syngr3 (synaptogyrin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SYNGR3 (synaptogyrin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SYNGR3 (synaptogyrin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Syngr3 (synaptogyrin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SYNGR3 (synaptogyrin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SYNGR3 (synaptogyrin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Syngr3 (synaptogyrin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	NARF (nuclear prelamin A recognition factor)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	SYNGR3 (synaptogyrin 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Syngr3 (synaptogyrin 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	syngr3a (synaptogyrin 3a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Danio rerio (zebrafish):	syngr3b (synaptogyrin 3b)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)
Drosophila melanogaster (fruit fly):	Syngr	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	sng-1	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	syngr3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	10	14,215,088 - 14,219,844 (-)	NCBI		GRCr8
mRatBN7.2	10	13,710,553 - 13,715,309 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	13,704,998 - 13,715,669 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	18,457,380 - 18,462,138 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	10	17,946,233 - 17,950,991 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	10	13,445,435 - 13,450,193 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	10	14,051,413 - 14,056,169 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	14,051,415 - 14,056,169 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	13,868,393 - 13,873,388 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	13,938,377 - 13,943,131 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	10	13,938,375 - 13,943,059 (-)	NCBI
Celera	10	13,390,479 - 13,395,233 (-)	NCBI		Celera
Cytogenetic Map	10	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

epilepsy (ISO)

idiopathic generalized epilepsy (ISO)

short-rib thoracic dysplasia 9 with or without polydactyly (ISO)

tuberous sclerosis 2 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

1,2-dimethylhydrazine (ISO)

1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (ISO)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

3,4-methylenedioxymethamphetamine (ISO)

acrylamide (EXP,ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

aristolochic acid A (ISO)

atrazine (ISO)

azoxystrobin (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

calcitriol (ISO)

carbamazepine (ISO)

chlorpyrifos (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

Enterolactone (ISO)

entinostat (ISO)

ethanol (ISO)

folic acid (ISO)

fulvestrant (ISO)

gentamycin (EXP)

heroin (ISO)

ivermectin (ISO)

lead(0) (ISO)

lipopolysaccharide (ISO)

mercury dibromide (ISO)

paracetamol (ISO)

phenylmercury acetate (ISO)

PhIP (ISO)

picoxystrobin (ISO)

quercetin (ISO)

resveratrol (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

SB 431542 (ISO)

silver atom (ISO)

silver(0) (ISO)

sodium arsenite (ISO)

sodium dodecyl sulfate (ISO)

sulforaphane (ISO)

tebufenpyrad (ISO)

testosterone (ISO)

thimerosal (ISO)

trichloroethene (EXP)

tris(2-butoxyethyl) phosphate (ISO)

valproic acid (ISO)

vorinostat (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

regulated exocytosis (ISO)

regulation of neurotransmitter uptake (IDA,IMP)

regulation of synaptic vesicle priming (ISO)

substantia nigra development (ISO)

Cellular Component

neuromuscular junction (IBA,ISO)

synapse (ISO)

synaptic vesicle (ISO)

synaptic vesicle membrane (IBA)

Molecular Function

protein binding (ISO)

SH2 domain binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Physical and functional interaction between the dopamine transporter and the synaptic vesicle protein synaptogyrin-3.	Egaña LA, etal., J Neurosci. 2009 Apr 8;29(14):4592-604. doi: 10.1523/JNEUROSCI.4559-08.2009.
2.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
4.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	GOA pipeline	RGD automated data pipeline
6.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:10383386	PMID:14755516	PMID:18706977	PMID:22926577

Genomics

Comparative Map Data

Syngr3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	10	14,215,088 - 14,219,844 (-)	NCBI		GRCr8
mRatBN7.2	10	13,710,553 - 13,715,309 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	13,704,998 - 13,715,669 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	18,457,380 - 18,462,138 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	10	17,946,233 - 17,950,991 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	10	13,445,435 - 13,450,193 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	10	14,051,413 - 14,056,169 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	14,051,415 - 14,056,169 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	13,868,393 - 13,873,388 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	13,938,377 - 13,943,131 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	10	13,938,375 - 13,943,059 (-)	NCBI
Celera	10	13,390,479 - 13,395,233 (-)	NCBI		Celera
Cytogenetic Map	10	q12	NCBI

