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Gene: Scfd2 (sec1 family domain containing 2) Rattus norvegicus

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Symbol:

Scfd2

Name:

sec1 family domain containing 2

RGD ID:

1562708

Description:

Predicted to be involved in intracellular protein transport and vesicle-mediated transport. Orthologous to human SCFD2 (sec1 family domain containing 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; flutamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC498353; sec1 family domain-containing protein 2; similar to Sec1 family domain containing protein 2 (Syntaxin binding protein 1-like 1) (Neuronal Sec1)

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):	SCFD2 (sec1 family domain containing 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Scfd2 (Sec1 family domain containing 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Scfd2 (sec1 family domain containing 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SCFD2 (sec1 family domain containing 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SCFD2 (sec1 family domain containing 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Scfd2 (sec1 family domain containing 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SCFD2 (sec1 family domain containing 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SCFD2 (sec1 family domain containing 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Scfd2 (sec1 family domain containing 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Scfd2 (sec1 family domain containing 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SCFD2 (sec1 family domain containing 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Scfd2 (Sec1 family domain containing 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	scfd2 (sec1 family domain containing 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	si:ch73-249k16.4	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	scfd2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	scfd2	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	34,037,392 - 34,369,423 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	14	34,037,430 - 34,363,436 (+)	Ensembl				GRCr8
mRatBN7.2	14	33,683,348 - 34,008,232 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	33,683,273 - 34,008,213 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	14	34,030,677 - 34,357,359 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	35,338,254 - 35,664,930 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	33,823,742 - 34,150,422 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	36,216,002 - 36,543,661 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	36,216,002 - 36,543,658 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	14	36,042,335 - 36,371,468 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	14	36,058,698 - 36,386,253 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	14	32,944,697 - 33,271,610 (+)	NCBI		Celera
Cytogenetic Map	14	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autism spectrum disorder (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

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

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

7,12-dimethyltetraphene (ISO)

acetylsalicylic acid (ISO)

aflatoxin B1 (ISO)

aristolochic acid A (ISO)

arsane (ISO)

arsenic atom (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

Butylbenzyl phthalate (ISO)

cadmium dichloride (ISO)

carbamazepine (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

chlorpyrifos (ISO)

choline (ISO)

chromium(6+) (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

dexamethasone (ISO)

dioxygen (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

epoxiconazole (ISO)

ethyl methanesulfonate (ISO)

flutamide (EXP)

folic acid (ISO)

formaldehyde (ISO)

fulvestrant (ISO)

genistein (ISO)

gentamycin (EXP)

glyphosate (EXP)

GSK-J4 (ISO)

hydroquinone (ISO)

indometacin (ISO)

ivermectin (ISO)

L-methionine (ISO)

methoxychlor (EXP)

methyl methanesulfonate (ISO)

methylmercury chloride (ISO)

mono(2-ethylhexyl) phthalate (ISO)

N,N-diethyl-m-toluamide (EXP)

N-nitrosomorpholine (EXP)

O-methyleugenol (ISO)

paracetamol (EXP,ISO)

permethrin (EXP)

pinostrobin (ISO)

potassium chromate (ISO)

quercetin (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trichostatin A (ISO)

triphenyl phosphate (ISO)

triptonide (ISO)

valproic acid (ISO)

vinclozolin (EXP)

zinc atom (ISO)

zinc(0) (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

intracellular protein transport (IBA)

protein transport (IEA)

vesicle-mediated transport (IBA,IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
2.	GOA pipeline	RGD automated data pipeline
3.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
5.	Comprehensive gene review and curation	RGD comprehensive gene curation
6.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Comparative Map Data

Scfd2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	34,037,392 - 34,369,423 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	14	34,037,430 - 34,363,436 (+)	Ensembl				GRCr8
mRatBN7.2	14	33,683,348 - 34,008,232 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	33,683,273 - 34,008,213 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	14	34,030,677 - 34,357,359 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	35,338,254 - 35,664,930 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	33,823,742 - 34,150,422 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	36,216,002 - 36,543,661 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	36,216,002 - 36,543,658 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	14	36,042,335 - 36,371,468 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	14	36,058,698 - 36,386,253 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	14	32,944,697 - 33,271,610 (+)	NCBI		Celera
Cytogenetic Map	14	p11	NCBI

