Srm (spermidine synthase) - Rat Genome Database

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

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Gene: Srm (spermidine synthase) Rattus norvegicus

Analyze

Symbol:

Srm

Name:

spermidine synthase

RGD ID:

620796

Description:

Enables spermidine synthase activity. Involved in spermidine biosynthetic process. Predicted to be active in cytosol. Orthologous to human SRM (spermidine synthase); PARTICIPATES IN spermidine metabolic pathway; glycine N-methyltransferase deficiency pathway; homocystinuria pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC100912604; LOC689673; similar to Spermidine synthase (Putrescine aminopropyltransferase) (SPDSY); spermidine synthase-like

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):	SRM (spermidine synthase)	HGNC	Ensembl, HomoloGene, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Srm (spermidine synthase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Srm (spermidine synthase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SRM (spermidine synthase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SRM (spermidine synthase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Srm (spermidine synthase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SRM (spermidine synthase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SRM (spermidine synthase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Srm (spermidine synthase)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SRM (spermidine synthase)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Srm (spermidine synthase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	srm (spermidine synthase)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	SpdS	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SPE3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	spds-1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

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	5	159,025,919 - 159,029,076 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	159,025,873 - 159,029,405 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	161,742,582 - 161,745,783 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	5	163,565,057 - 163,568,258 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	5	163,521,402 - 163,524,603 (+)	NCBI	Rnor_WKY
Rnor_6.0	5	165,405,168 - 165,408,325 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	14,588,870 - 14,591,974 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0 Ensembl	5	165,405,168 - 165,408,320 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	169,061,769 - 169,064,926 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	165,672,516 - 165,675,673 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	165,682,703 - 165,685,859 (+)	NCBI
Celera	5	157,302,130 - 157,305,203 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Animal Disease Models (ISO)

Familial Atrial Fibrillation 6 (ISO)

immunodeficiency 14 (ISO)

lung adenocarcinoma (ISO)

Peroxisome Biogenesis Disorder, Complementation Group K (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(-)-alpha-phellandrene (ISO)

(-)-demecolcine (ISO)

1,2-dimethylhydrazine (ISO)

1-chloro-2,4-dinitrobenzene (ISO)

14-Deoxy-11,12-didehydroandrographolide (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

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

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

2,4,6-trinitrobenzenesulfonic acid (ISO)

2,4,6-trinitrotoluene (EXP)

2,4-dinitrotoluene (EXP)

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

3-chloropropane-1,2-diol (EXP)

4-amino-2,6-dinitrotoluene (EXP)

5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole (EXP)

6-propyl-2-thiouracil (EXP)

acrylamide (ISO)

afimoxifene (ISO)

all-trans-retinoic acid (ISO)

alpha-phellandrene (ISO)

amiodarone (EXP)

ammonium chloride (EXP)

amphetamine (EXP)

azoxystrobin (ISO)

beauvericin (ISO)

benzbromarone (EXP)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (EXP)

caffeine (ISO)

calcitriol (ISO)

carbon nanotube (ISO)

choline (ISO)

ciguatoxin CTX1B (ISO)

cisplatin (ISO)

clobetasol (ISO)

clofibrate (EXP,ISO)

clofibric acid (EXP)

cobalt dichloride (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

coumestrol (ISO)

curcumin (ISO)

cyclophosphamide (ISO)

cyclosporin A (ISO)

cypermethrin (ISO)

dibutyl phthalate (ISO)

dicrotophos (ISO)

dioxygen (ISO)

doxorubicin (ISO)

Enterolactone (ISO)

epoxiconazole (ISO)

ethanol (ISO)

ethyl methanesulfonate (ISO)

fenthion (ISO)

flutamide (EXP)

folic acid (ISO)

genistein (EXP,ISO)

glafenine (EXP)

hydrogen peroxide (ISO)

isoprenaline (ISO)

ivermectin (ISO)

L-ethionine (EXP)

L-methionine (ISO)

metformin (EXP)

methidathion (ISO)

methotrexate (ISO)

methyl methanesulfonate (ISO)