SYNGR3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	16	1,989,970 - 1,994,275 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	16	1,989,660 - 1,994,275 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	16	2,039,971 - 2,044,276 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	16	1,979,969 - 1,984,277 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	16	1,979,968 - 1,984,276	NCBI
Celera	16	2,252,147 - 2,256,455 (+)	NCBI		Celera
Cytogenetic Map	16	p13.3	NCBI
HuRef	16	1,965,975 - 1,968,276 (+)	NCBI		HuRef
CHM1_1	16	2,039,872 - 2,044,202 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	16	2,009,915 - 2,014,220 (+)	NCBI		T2T-CHM13v2.0

Syngr3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	24,904,066 - 24,908,923 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	24,904,066 - 24,908,929 (-)	Ensembl		GRCm39 Ensembl
GRCm38	17	24,685,092 - 24,689,949 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	24,685,092 - 24,689,955 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	24,822,037 - 24,826,894 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	17	24,412,692 - 24,417,549 (-)	NCBI		MGSCv36	mm8
Celera	17	25,208,003 - 25,212,868 (-)	NCBI		Celera
Cytogenetic Map	17	A3.3	NCBI
cM Map	17	12.47	NCBI

Syngr3
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955442	15,272,692 - 15,277,765 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955442	15,273,597 - 15,277,740 (-)	NCBI	ChiLan1.0	ChiLan1.0

SYNGR3
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	18	2,353,140 - 2,357,479 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	16	6,134,807 - 6,139,120 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	16	710,090 - 714,421 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	16	2,078,770 - 2,083,100 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	16	2,078,645 - 2,083,100 (+)	Ensembl	panpan1.1		panPan2

SYNGR3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	6	38,941,933 - 38,944,110 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	6	40,181,673 - 40,186,094 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	6	39,258,991 - 39,263,413 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	6	39,258,989 - 39,263,455 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	6	38,935,781 - 38,940,202 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	6	38,908,091 - 38,912,507 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	6	39,386,965 - 39,391,391 (-)	NCBI		UU_Cfam_GSD_1.0

Syngr3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409344	104,661,355 - 104,665,817 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936694	2,043,657 - 2,047,883 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936694	2,043,646 - 2,047,897 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SYNGR3
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	39,975,069 - 39,979,217 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	39,975,067 - 39,981,537 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	42,202,480 - 42,206,646 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SYNGR3
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	5	1,886,899 - 1,891,293 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	5	1,886,864 - 1,891,368 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666068	29,176,621 - 29,181,012 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Syngr3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624913	265,316 - 270,491 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624913	266,296 - 270,420 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Syngr3
5 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	76
Count of miRNA genes:	60
Interacting mature miRNAs:	74
Transcripts:	ENSRNOT00000017833
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
737820	Alc9	Alcohol consumption QTL 9	2.2		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	10	5144027	19233348	Rat
631660	Hcar1	Hepatocarcinoma resistance QTL 1	3.4	0.0001	liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	10	6154182	15990232	Rat
9590310	Scort19	Serum corticosterone level QTL 19	6.3	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	11474010	56474010	Rat
631554	Bp133	Blood pressure QTL 133		0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	743364	63851208	Rat
634327	Hc4	Hypercalciuria QTL 4	2.4		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	10	1	38328221	Rat
634329	Pia15	Pristane induced arthritis QTL 15	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	1	24158324	Rat
9590268	Scort13	Serum corticosterone level QTL 13	3.26	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	10	11474010	56474010	Rat
7411611	Foco17	Food consumption QTL 17	18.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	10	1	42315980	Rat
8662860	Vetf10	Vascular elastic tissue fragility QTL 10			artery integrity trait (VT:0010639)	number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)	10	6154182	73453136	Rat
9589136	Insul27	Insulin level QTL 27	10.46	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	10	11474010	56474010	Rat
1576304	Schws7	Schwannoma susceptibility QTL 7		0.0115	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	10	4765527	19816042	Rat
1578761	Stresp21	Stress response QTL 21	3.3		thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	10	6375746	51375746	Rat
631828	Alc5	Alcohol consumption QTL 5	2.4		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	10	5144027	17245662	Rat
61427	Cia16	Collagen induced arthritis QTL 16	3.2		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	10	6357896	96121100	Rat
70223	Bp57	Blood pressure QTL 57	5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	10	1	80676123	Rat
2298544	Neuinf9	Neuroinflammation QTL 9	4.6		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	10	5801990	62146030	Rat
2313064	Bmd71	Bone mineral density QTL 71	0.9	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	10	5387014	50387014	Rat
2303118	Mamtr7	Mammary tumor resistance QTL 7		0.003	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	10	9658275	104670812	Rat
2313095	Bss62	Bone structure and strength QTL 62	1.5	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	10	5387014	50387014	Rat
2293680	Bss40	Bone structure and strength QTL 40	5.66	0.0001	femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	10	1	35225947	Rat
2313081	Bss64	Bone structure and strength QTL 64	1.3	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	10	5387014	50387014	Rat
10401803	Kidm50	Kidney mass QTL 50			kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	10	418344	45418344	Rat
2313066	Bss63	Bone structure and strength QTL 63	1.4	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	10	5387014	50387014	Rat
2313104	Bss61	Bone structure and strength QTL 61	0.9	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	10	5387014	50387014	Rat