SCFD2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	52,872,982 - 53,366,061 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	52,872,982 - 53,366,072 (-)	Ensembl			hg38	GRCh38
GRCh37	4	53,739,149 - 54,232,228 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	53,433,906 - 53,926,999 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	4	53,580,079 - 54,073,170	NCBI
Celera	4	51,235,702 - 51,729,727 (-)	NCBI		Celera
Cytogenetic Map	4	q12	NCBI
HuRef	4	49,683,229 - 50,177,390 (-)	NCBI		HuRef
CHM1_1	4	53,775,094 - 54,267,978 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	4	56,359,861 - 56,853,303 (-)	NCBI		T2T-CHM13v2.0

Scfd2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	74,365,477 - 74,692,436 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	74,365,477 - 74,692,420 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	5	74,204,816 - 74,531,742 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	74,204,816 - 74,531,759 (-)	Ensembl			mm10	GRCm38
MGSCv37	5	74,600,841 - 74,927,774 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	5	74,738,076 - 74,813,448 (-)	NCBI		MGSCv36	mm8
Celera	5	71,468,013 - 71,796,817 (-)	NCBI		Celera
Cytogenetic Map	5	C3.3	NCBI
cM Map	5	39.44	NCBI

Scfd2
(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_004955447	17,341,813 - 17,748,522 (+)	Ensembl
ChiLan1.0	NW_004955447	17,341,990 - 17,748,735 (+)	NCBI	ChiLan1.0	ChiLan1.0

SCFD2
(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	3	76,434,638 - 76,948,776 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	4	76,639,598 - 77,153,397 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	4	70,590,252 - 71,095,567 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	4	77,144,483 - 77,649,669 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	77,144,648 - 77,614,966 (+)	Ensembl			panPan2	panpan1.1

SCFD2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	13	45,590,730 - 46,002,618 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	13	45,589,254 - 46,002,647 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	13	45,541,179 - 45,959,715 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	13	46,198,021 - 46,612,135 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	13	46,197,639 - 46,612,113 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	13	45,866,687 - 46,285,626 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	13	45,400,724 - 45,817,688 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	13	46,276,821 - 46,690,640 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Scfd2
(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_024405285	30,182,027 - 30,555,409 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936482	15,743,722 - 16,116,068 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936482	15,743,390 - 16,116,068 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SCFD2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	8	39,715,528 - 40,145,887 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	8	39,715,528 - 40,145,904 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	41,841,759 - 42,271,310 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SCFD2
(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	7	15,155,880 - 15,624,275 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	7	15,156,367 - 15,364,322 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666066	16,036,184 - 16,562,354 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Scfd2
(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_004624761	16,152,548 - 16,755,711 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624761	16,152,640 - 16,757,462 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Scfd2
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	11	30,996,644 - 31,301,710 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Scfd2
2212 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	20
Count of miRNA genes:	17
Interacting mature miRNAs:	20
Transcripts:	ENSRNOT00000038506
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
631528	Scl11	Serum cholesterol level QTL 11	4.9		blood cholesterol amount (VT:0000180)	blood total cholesterol level (CMO:0000051)	14	17875645	36079022	Rat
7411573	Bw139	Body weight QTL 139	4.7	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	14	1	40068101	Rat
9589814	Gluco67	Glucose level QTL 67	4.54	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	14	1	40068101	Rat
731183	Pia20	Pristane induced arthritis QTL 20	3.55		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	14	9393298	39411170	Rat
1300154	Bp189	Blood pressure QTL 189	3.04		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	14	31238080	72970315	Rat
70187	Pancm5	Pancreatic morphology QTL 5	16.7		pancreas mass (VT:0010144)	pancreas weight to body weight ratio (CMO:0000630)	14	30674469	85041098	Rat
2324617	Coatc2	Coat color QTL 2		0.001	coat/hair pigmentation trait (VT:0010463)	pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)	14	31121333	39507682	Rat
631523	Pia13	Pristane induced arthritis QTL 13	3.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	14	33424686	102238540	Rat
1358296	Ael3	Aortic elastin QTL 3	3.7	0.00051	aorta elastin amount (VT:0003905)	aortic elastin	14	8621398	53621398	Rat
61420	Pia6	Pristane induced arthritis QTL 6	4.9		joint integrity trait (VT:0010548)	arthritic paw count (CMO:0001460)	14	18915454	42433608	Rat
7387267	Uae42	Urinary albumin excretion QTL 42		0.61	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	14	22521517	67521517	Rat
631839	Niddm37	Non-insulin dependent diabetes mellitus QTL 37	3.37		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	14	11334716	100078267	Rat
2313397	Coatc1	Coat color QTL1			coat/hair pigmentation trait (VT:0010463)	coat/hair color measurement (CMO:0001808)	14	18895192	63895192	Rat
631262	Tcas4	Tongue tumor susceptibility QTL 4	7.29		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	14	17906726	54251504	Rat
634352	Apr6	Acute phase response QTL 6	3.7		blood interleukin-6 amount (VT:0008595)	plasma interleukin-6 level (CMO:0001927)	14	1	41415516	Rat
2302045	Pia39	Pristane induced arthritis QTL 39	4.9	0.001	blood immunoglobulin amount (VT:0002460)	serum immunoglobulin G2a level (CMO:0002116)	14	8621398	53621398	Rat