N-(6-acetamidohexyl)acetamide (ISO)

N-methyl-4-phenylpyridinium (EXP)

N-nitrosodiethylamine (EXP)

nefazodone (EXP)

nickel atom (ISO)

nimesulide (EXP)

omeprazole (EXP)

ozone (ISO)

paracetamol (EXP,ISO)

paraquat (EXP)

phenobarbital (ISO)

PhIP (EXP)

pirinixic acid (EXP,ISO)

propiconazole (ISO)

pyrazinecarboxamide (EXP)

rotenone (EXP)

silicon dioxide (ISO)

sodium arsenite (ISO)

sodium dichromate (EXP)

Soman (EXP)

tamoxifen (ISO)

tebufenpyrad (ISO)

testosterone (ISO)

tetrachloroethene (ISO)

tetrachloromethane (EXP,ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

trichloroethene (EXP,ISO)

triptonide (ISO)

trovafloxacin (EXP)

urethane (ISO)

valdecoxib (EXP)

valproic acid (EXP,ISO)

vincristine (ISO)

zinc dichloride (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to leukemia inhibitory factor (ISO)

polyamine biosynthetic process (IBA)

spermidine biosynthetic process (IBA,IDA,IMP,ISO)

Molecular Function

identical protein binding (ISO)

protein binding (ISO)

protein homodimerization activity (ISO)

spermidine synthase activity (IBA,IDA,IMP,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

arginine and proline metabolic pathway (IEA)

beta-alanine metabolic pathway (IEA)

cysteine and methionine metabolic pathway (IEA)

glutathione metabolic pathway (IEA)

glycine N-methyltransferase deficiency pathway (ISO)

homocystinuria pathway (ISO)

hypermethioninemia pathway (ISO)

methionine cycle/metabolic pathway (ISO)

methylenetetrahydrofolate reductase deficiency pathway (ISO)

polyamine metabolic pathway (ISO)

spermidine metabolic pathway (IDA,IMP,ISO)

spermine metabolic pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Synthetic decarboxylated S-adenosyl-L-methionine as a substrate for aminopropyl transferases.	Dejima H, etal., Biol Pharm Bull 2003 Jul;26(7):1005-8.
2.	Aminooxy analogues of spermidine as inhibitors of spermine synthase and substrates of hepatic polyamine acetylating activity.	Eloranta TO, etal., J Biochem. 1990 Oct;108(4):593-8.
3.	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.
4.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
5.	KEGG: Kyoto Encyclopedia of Genes and Genomes	KEGG
6.	S-adenosylmethionine in liver health, injury, and cancer.	Lu SC and Mato JM, Physiol Rev. 2012 Oct;92(4):1515-42. doi: 10.1152/physrev.00047.2011.
7.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
8.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
9.	SMPDB Annotation Import Pipeline	Pipeline to import SMPDB annotations from SMPDB into RGD
10.	GOA pipeline	RGD automated data pipeline
11.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
12.	Assay for spermidine synthase activity by micellar electrokinetic chromatography with laser-induced fluorescence detection.	Sano M and Nishino I, J Chromatogr B Analyt Technol Biomed Life Sci. 2007 Jan 1;845(1):80-3. Epub 2006 Aug 23.
13.	Effects of inhibitors of spermidine synthase and spermine synthase on polyamine synthesis in rat tissues.	Shirahata A, etal., Biochem Pharmacol. 1993 May 5;45(9):1897-903.
14.	A perspective of polyamine metabolism.	Wallace HM, etal., Biochem J. 2003 Nov 15;376(Pt 1):1-14.

