Scg5 (secretogranin V) - Rat Genome Database

Name: Scg5
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Scg5 (secretogranin V) Rattus norvegicus

Analyze

Symbol:

Scg5

Name:

secretogranin V

RGD ID:

3669

Description:

Predicted to enable enzyme inhibitor activity and unfolded protein binding activity. Predicted to be involved in intracellular protein transport; peptide hormone processing; and regulation of hormone secretion. Predicted to be located in secretory granule. Predicted to be active in nucleus. Orthologous to human SCG5 (secretogranin V); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,4-methylenedioxymethamphetamine.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

7B2; neuroendocrine protein 7B2; secretogranin V (7B2 protein); secretogranin-5; secretory granule endocrine protein I; secretory granule neuroendocrine protein 1; Secretory granule neuroendocrine protein 1 (7B2 protein); Secretory granule neuroendocrine, protein 1 (7B2 protein); Sgne1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

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):	SCG5 (secretogranin V)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Scg5 (secretogranin V)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Scg5 (secretogranin V)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SCG5 (secretogranin V)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SCG5 (secretogranin V)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Scg5 (secretogranin V)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SCG5 (secretogranin V)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SCG5 (secretogranin V)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Scg5 (secretogranin V)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SCG5 (secretogranin V)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Scg5 (secretogranin V)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	scg5 (secretogranin V)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	7B2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)
Caenorhabditis elegans (roundworm):	sbt-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	scg5	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|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
mRatBN7.2	3	100,544,101 - 100,588,558 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	100,544,099 - 100,588,463 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	104,171,047 - 104,215,378 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	3	112,770,077 - 112,814,414 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	3	110,459,966 - 110,504,303 (-)	NCBI	Rnor_WKY
Rnor_6.0	3	105,235,065 - 105,279,475 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	105,235,050 - 105,279,462 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	111,811,718 - 111,856,212 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	99,629,194 - 99,674,523 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	99,525,619 - 99,570,949 (-)	NCBI
Celera	3	99,515,552 - 99,558,902 (-)	NCBI		Celera
RH 3.4 Map	3	840.41	RGD
Cytogenetic Map	3	q35	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Bloom syndrome (ISO)

colorectal cancer (ISO)

Colorectal Neoplasms (ISO)

genetic disease (ISO)

hereditary mixed polyposis syndrome (ISO)

hereditary mixed polyposis syndrome 1 (ISO)

medulloblastoma (ISO)

pituitary-dependent Cushing's disease (ISS)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

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

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

2,4-dibromophenyl 2,4,5-tribromophenyl ether (ISO)

3,3',4,4',5-pentachlorobiphenyl (ISO)

3,4-dichloroaniline (ISO)

3,4-methylenedioxymethamphetamine (EXP)

3,7-dihydropurine-6-thione (EXP)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (EXP)

5-aza-2'-deoxycytidine (ISO)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP)

bisphenol F (EXP)

buta-1,3-diene (ISO)

butanal (ISO)

cadmium dichloride (ISO)

carbamazepine (ISO)

chlordecone (ISO)

chloropicrin (ISO)

cisplatin (ISO)

copper atom (ISO)

copper(0) (ISO)

cyclosporin A (ISO)

dibutyl phthalate (EXP)

diuron (ISO)

ethanol (ISO)

fenvalerate (EXP)

folic acid (ISO)

formaldehyde (EXP,ISO)

furan (EXP)

hydroquinone (ISO)

mercaptopurine (EXP)

methylisothiazolinone (ISO)

mitomycin C (ISO)

monosodium L-glutamate (ISO)

paclitaxel (EXP,ISO)

paracetamol (EXP,ISO)