Markers in Region

D14Got42

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	14	34,332,652 - 34,332,900 (+)	Marker Load Pipeline
mRatBN7.2	14	33,978,545 - 33,978,795 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	36,514,386 - 36,514,633	NCBI	Rnor6.0
Rnor_5.0	14	36,341,735 - 36,341,982	UniSTS	Rnor5.0
RGSC_v3.4	14	36,355,891 - 36,356,139	RGD	RGSC3.4
RGSC_v3.4	14	36,355,892 - 36,356,139	UniSTS	RGSC3.4
Celera	14	33,241,941 - 33,242,188	UniSTS
RGSC_v3.1	14	36,358,326 - 36,358,574	RGD
RH 2.0 Map	14	407.2	RGD
Cytogenetic Map	14	p11	UniSTS

BI289920

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	33,942,977 - 33,943,081 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	36,478,750 - 36,478,853	NCBI	Rnor6.0
Rnor_5.0	14	36,306,379 - 36,306,482	UniSTS	Rnor5.0
RGSC_v3.4	14	36,319,716 - 36,319,819	UniSTS	RGSC3.4
Celera	14	33,206,369 - 33,206,472	UniSTS
RH 3.4 Map	14	433.19	UniSTS
Cytogenetic Map	14	p11	UniSTS

UniSTS:142632

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	33,774,497 - 33,775,914 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	36,307,157 - 36,308,573	NCBI	Rnor6.0
Rnor_5.0	14	36,132,919 - 36,134,335	UniSTS	Rnor5.0
RGSC_v3.4	14	36,149,853 - 36,151,269	UniSTS	RGSC3.4
Celera	14	33,037,631 - 33,039,047	UniSTS
Cytogenetic Map	14	p11	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	164	91	90	59	90	59	6	354	190	11	143	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001017499	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_010057401	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC099101	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC114452	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AC128952	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC085889	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473981	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000038506 ⟹ ENSRNOP00000037023

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	14	34,037,430 - 34,335,586 (+)	Ensembl
mRatBN7.2 Ensembl	14	33,683,273 - 34,008,213 (+)	Ensembl
Rnor_6.0 Ensembl	14	36,216,002 - 36,543,658 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000108929 ⟹ ENSRNOP00000084656

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	14	34,037,430 - 34,362,121 (+)	Ensembl
mRatBN7.2 Ensembl	14	33,683,273 - 34,008,016 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000157348 ⟹ ENSRNOP00000101405

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	14	34,037,430 - 34,363,436 (+)	Ensembl

RefSeq Acc Id:

NM_001017499 ⟹ NP_001017499

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	34,037,479 - 34,362,337 (+)	NCBI
mRatBN7.2	14	33,683,348 - 34,008,232 (+)	NCBI
Rnor_6.0	14	36,216,002 - 36,543,661 (+)	NCBI
Rnor_5.0	14	36,042,335 - 36,371,468 (+)	NCBI
RGSC_v3.4	14	36,058,698 - 36,386,253 (+)	RGD
Celera	14	32,944,697 - 33,271,610 (+)	RGD

Sequence:

show sequence

TGCGTTCTGACCGAGGTTCCTGCGCATCCGCCGGTGAGACTCCTGGCCAGACTGCGCCTACCGA
ATCATGAGTGCCGTGGGCGTACTGTCTTTTGCCCAGCAAGGCTGGGAGCAGGTGCTGGCCAAAG
TGAAGTGGTCCGTGGTCTACCTGGACGCTGCCTGCGCGGAGAGCCTGCACTGGAGCTGCGGTTC
AAGCAGGCTTCTGGAGGCGGTGAAGGGTCCTGCGTGCAACCTGAGGGAATTTGAACCCCATGCA
ATAGGCGGTGGGGCCAAGCAGCCCCGGGCGGTGTTCGTTTTGAGCAGCCTGCTGAAAGGCCGCA
TAGTAGACACTCTACAAGACATCATTTGCCGCAGTCACTTTCAGCACTGTGTGGTGGTCACAGC
CGTGAGCCACCCAGTCCACCTCACTGCTAACCATGTACCAGCAGCTGCAGCGGCCGAGCTAGAG
GGGCAGCAGCCGGTGTTCGAACAGCTGGAGGAGAAGCTCTGTGAGTGGATGGGCAACATGAACT
ACACAGCTGAGGTGCTCCACGTCCCGTTGTTGCTCGCCCCTGCTGCTCCCCACCTTGCCTTTAC
TCCAGCCTTTGCTACCCTTTTCCCACTGCTACCTCAGGATGTGCATGTTCTTAATAATGCCAGA
CCCGACAAGAGGAGACTGAACAGCTTGGGTGAGGTGGATGCCACTGCCCTAACCCCAGAGCTGC
TGCTGTACATTAGATGCCTCGTGTCAGGCCTCAGTTCTCTGTGTGAACATCTAGGGGTACGAGA
GGAGTGTTTCGCTGTGGGTTCCCTCAGTCGGGTCATCGCTACAGATCTGGCAAATTATGCCCCT
GCCAAGAACAGGAGAAAGACTGCTACAGGCAGGGCTTCCGTGGTCTTTGTGGATAGAACTCTGG
ATCTCACGGGAGCGGTTGGACACCATGGAGACAACTTAGTAGAGAAGATCATTTCAGCACTTCC
ACAGCTTCCGGGCCACACCAACGACGTGATGGTCAACATGGCAGAGCTCACGGCTGTCCAGGCT
GTGGAGGAAAACCAGACCGTGATTGCACCAGGCTGCCTTGCGCCATCCAATGATGCCTCAGCCA
AGGCCCTCTGGGAAGCCTTACTGAACACCAAGCACAAAGAGGCGGTGATGGAAGTCCGGAGACA
TCTAGTGGAAGCAGCCAGCAGAGAGAACCTGCCCATCAAGATGAGTATGGGGAGAGTCACTCCA
GGGCAGCTCATGTCCTATATTCAGCTCTTCAAGAACAACCTCAGAGCTCTTACAAATCATTGTG
GGCTTCTACAGCTAGGGATGGCCACAGTTCAAACTCTGAAGCACCCACAGACTGCCAAGTGGGA
TAACTTCCTGGCATTTGAAAGGCTTCTTCTACAGAGTCTTGGGGATTCAACCATGGCTGGTGTG
CTAAATCAGCTGCTACCCTTGATTAAGTCCTCAAGCCAGAGAACCAGGGACGACTACAGCCCCG
AGGAGCTGCTAATCCTCCTCATATACATCTACTCGGTCACTGGGGAATGCACGCGGGACACAGA
CCTGGGAGACGTGGAAGAGAAGGTGAGGAGAGCACTGGCCAGTGTCTTCTCTGAGGAGTCTGAG
CTGTCCCCTTTGCTGCAGAAGATCACAGGCTGTGACTCTGCAATCGACCTGACATTGCCCAAAT
CCCAAACTGCTGTGAATGATGTCTTCACGGCTCTCCGGGAGATCGCTGGAGCTAGGAATCTCCT
GAGACAGTTCAAATCGGTGTATGTTCCTGGAAATAGTACCCATCAGGCAGCCTATAAGCCACTG
TTGAAGCAGGTTGTGGAAGAAATATTTAATCCTGAGAAGCCAGATCCCATTGACATTGAACATA
TGTCCTCAGGCCTCACTGATCTCCTTAAAACTGGATTCAGCATGTTCATGAAGGTGAGCCGGCC
CCATCCCAGTGACCATCCCCTCTTGATCCTCTTTGTGGTGGGCGGCGTCACAGTTGCTGAAGCC
AAAATGGTCAAAGACCTTGTAGCATCTCTGAAGCCAGGAACCCAGGTGATGGTGCTGTCCACAA
GACTCCTGAAGCCACTTAACATTCCTGAGCTGCTCTTTGCAACTGACCGGCTACACCCAGACCT
TGGCTTCTGACATCTAAGAGAAGATTAGACCTGTTTGAGCTGGAAATACCAATACCCATTGGTC
ACCGCTCCAGATATGCCTCCAAAGGCTGTGTCCCGGTTACTAATTATAGGTATGACTTAATTCT
ACCAGAGATCTGCATAACTGCATGGAAGGCAGTTTGTTTGGACTGCTCCCGTTCTTCAAAAGCA
AAATAAAGACTTGTGTTCTCATTCTTCTTCTAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XR_010057401