Markers in Region

RH134049

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	10	13,710,584 - 13,710,794 (+)	MAPPER	mRatBN7.2
Rnor_6.0	10	14,051,445 - 14,051,654	NCBI	Rnor6.0
Rnor_5.0	10	13,868,425 - 13,868,634	UniSTS	Rnor5.0
RGSC_v3.4	10	13,938,407 - 13,938,616	UniSTS	RGSC3.4
Celera	10	13,390,509 - 13,390,718	UniSTS
RH 3.4 Map	10	171.5	UniSTS
Cytogenetic Map	10	q12	UniSTS

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium									62
Low	3	4	20	12	2	12	1	1	10	26	32	11	1
Below cutoff		39	28	22	15	22	7	8	2	9	9		7

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106985	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC093937	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473948	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000010	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000017833 ⟹ ENSRNOP00000017833

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	13,710,556 - 13,715,669 (-)	Ensembl
Rnor_6.0 Ensembl	10	14,051,415 - 14,056,169 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000101849 ⟹ ENSRNOP00000097621

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	10	13,704,998 - 13,715,669 (-)	Ensembl

RefSeq Acc Id:

NM_001106985 ⟹ NP_001100455

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	10	14,215,088 - 14,219,844 (-)	NCBI
mRatBN7.2	10	13,710,553 - 13,715,309 (-)	NCBI
Rnor_6.0	10	14,051,415 - 14,056,169 (-)	NCBI
Rnor_5.0	10	13,868,393 - 13,873,388 (-)	NCBI
RGSC_v3.4	10	13,938,377 - 13,943,131 (-)	RGD
Celera	10	13,390,479 - 13,395,233 (-)	RGD

Sequence:

show sequence

AGCCGACGCGCGCTCCCGGGAGGCGGCGGCAGAGGCAGCAGCATCCACAGCATCAGCAGCCTCA
GCATCAGCCCTGGGAGGTCTCCGGCAGGGCAGGCCGGTGGGACAAACGGACAGAAGGCACAGGT
CCCGCAATGGAAGGAGCATCCTTTGGCGCGGGCCGTGCGGGAGCTGCCTTTGATCCCGTGAGCT
TTGCGCAGCGGCCCCAGACCCTGTTGCGGGTCGTGTCCTGGGTGTTTTCTATAGCCGTGTTCGG
GCCGATTGTCAATGAGGGCTACGTGAACTCGGACAGCGGTCCAGAACTGCGCTGCGTCTTCAAT
GGAAACGCGGGAGCCTGCCGCTTCGGCGTCGTACTAGGTCTAGGGGCTTTCATCGCCTGCGTGG
CCTTCCTGCTGCTGGACGTGCGCTTTCAGCAGATCAGCAGCGTCCGAGACCGCCGTCGTGCAGT
GCTACTGGATCTGGGCTTCTCAGGGGTCTGGTCCTTCCTGTGGTTCGTAGGCTTCTGTTTCCTC
ACCAATCAGTGGCAACGTACAGCACCAGGGCCAGGCACCGCGCAGGCTGGGGATGCGGCACGTG
CCGCCATCGCTTTCAGCTTCTTCTCCATCCTCAGCTGGGTGGCGCTCACCGTGAAGGCCCTGCA
GCGGTTCCGTCTAGGCACCGATATGTCTCTCTTTGCCACAGATCAGCTAGGCCTGGGCACCTGC
CCTTCAGTTAGACATTCCCTAGGGAACTGATAGCTGGGTGCCTGGGTGCCAGGCAAGACAAGTC
TCTTACAAGGAGAGGACTAAAGGTCTCATCTGCCCAGGGTGTCACTAAAGAGAGTCGTTCCTAT
AAATGGCTTAACCTTGGCTTCCTGAACAAGTCCCTCCCCAGTCTATCCCCTTTTAAGACCCAGA
CCAGGTGTGGGTCCTTGTGCGTAGCTGACTACTCATGCATTGCTTGAAGCTGGCTTTTCATATC
AAGTCAAAACCAAACGCGTTGCCATATCTCATCCTTCCAGACAAAATGCCTCCCTGTGGAGTTG
CAGTTGAATGACAACCCCTGTACGTTGTAGCATAGACCAATTATGTGGATATTTAAGTGAATAT
GTTTACAATTTTTGTATATATGGGATCTATTCCTCTCTCTTCTGAAAGAACAATCCGTGATTGT
GTATTTTCAGTGTCCCCTGTCACAACTGCAACGTCTTTACAATAAAGACTGTAAATGCATTGAC
CAT

hide sequence

Protein Sequences


Protein RefSeqs	NP_001100455	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDM03856	(Get FASTA)	NCBI Sequence Viewer
	EDM03857	(Get FASTA)	NCBI Sequence Viewer
	EDM03858	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000017833.5
	ENSRNOP00000097621.1

RefSeq Acc Id:

NP_001100455 ⟸ NM_001106985

- UniProtKB:

A6HCV2 (UniProtKB/TrEMBL), A6HCV1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MEGASFGAGRAGAAFDPVSFAQRPQTLLRVVSWVFSIAVFGPIVNEGYVNSDSGPELRCVFNGN
AGACRFGVVLGLGAFIACVAFLLLDVRFQQISSVRDRRRAVLLDLGFSGVWSFLWFVGFCFLTN
QWQRTAPGPGTAQAGDAARAAIAFSFFSILSWVALTVKALQRFRLGTDMSLFATDQLGLGTCPS
VRHSLGN

hide sequence

RefSeq Acc Id:

ENSRNOP00000017833 ⟸ ENSRNOT00000017833

RefSeq Acc Id:

ENSRNOP00000097621 ⟸ ENSRNOT00000101849

Protein Domains

MARVEL

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4ABK1-F1-model_v2	AlphaFold	D4ABK1	1-199	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13697021

Promoter ID:

EPDNEW_R7546

Type:

single initiation site

Name:

Syngr3_1

Description:

synaptogyrin 3

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	10	14,056,139 - 14,056,199	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311801	AgrOrtholog
BioCyc Gene	G2FUF-25838	BioCyc
Ensembl Genes	ENSRNOG00000012620	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000017833.6	UniProtKB/TrEMBL
	ENSRNOT00000101849.1	UniProtKB/TrEMBL
InterPro	Marvel	UniProtKB/TrEMBL
	Synaptogyrin	UniProtKB/TrEMBL
KEGG Report	rno:302975	UniProtKB/TrEMBL
NCBI Gene	302975	ENTREZGENE
PANTHER	PTHR10838	UniProtKB/TrEMBL
	SYNAPTOGYRIN-3	UniProtKB/TrEMBL
Pfam	MARVEL	UniProtKB/TrEMBL
PhenoGen	Syngr3	PhenoGen
PIRSF	Synaptogyrin	UniProtKB/TrEMBL
PROSITE	MARVEL	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000012620	RatGTEx
UniProt	A0A8I6AUM8_RAT	UniProtKB/TrEMBL
	A6HCV1	ENTREZGENE, UniProtKB/TrEMBL
	A6HCV2	ENTREZGENE, UniProtKB/TrEMBL
	D4ABK1_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Syngr3	synaptogyrin 3	Syngr3_predicted	synaptogyrin 3 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Syngr3_predicted	synaptogyrin 3 (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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