PD 0325901 (ISO)

perfluorononanoic acid (ISO)

pirinixic acid (ISO)

purine-6-thiol (EXP)

quercetin (ISO)

silicon dioxide (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

Soman (EXP)

sunitinib (ISO)

tamoxifen (ISO)

taurine (ISO)

temozolomide (ISO)

tert-butyl hydroperoxide (ISO)

urethane (ISO)

valproic acid (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

intracellular protein transport (IEA,ISO,ISS)

neuropeptide signaling pathway (IEA)

peptide hormone processing (IEA,ISO,ISS)

regulation of hormone secretion (IBA,IEA,ISO,ISS)

Cellular Component

extracellular region (IEA)

nucleus (IEA,ISO)

secretory granule (IEA,ISO,ISS)

Molecular Function

enzyme inhibitor activity (IEA,ISO,ISS)

enzyme regulator activity (IBA)

protein binding (IPI,ISO)

unfolded protein binding (IEA,ISO,ISS)

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.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence.	Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
4.	Neuroendocrine protein 7B2 can be inactivated by phosphorylation within the secretory pathway.	Lee SN, etal., J Biol Chem. 2006 Feb 10;281(6):3312-20. Epub 2005 Nov 14.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	GOA pipeline	RGD automated data pipeline
8.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
10.	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.
11.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
12.	Cloning and characterization of the rat complementary deoxyribonucleic acid and gene encoding the neuroendocrine peptide 7B2.	Waldbieser GC, etal., Endocrinology 1991 Jun;128(6):3228-36.

Additional References at PubMed

PMID:6514132	PMID:7913882	PMID:8016065	PMID:9348280	PMID:10089884	PMID:11439082	PMID:15489334	PMID:21805245	PMID:25002582	PMID:27914912

Genomics

Comparative Map Data

Scg5
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	100,544,101 - 100,588,558 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	100,544,099 - 100,588,463 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	104,171,047 - 104,215,378 (-)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	3	112,770,077 - 112,814,414 (-)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	3	110,459,966 - 110,504,303 (-)	NCBI	Rnor_WKY
Rnor_6.0	3	105,235,065 - 105,279,475 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	105,235,050 - 105,279,462 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	111,811,718 - 111,856,212 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	99,629,194 - 99,674,523 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	99,525,619 - 99,570,949 (-)	NCBI
Celera	3	99,515,552 - 99,558,902 (-)	NCBI		Celera
RH 3.4 Map	3	840.41	RGD
Cytogenetic Map	3	q35	NCBI

SCG5
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	15	32,641,710 - 32,697,092 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	15	32,641,676 - 32,697,098 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	15	32,933,911 - 32,989,293 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	15	30,721,252 - 30,776,590 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	15	30,721,251 - 30,776,590	NCBI
Celera	15	9,735,550 - 9,791,154 (+)	NCBI		Celera
Cytogenetic Map	15	q13.3	NCBI
HuRef	15	9,796,189 - 9,851,652 (+)	NCBI		HuRef
CHM1_1	15	33,051,914 - 33,107,353 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	15	30,438,200 - 30,493,619 (+)	NCBI		T2T-CHM13v2.0

Scg5
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	113,606,658 - 113,659,436 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	113,606,707 - 113,659,466 (-)	Ensembl		GRCm39 Ensembl
GRCm38	2	113,776,313 - 113,829,091 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	113,776,362 - 113,829,121 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	113,616,470 - 113,669,248 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	113,577,206 - 113,629,965 (-)	NCBI		MGSCv36	mm8
Celera	2	114,909,627 - 114,958,933 (-)	NCBI		Celera
Cytogenetic Map	2	E4	NCBI
cM Map	2	57.45	NCBI

Scg5
(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_004955416	1,866,997 - 1,914,640 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955416	1,867,848 - 1,914,505 (-)	NCBI	ChiLan1.0	ChiLan1.0

SCG5
(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	15	26,131,284 - 26,187,027 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	15	11,136,920 - 11,192,606 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	15	29,974,633 - 30,030,291 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	15	29,974,633 - 30,030,291 (+)	Ensembl	panpan1.1		panPan2