Additional References at PubMed

PMID:12477932	PMID:16515550	PMID:17585781	PMID:20439489	PMID:29892012	PMID:31515488

Genomics

Comparative Map Data

Srm
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	5	159,025,919 - 159,029,076 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	159,025,873 - 159,029,405 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	161,742,582 - 161,745,783 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	5	163,565,057 - 163,568,258 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	5	163,521,402 - 163,524,603 (+)	NCBI	Rnor_WKY
Rnor_6.0	5	165,405,168 - 165,408,325 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	14,588,870 - 14,591,974 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0 Ensembl	5	165,405,168 - 165,408,320 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	169,061,769 - 169,064,926 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	165,672,516 - 165,675,673 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	165,682,703 - 165,685,859 (+)	NCBI
Celera	5	157,302,130 - 157,305,203 (+)	NCBI		Celera
Cytogenetic Map	5	q36	NCBI

SRM
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	11,054,589 - 11,060,018 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	1	11,054,584 - 11,060,020 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	11,114,646 - 11,120,075 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	11,037,236 - 11,042,678 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	1	11,048,942 - 11,054,347	NCBI
Celera	1	10,226,954 - 10,232,396 (-)	NCBI		Celera
Cytogenetic Map	1	p36.22	NCBI
HuRef	1	10,266,094 - 10,271,363 (-)	NCBI		HuRef
CHM1_1	1	11,102,556 - 11,108,076 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	1	10,596,153 - 10,601,582 (-)	NCBI		T2T-CHM13v2.0

Srm
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	148,675,970 - 148,679,076 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	148,675,960 - 148,679,450 (+)	Ensembl		GRCm39 Ensembl
GRCm38	4	148,591,513 - 148,594,619 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	148,591,503 - 148,594,993 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	147,965,622 - 147,968,728 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	4	147,435,313 - 147,438,419 (+)	NCBI		MGSCv36	mm8
Celera	4	150,853,070 - 150,856,182 (+)	NCBI		Celera
Cytogenetic Map	4	E2	NCBI

Srm
(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_004955486	2,631,586 - 2,634,527 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955486	2,631,579 - 2,634,779 (+)	NCBI	ChiLan1.0	ChiLan1.0

SRM
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	1	11,038,452 - 11,043,186 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
Mhudiblu_PPA_v0	1	9,817,765 - 9,823,244 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3

SRM
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	2	84,968,833 - 84,973,111 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	2	84,967,570 - 84,973,087 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	2	81,499,046 - 81,502,445 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	2	85,631,078 - 85,634,460 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	2	85,631,106 - 85,636,493 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	2	82,379,185 - 82,382,581 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	2	83,380,647 - 83,384,031 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	2	84,443,471 - 84,446,868 (+)	NCBI		UU_Cfam_GSD_1.0