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	34,037,392 - 34,369,423 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001017499	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH85889	(Get FASTA)	NCBI Sequence Viewer
	EDL89941	(Get FASTA)	NCBI Sequence Viewer
	EDL89942	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000037023.4
	ENSRNOP00000084656.1
	ENSRNOP00000101405
	ENSRNOP00000101405.1

RefSeq Acc Id:

NP_001017499 ⟸ NM_001017499

- UniProtKB:

Q5U2R9 (UniProtKB/TrEMBL), A0A8I6A025 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSAVGVLSFAQQGWEQVLAKVKWSVVYLDAACAESLHWSCGSSRLLEAVKGPACNLREFEPHAI
GGGAKQPRAVFVLSSLLKGRIVDTLQDIICRSHFQHCVVVTAVSHPVHLTANHVPAAAAAELEG
QQPVFEQLEEKLCEWMGNMNYTAEVLHVPLLLAPAAPHLAFTPAFATLFPLLPQDVHVLNNARP
DKRRLNSLGEVDATALTPELLLYIRCLVSGLSSLCEHLGVREECFAVGSLSRVIATDLANYAPA
KNRRKTATGRASVVFVDRTLDLTGAVGHHGDNLVEKIISALPQLPGHTNDVMVNMAELTAVQAV
EENQTVIAPGCLAPSNDASAKALWEALLNTKHKEAVMEVRRHLVEAASRENLPIKMSMGRVTPG
QLMSYIQLFKNNLRALTNHCGLLQLGMATVQTLKHPQTAKWDNFLAFERLLLQSLGDSTMAGVL
NQLLPLIKSSSQRTRDDYSPEELLILLIYIYSVTGECTRDTDLGDVEEKVRRALASVFSEESEL
SPLLQKITGCDSAIDLTLPKSQTAVNDVFTALREIAGARNLLRQFKSVYVPGNSTHQAAYKPLL
KQVVEEIFNPEKPDPIDIEHMSSGLTDLLKTGFSMFMKVSRPHPSDHPLLILFVVGGVTVAEAK
MVKDLVASLKPGTQVMVLSTRLLKPLNIPELLFATDRLHPDLGF

hide sequence

Ensembl Acc Id:

ENSRNOP00000037023 ⟸ ENSRNOT00000038506

Ensembl Acc Id:

ENSRNOP00000084656 ⟸ ENSRNOT00000108929

Ensembl Acc Id:

ENSRNOP00000101405 ⟸ ENSRNOT00000157348

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5U2R9-F1-model_v2	AlphaFold	Q5U2R9	1-684	view protein structure

Transcriptome

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

Promoters

RGD ID:

13699286

Promoter ID:

EPDNEW_R9811

Type:

multiple initiation site

Name:

Scfd2_1

Description:

sec1 family domain containing 2

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	14	36,215,987 - 36,216,047	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1562708	AgrOrtholog
BioCyc Gene	G2FUF-15915	BioCyc
Ensembl Genes	ENSRNOG00000026828	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000038506.5	UniProtKB/TrEMBL
	ENSRNOT00000108929.2	UniProtKB/TrEMBL
	ENSRNOT00000157348	ENTREZGENE
	ENSRNOT00000157348.1	UniProtKB/TrEMBL
Gene3D-CATH	3.40.50.1910	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7192440	IMAGE-MGC_LOAD
InterPro	Sec-1-like_dom2	UniProtKB/TrEMBL
	Sec1-like	UniProtKB/TrEMBL
	Sec1-like_sf	UniProtKB/TrEMBL
KEGG Report	rno:498353	UniProtKB/TrEMBL
MGC_CLONE	MGC:94680	IMAGE-MGC_LOAD
NCBI Gene	498353	ENTREZGENE
PANTHER	Sec1-like	UniProtKB/TrEMBL
Pfam	Sec1	UniProtKB/TrEMBL
PhenoGen	Scfd2	PhenoGen
RatGTEx	ENSRNOG00000026828	RatGTEx
Superfamily-SCOP	Sec1-like	UniProtKB/TrEMBL
UniProt	A0A8I6A025	ENTREZGENE, UniProtKB/TrEMBL
	F7ENF3_RAT	UniProtKB/TrEMBL
	Q5U2R9	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2009-08-12	Scfd2	sec1 family domain containing 2	LOC498353	similar to Sec1 family domain containing protein 2 (Syntaxin binding protein 1-like 1) (Neuronal Sec1)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-02-09	LOC498353	similar to Sec1 family domain containing protein 2 (Syntaxin binding protein 1-like 1) (Neuronal Sec1)			Symbol and Name status set to provisional	70820	PROVISIONAL

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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