SCG5
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	30	2,261,144 - 2,315,315 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	30	2,261,189 - 2,315,213 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	30	2,310,629 - 2,364,774 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	30	2,373,662 - 2,427,835 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	30	2,373,665 - 2,427,885 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	30	2,310,404 - 2,364,530 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	30	2,409,276 - 2,463,487 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	30	2,537,616 - 2,591,809 (-)	NCBI		UU_Cfam_GSD_1.0

Scg5
(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_024408640	80,784,633 - 80,839,707 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936673	1,311,861 - 1,367,237 (+)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936673	1,312,183 - 1,367,205 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SCG5
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	136,525,944 - 136,593,583 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	136,525,920 - 136,590,021 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	152,695,828 - 152,711,796 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SCG5
(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	26	50,182,966 - 50,243,284 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	26	50,189,473 - 50,243,282 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666048	90,640,439 - 90,694,840 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Scg5
(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 1.0	NW_004624804	1,660,371 - 1,711,169 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Scg5
120 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	67
Count of miRNA genes:	50
Interacting mature miRNAs:	60
Transcripts:	ENSRNOT00000010679
Prediction methods:	Miranda, 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
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
737818	Hcar12	Hepatocarcinoma resistance QTL 12	2.6		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	3	29463235	118376539	Rat
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	31172320	163586636	Rat
1354604	Bw36	Body weight QTL 36	2.9		body mass (VT:0001259)	body weight (CMO:0000012)	3	33703347	104104347	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	38192233	133483320	Rat
1354597	Kidm13	Kidney mass QTL 13	2.9		kidney mass (VT:0002707)	right kidney wet weight (CMO:0000082)	3	41874578	104104347	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	41874578	155617519	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	41874578	155617519	Rat
1581503	Cm58	Cardiac mass QTL 58	2.7	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	43827364	121056321	Rat
1559282	Emca5	Estrogen-induced mammary cancer QTL 5	3.9		mammary gland integrity trait (VT:0010552)	percentage of study population developing mammary tumors during a period of time (CMO:0000948)	3	43827364	169034231	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	47233211	147415807	Rat
1358186	Ept2	Estrogen-induced pituitary tumorigenesis QTL 2	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
2292613	Ept16	Estrogen-induced pituitary tumorigenesis QTL 16	8.3		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	3	47233430	110362260	Rat
631665	Bw8	Body weight QTL 8	5.5		body mass (VT:0001259)	body weight (CMO:0000012)	3	50437042	119183768	Rat
724523	Tsu1	Thymus enlargement suppressive QTL 1	3.84		thymus mass (VT:0004954)	thymus weight to body weight ratio (CMO:0000612)	3	50437504	115638231	Rat
1582218	Bw74	Body weight QTL 74	3.9	0.0021	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582238	Bw68	Body weight QTL 68	3.2	0.0064	body mass (VT:0001259)	body weight (CMO:0000012)	3	53184593	115665732	Rat
1582239	Epfw1	Epididymal fat weight QTL 1	4.5	0.0006	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	3	53184593	115665732	Rat
1581568	Rf53	Renal function QTL 53			urine total protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	56395968	161299569	Rat
8662816	Vetf4	Vascular elastic tissue fragility QTL 4	4		renal artery integrity trait (VT:0010642)	number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)	3	59242096	157323038	Rat
1300111	Rf12	Renal function QTL 12	3.78		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	61017749	121056321	Rat
1582210	Bw71	Body weight QTL 71	3.3	0.0012	body mass (VT:0001259)	body weight (CMO:0000012)	3	64655305	115665732	Rat
1582221	Kidm30	Kidney mass QTL 30	3.5	0.0008	kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	3	64655305	115665732	Rat
12879848	Bw181	Body weght QTL 181		0.015	body mass (VT:0001259)	body weight (CMO:0000012)	3	70348525	121056321	Rat
2301414	Kidm37	Kidney mass QTL 37		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	70653097	121056321	Rat
1600376	Arunc5	Aerobic running capacity QTL 5		0.21	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	73376539	118376539	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	urine total protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	78196190	146592722	Rat
2302273	Gluco35	Glucose level QTL 35	5.3	0.001	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	80800231	114297550	Rat
631649	Bp123	Blood pressure QTL 123	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	89772419	134772419	Rat
8694437	Bw167	Body weight QTL 167	22.46	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	3	91797474	136797474	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	94856903	159898684	Rat
724532	Cm17	Cardiac mass QTL 17	2		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	3	95735366	140735366	Rat
1582252	Sual1	Serum uric acid level QTL 1	3.4	0.0123	blood uric acid amount (VT:0010302)	blood uric acid level (CMO:0000501)	3	96127817	102200699	Rat
1582219	Bw63	Body weight QTL 63	3.8	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	3	96127817	115665732	Rat
1354611	Despr2	Despair related QTL 2	3.03	0.0028	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	3	97084464	142084464	Rat
2293087	Iddm27	Insulin dependent diabetes mellitus QTL 27	2.68		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	97551417	147415807	Rat
2312659	Slep7	Serum leptin concentration QTL 7		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	3	98535255	168026850	Rat
2312670	Bw94	Body weight QTL 94		0.01	inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	3	98535255	168026850	Rat
2312673	Scl63	Serum cholesterol level QTL 63		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	98535255	168026850	Rat
2302373	Gluco39	Glucose level QTL 39	5.01		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	3	98535386	161695835	Rat