Srm
(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_024405058	34,294,112 - 34,300,103 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936474	118,000 - 124,963 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936474	121,135 - 124,894 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SRM
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	71,246,876 - 71,253,508 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	71,246,895 - 71,253,534 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	65,154,834 - 65,158,866 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SRM
(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	20	120,718,265 - 120,723,694 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	120,718,424 - 120,723,944 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666054	24,626,079 - 24,631,446 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Srm
(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_004624818	1,725,480 - 1,732,186 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624818	1,725,614 - 1,729,374 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Srm
14 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	129
Count of miRNA genes:	56
Interacting mature miRNAs:	75
Transcripts:	ENSRNOT00000014934, ENSRNOT00000071712
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
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	Rat
1578766	Tcas11	Tongue tumor susceptibility QTL 11	4.12		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	5	46711509	161317411	Rat
61393	Bp7	Blood pressure QTL 7	4.5	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	60293434	161481680	Rat
1302790	Scl20	Serum cholesterol level QTL 20	6.4	0.0001	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	82394392	166664054	Rat
1641920	Colcs1	Colorectal carcinoma susceptibility QTL 1	2.99	0.0055	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	5	121846814	166846814	Rat
10053720	Scort26	Serum corticosterone level QTL 26	2.06	0.0147	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	5	124965598	166875058	Rat
724525	Bp147	Blood pressure QTL 147	4.3	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	126424772	166875058	Rat
1598819	Bp292	Blood pressure QTL 292	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	127798274	166875058	Rat
1598861	Cm64	Cardiac mass QTL 64	2.9		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	127798274	166875058	Rat
8552908	Pigfal4	Plasma insulin-like growth factor 1 level QTL 4	6.6		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	128506074	166875058	Rat
8694169	Bw148	Body weight QTL 148	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	128506074	166875058	Rat
634349	Bp139	Blood pressure QTL 139		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	128924607	166875058	Rat
738018	Anxrr4	Anxiety related response QTL 4	5.1		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	5	130130159	166875058	Rat
7794791	Mcs33	Mammary carcinoma susceptibility QTL 33	1.93		mammary gland integrity trait (VT:0010552)	mammary tumor incidence/prevalence measurement (CMO:0000946)	5	131345754	166875058	Rat
631505	Bp103	Blood pressure QTL 103	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	132717196	165560427	Rat
631562	Apr2	Acute phase response QTL 2	3.7		blood murinoglobulin 1 amount (VT:0010597)	plasma murinoglobulin 1 level (CMO:0001931)	5	135927956	166875058	Rat
61444	Strs2	Sensitivity to stroke QTL 2	4.7		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	5	135929696	166875058	Rat
1331721	Bp210	Blood pressure QTL 210	3.413		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	5	143069996	166846814	Rat
2302369	Scl60	Serum cholesterol level QTL 60	3.13		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	143608201	161165651	Rat
2313096	Bmd78	Bone mineral density QTL 78	3.1	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	5	144377876	161317411	Rat
1298090	Bp155	Blood pressure QTL 155	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	151006154	161165494	Rat
1354631	Swd2	Spike wave discharge measurement QTL 2	3.64	0.0002	brain electrophysiology trait (VT:0010557)	brain total spike-and-wave discharge duration (CMO:0001740)	5	151113452	164465185	Rat
631272	Lanf1	Left ventricular atrial natriuretic factor QTL 1	12		heart left ventricle natriuretic peptide A amount (VT:0010596)	heart left ventricle natriuretic peptide A level (CMO:0002165)	5	151113452	166875058	Rat
1549904	Neuinf1	Neuroinflammation QTL 1	3	0	nervous system integrity trait (VT:0010566)	blood T lymphocyte count (CMO:0000110)	5	154828214	166875058	Rat

Markers in Region

AA858619

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	159,028,823 - 159,029,024 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	14,591,720 - 14,591,920	NCBI	Rnor6.0
Rnor_6.0	5	165,408,073 - 165,408,273	NCBI	Rnor6.0
Rnor_5.0	5	169,064,674 - 169,064,874	UniSTS	Rnor5.0
Rnor_5.0	3	19,903,052 - 19,903,252	UniSTS	Rnor5.0
RGSC_v3.4	5	165,675,421 - 165,675,621	UniSTS	RGSC3.4
Celera	5	157,304,951 - 157,305,151	UniSTS
RH 3.4 Map	5	1114.4	UniSTS
Cytogenetic Map	5	q36	UniSTS

Srm

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	159,028,206 - 159,028,887 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	14,591,103 - 14,591,783	NCBI	Rnor6.0
Rnor_6.0	5	165,407,456 - 165,408,136	NCBI	Rnor6.0
Rnor_5.0	3	19,902,435 - 19,903,115	UniSTS	Rnor5.0
Rnor_5.0	5	169,064,057 - 169,064,737	UniSTS	Rnor5.0
Celera	5	157,304,334 - 157,305,014	UniSTS
Celera	3	13,422,895 - 13,423,336	UniSTS
Cytogenetic Map	5	q36	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
Low	3	24	24	24	4	24		4	96	30	38	2
Below cutoff	2	41	57	40	17	40	8	9	39	26	28	11	8

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053464	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF337636	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC128733	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000162	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000014934 ⟹ ENSRNOP00000014934

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	159,025,873 - 159,029,069 (+)	Ensembl
Rnor_6.0 Ensembl	5	165,405,168 - 165,408,320 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000071712 ⟹ ENSRNOP00000067465

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	159,025,873 - 159,029,405 (+)	Ensembl
Rnor_6.0 Ensembl	3	14,588,870 - 14,591,974 (+)	Ensembl

RefSeq Acc Id:

NM_053464 ⟹ NP_445916

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	5	159,025,919 - 159,029,076 (+)	NCBI
Rnor_6.0	5	165,405,168 - 165,408,325 (+)	NCBI
Rnor_5.0	5	169,061,769 - 169,064,926 (+)	NCBI
RGSC_v3.4	5	165,672,516 - 165,675,673 (+)	RGD
Celera	5	157,302,130 - 157,305,203 (+)	RGD

Sequence:

show sequence

GTTGTGCTGGGGCTCCGCGCGGCCTGCAGTCCCGGGCCCGCGACGCGCGCCGCCCGCCCGCCAT
GGAGCCTGGCCCCGACGGCCCAGCCGCGCCCGGCCCCGCCGCCATCCGTGAGGGTTGGTTCCGA
GAGACCTGCAGCCTGTGGCCTGGCCAGGCCCTGTCGCTGCAAGTGGAGCAGCTGCTGCACCACC
GGCGCTCGCGGTACCAAGACATCCTCGTCTTCCGCAGTAAAACCTACGGCAACGTGCTGGTTCT
GGATGGCGTCATCCAGTGTACCGAGAGGGACGAGTTCTCCTACCAGGAGATGATAGCCAACCTG
CCGCTCTGCAGCCACCCCAACCCGCGGAAGGTGCTGATCATCGGGGGTGGAGATGGGGGCGTCC
TACGGGAAGTGGTGAAGCACCCCTCTGTGGAGTCTGTGGTCCAGTGCGAGATCGATGAGGATGT
CATTGAGGTCTCTAAGAAGTTCCTGCCTGGCATGGCCGTTGGCTACTCCAGCTCAAAGCTGACT
CTCCACGTGGGCGATGGCTTTGAGTTCATGAAGCAGAACCAAGATGCCTTTGATGTCATCATCA
CCGACTCCTCAGACCCCATGGGCCCTGCTGAGAGCCTCTTCAAGGAGTCCTATTACCAGCTCAT
GAAGACAGCCCTCAAAGAAGATGGCATCCTCTGTTGCCAGGGCGAGTGCCAGTGGCTGCACCTG
GACCTCATCAAGGAGATGAGGCATTTCTGCAAGTCTCTCTTCCCTGTGGTGAGCTATGCCTACT
GTACCATTCCCACCTATCCCAGTGGCCAGATCGGCTTCATGCTGTGTAGCAAAAACCCGAGCAC
CAACTTCCGGGAGCCCGTGCAGCAGCTGACACAGGCCCAGGTAGAGCAGATGCAGCTGAAGTAC
TATAACTCAGACATGCACCGCGCGGCCTTCGTGCTGCCAGAGTTCACCCGAAAGGCCCTGAATG
ACATAAGCTGAATCCAGTGCCACTGTAACACCACCCGAGACCTCAGTTGGATTGGACCAAGGAG
CTTCCAAGCTGTCTGGGACCACCAGTCCTGGACCAAACTCCCAGATGACTCTTGCCCACCAACC
AAGTGTTACAGGCCCCAGAATGCTGCCTGGCCTGCCCTGCTGGGTGGACTCAGTCTCTGTGTCT
GTCTATCTCTGTGGCGTTCAGCCCCACGCCTATACCAGCTCTGTACAGCACCACCTATGCCCTG
TGACCCAACAAAAAACACGTGTATTTATAACAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_445916	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI28734	(Get FASTA)	NCBI Sequence Viewer
	AAK21288	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_445916 ⟸ NM_053464

- UniProtKB:

Q99MI5 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MEPGPDGPAAPGPAAIREGWFRETCSLWPGQALSLQVEQLLHHRRSRYQDILVFRSKTYGNVLV
LDGVIQCTERDEFSYQEMIANLPLCSHPNPRKVLIIGGGDGGVLREVVKHPSVESVVQCEIDED
VIEVSKKFLPGMAVGYSSSKLTLHVGDGFEFMKQNQDAFDVIITDSSDPMGPAESLFKESYYQL
MKTALKEDGILCCQGECQWLHLDLIKEMRHFCKSLFPVVSYAYCTIPTYPSGQIGFMLCSKNPS
TNFREPVQQLTQAQVEQMQLKYYNSDMHRAAFVLPEFTRKALNDIS

hide sequence

RefSeq Acc Id:

ENSRNOP00000014934 ⟸ ENSRNOT00000014934

RefSeq Acc Id:

ENSRNOP00000067465 ⟸ ENSRNOT00000071712

Protein Domains

PABS

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q99MI5-F1-model_v2	AlphaFold	Q99MI5	1-302	view protein structure

Transcriptome

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

Promoters

RGD ID:

13694263

Promoter ID:

EPDNEW_R4788

Type:

initiation region

Name:

Srm_1

Description:

spermidine synthase

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	5	165,405,160 - 165,405,220	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620796	AgrOrtholog
BioCyc Gene	G2FUF-39160	BioCyc
BioCyc Pathway	BSUBPOLYAMSYN-PWY [spermidine biosynthesis I]	BioCyc
Ensembl Genes	ENSRNOG00000011078	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
	ENSRNOG00000046379	Ensembl
Ensembl Protein	ENSRNOP00000014934	ENTREZGENE
	ENSRNOP00000014934.2	UniProtKB/TrEMBL
	ENSRNOP00000067465.2	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000014934	ENTREZGENE
	ENSRNOT00000014934.5	UniProtKB/TrEMBL
	ENSRNOT00000071712.3	UniProtKB/TrEMBL
Gene3D-CATH	2.30.140.10	UniProtKB/TrEMBL
	3.40.50.150	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:8366755	IMAGE-MGC_LOAD
InterPro	PABS	UniProtKB/TrEMBL
	PABS_CS	UniProtKB/TrEMBL
	SAM-dependent_MTases-like	UniProtKB/TrEMBL
	Spermi_synthase_euk	UniProtKB/TrEMBL
	Spermidine_synt_N	UniProtKB/TrEMBL
	Spermidine_synt_N_sf	UniProtKB/TrEMBL
	Sprmine_synthase	UniProtKB/TrEMBL
KEGG Report	rno:84596	UniProtKB/TrEMBL
MGC_CLONE	MGC:156617	IMAGE-MGC_LOAD
NCBI Gene	84596	ENTREZGENE
PANTHER	PTHR11558	UniProtKB/TrEMBL
Pfam	Spermine_synt_N	UniProtKB/TrEMBL
PhenoGen	Srm	PhenoGen
PIRSF	Spermidine_synth	UniProtKB/TrEMBL
PROSITE	SPERMIDINE_SYNTHASE_1	UniProtKB/TrEMBL
	SPERMIDINE_SYNTHASE_2	UniProtKB/TrEMBL
Superfamily-SCOP	SSF53335	UniProtKB/TrEMBL
TIGRFAMs	speE	UniProtKB/TrEMBL
UniProt	M0RCX8_RAT	UniProtKB/TrEMBL
	Q99MI5	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2021-03-09	Srm	spermidine synthase	LOC100912604	spermidine synthase-like	Data Merged	737654	PROVISIONAL
2015-07-29	LOC100912604	spermidine synthase-like	LOC689673	similar to Spermidine synthase (Putrescine aminopropyltransferase) (SPDSY)	Data Merged	737654	PROVISIONAL
2012-07-05	LOC100912604	spermidine synthase-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2008-01-09	LOC689673	similar to Spermidine synthase (Putrescine aminopropyltransferase) (SPDSY)	LOC687838	similar to Spermidine synthase (Putrescine aminopropyltransferase) (SPDSY)	Data Merged	1643240	APPROVED
2006-11-20	LOC689673	similar to Spermidine synthase (Putrescine aminopropyltransferase) (SPDSY)			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-20	LOC687838	similar to Spermidine synthase (Putrescine aminopropyltransferase) (SPDSY)			Symbol and Name status set to provisional	70820	PROVISIONAL
2004-02-26	Srm	spermidine synthase			Symbol and Name status set to approved	625702	APPROVED
2002-08-07	Srm	spermidine synthase			Symbol and Name status set to provisional	70820	PROVISIONAL

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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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

RGD Manual Annotations

Imported Annotations - SMPDB

Imported Annotations - KEGG (archival)