Markers in Region

RH94440

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	100,544,122 - 100,544,280 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	105,235,087 - 105,235,244	NCBI	Rnor6.0
Rnor_5.0	3	111,811,743 - 111,811,900	UniSTS	Rnor5.0
RGSC_v3.4	3	99,629,212 - 99,629,369	UniSTS	RGSC3.4
Celera	3	99,515,570 - 99,515,727	UniSTS
RH 3.4 Map	3	840.41	UniSTS
Cytogenetic Map	3	q34	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			7						68		1
Low	3	31	19	10	18	10	3	3	6	35	36	11	3
Below cutoff		12	30	30	1	30	5	7			3		5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_013175	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006234701	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC061560	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212495	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213081	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213100	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213673	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	M63901	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000010679 ⟹ ENSRNOP00000010679

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	100,544,099 - 100,588,463 (-)	Ensembl
Rnor_6.0 Ensembl	3	105,235,050 - 105,279,462 (-)	Ensembl

RefSeq Acc Id:

NM_013175 ⟹ NP_037307

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	100,544,105 - 100,588,437 (-)	NCBI
Rnor_6.0	3	105,235,069 - 105,279,399 (-)	NCBI
Rnor_5.0	3	111,811,718 - 111,856,212 (-)	NCBI
RGSC_v3.4	3	99,629,194 - 99,674,523 (-)	RGD
Celera	3	99,515,552 - 99,558,902 (-)	RGD

Sequence:

show sequence

AGATTGCTAGACGCTCGCCCGCGGCCACACGGTTAAAAATGACCTCAAGGATGGCCATACTATC
TGGTCTTTTGTTTTGGCTGCTGCTTGAGTGGAATCCAGCATTCGCTTATAGTCCACGGACTCCT
GACCGGGTCTCAGAGACAGACATCCAGAGGCTGCTGCATGGAGTCATGGAGCAGCTGGGCATTG
CCAGGCCACGTGTGGAGTACCCAGCCCACCAGGCCATGAATCTTGTTGGGCCGCAGAGCATCGA
AGGGGGAGCTCACGAGGGTCTTCAGCATCTGGGTCCTTTCGGCAACATCCCCAACATCGTGGCA
GAGTTGACTGGCGACAATATTCCTAAGGACTTCAGTGAGGACCAAGGCTACCCAGACCCTCCAA
ATCCCTGTCCTCTTGGGAAAACTGCAGATGACGGATGTCTAGAAAACGCCCCTGACACTGCAGA
GTTCAGCCGAGAATTCCAGTTAGACCAGCACCTTTTTGATCCAGAACATGACTACCCAGGTTTG
GGCAAGTGGAACAAGAAACTCCTTTATGAGAAGATGAAGGGAGGACAGAGGCGGAAGCGGAGGA
GTGTCAATCCCTATCTACAAGGAAAGAGGCTGGACAATGTTGTGGCAAAGAAATCTGTCCCCCA
CTTCTCAGAAGAGGAGAAGGAGCCAGAATAAAGAGAAGACAGTAGGTGGAAACCCATACAATGC
TTATGTATGTGCATGTTAGCAGAGCCCGTGAGTGACAGCATGCATTTTACATATTTATGGATGA
AAAACAGCTGTCCTTGTCTCCATAGCAATGCCTGAGCTTTCTGCTAAATTAGAATAAAAGCTCC
TTTCCTTTTGGGGATTTTTTGATGTGGATCTGCAAGAAACATTACAATTAAAATGTATATGTCA
AGTATAATAAAAACACGGATATGAAATACTCTGATTTCTTGCCGTTTTGGGTTGTGCTGTTTGG
GCCAAGTCTGTAAAAAGCTAGCATTTGATTTTGATTATGTAGTGTATCTAGCCCTTGGGCCTTG
TTACACACCAATAAAGAAGTTTGTACTCAAGGGGAGGGGCTGACACATCTCACTCTGCTGCTTC
TTAATAAATGTATGTGCAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_006234701 ⟹ XP_006234763

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	100,544,101 - 100,588,558 (-)	NCBI
Rnor_6.0	3	105,235,065 - 105,279,475 (-)	NCBI
Rnor_5.0	3	111,811,718 - 111,856,212 (-)	NCBI

Sequence:

show sequence

GGGGCCTGGGTGGAGCTTGGTTGCGGAGGGAGGTGACGCAGGAGCTATCCAGCACGTCAGCTCC
CTGTTTTGGCCCAGATTGCTAGACGCCCGCCCGCGGCCACACGGTTAAAAATGACCTCAAGGAT
GGTCATACTATCTGGTCTTTTGTTTTGGCTGCTGCTTGAGTGGAATCCAGCATTCGCTTATAGT
CCACGGACTCCTGACCGGGTCTCAGAGACAGACATCCAGAGGCTGCTGCATGGAGTCATGGAGC
AGCTGGGCATTGCCAGGCCACGTGTGGAGTACCCAGCCCACCAGGCCATGAATCTTGTTGGGCC
GCAGAGCATCGAAGGGGGAGCTCACGAGGGTCTTCAGCATCTGGGTCCTTTCGGCAACATCCCC
AACATCGTGGCAGAGTTGACTGGCGACAATATTCCTAAGGACTTCAGTGAGGACCAAGGCTACC
CAGACCCTCCAAATCCCTGTCCTCTTGGGAAAACTGATGACGGATGTCTAGAAAACGCCCCTGA
CACTGCAGAGTTCAGCCGAGAATTCCAGTTAGACCAGCACCTTTTTGATCCAGAACATGACTAC
CCAGGTTTGGGCAAGTGGAACAAGAAACTCCTTTATGAGAAGATGAAGGGAGGACAGAGGCGGA
AGCGGAGGAGTGTCAATCCCTATCTACAAGGAAAGAGGCTGGACAATGTTGTGGCAAAGAAATC
TGTCCCCCACTTCTCAGAAGAGGAGAAGGAGCCAGAATAAAGAGAAGACAGTAGGTGGAAACCC
ATACAATGCTTATGTATGTGCATGTTAGCAGAGCCCGTGAGTGACAGCATGCATTTTACATATT
TATGGATGAAAAACAGCTGTCCTTGTCTCCATAGCAATGCCTGAGCTTTCTGCTAAATTAGAAT
AAAAGCTCCTTTCCTTTTGGGGATTTTTTGATGTGGATCTGCAAGAAACATTACAATTAAAATG
TATATGTCAAGTATAATAAAAACACGGATATGAAATACTCTGATTTCTTGCCGTTTTGGGTTGT
GCTGTTTGGGCCAAGTCTGTAAAAAGCTAGCATTTGATTTTGATTATGTAGTGTATCTAGCCCT
TGGGCCTTGTTACACACCAATAAAGAAGTTTGTACTCAAGGGGAGGGGCTGACACATCTCACTC
TGCTGCTTCTTAATAAATGTATGTGCAAGCAT

hide sequence

Protein Sequences


Protein RefSeqs	NP_037307	(Get FASTA)	NCBI Sequence Viewer
	XP_006234763	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA40626	(Get FASTA)	NCBI Sequence Viewer
	AAH61560	(Get FASTA)	NCBI Sequence Viewer
	EDL79818	(Get FASTA)	NCBI Sequence Viewer
	P27682	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_037307 ⟸ NM_013175
- Peptide Label:	precursor
- UniProtKB:	G3V714 (UniProtKB/TrEMBL)
- Sequence:	show sequence MTSRMAILSGLLFWLLLEWNPAFAYSPRTPDRVSETDIQRLLHGVMEQLGIARPRVEYPAHQAM NLVGPQSIEGGAHEGLQHLGPFGNIPNIVAELTGDNIPKDFSEDQGYPDPPNPCPLGKTADDGC LENAPDTAEFSREFQLDQHLFDPEHDYPGLGKWNKKLLYEKMKGGQRRKRRSVNPYLQGKRLDN VVAKKSVPHFSEEEKEPE hide sequence

RefSeq Acc Id:

XP_006234763 ⟸ XM_006234701

- Peptide Label:

isoform X1

- Sequence:

show sequence

MTSRMVILSGLLFWLLLEWNPAFAYSPRTPDRVSETDIQRLLHGVMEQLGIARPRVEYPAHQAM
NLVGPQSIEGGAHEGLQHLGPFGNIPNIVAELTGDNIPKDFSEDQGYPDPPNPCPLGKTDDGCL
ENAPDTAEFSREFQLDQHLFDPEHDYPGLGKWNKKLLYEKMKGGQRRKRRSVNPYLQGKRLDNV
VAKKSVPHFSEEEKEPE

hide sequence

RefSeq Acc Id:

ENSRNOP00000010679 ⟸ ENSRNOT00000010679

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P27682-F1-model_v2	AlphaFold	P27682	1-210	view protein structure

Transcriptome

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

Promoters

RGD ID:

13692296

Promoter ID:

EPDNEW_R2821

Type:

multiple initiation site

Name:

Scg5_1

Description:

secretogranin V

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	3	105,279,399 - 105,279,459	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3669	AgrOrtholog
BioCyc Gene	G2FUF-48360	BioCyc
Ensembl Genes	ENSRNOG00000007542	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000010679	ENTREZGENE
	ENSRNOP00000010679.5	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000010679	ENTREZGENE
	ENSRNOT00000010679.7	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:6918342	IMAGE-MGC_LOAD
InterPro	Secretogranin_V	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:25719	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:72901	IMAGE-MGC_LOAD
NCBI Gene	25719	ENTREZGENE
PANTHER	NEUROENDOCRINE PROTEIN 7B2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR12738	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Secretogranin_V	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Scg5	PhenoGen
TIGR	TC228445
UniProt	7B2_RAT	UniProtKB/Swiss-Prot
	G3V714	ENTREZGENE, UniProtKB/TrEMBL
	P27682	ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-03-26	Scg5	secretogranin V	Scg5	secretogranin V (7B2 protein)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2012-02-02	Scg5	secretogranin V (7B2 protein)	Scg5	secretogranin V	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-02-12	Scg5	secretogranin V	Sgne1	secretory granule neuroendocrine protein 1	Symbol and Name updated to reflect Human and Mouse nomenclature	1299863	APPROVED
2002-06-10	Sgne1	Secretory granule neuroendocrine, protein 1 (7B2 protein)			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_expression	expressed in the pituitary and in brain	729678

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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