Ssbp4 (single stranded DNA binding protein 4)

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Gene: Ssbp4 (single stranded DNA binding protein 4) Rattus norvegicus

Analyze

Symbol:

Ssbp4

Name:

single stranded DNA binding protein 4

RGD ID:

1359619

Description:

Predicted to enable single-stranded DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human SSBP4 (single stranded DNA binding protein 4); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC364534; similar to RIKEN cDNA 1210002E11; single-stranded DNA-binding protein 4

RGD Orthologs

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):	SSBP4 (single stranded DNA binding protein 4)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Ssbp4 (single stranded DNA binding protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Ssbp4 (single stranded DNA binding protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SSBP4 (single stranded DNA binding protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SSBP4 (single stranded DNA binding protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Ssbp4 (single stranded DNA binding protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SSBP4 (single stranded DNA binding protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SSBP4 (single stranded DNA binding protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Ssbp4 (single stranded DNA binding protein 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	SSBP3 (single stranded DNA binding protein 3)	HGNC	OrthoDB
Alliance orthologs ³
Homo sapiens (human):	SSBP4 (single stranded DNA binding protein 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Ssbp4 (single stranded DNA binding protein 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	zgc:110158	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Danio rerio (zebrafish):	ssbp4 (single stranded DNA binding protein 4)	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Caenorhabditis elegans (roundworm):	sam-10	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Ssdp	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	ssbp4	Alliance	DIOPT (Ensembl Compara\|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	16	18,828,014 - 18,838,941 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	16	18,828,054 - 18,838,947 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	16	18,869,738 - 18,880,637 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	16	20,002,544 - 20,013,421 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	16	18,922,700 - 18,933,599 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	16	20,578,111 - 20,589,295 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	20,578,131 - 20,589,290 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	20,433,829 - 20,445,004 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	19,334,216 - 19,345,098 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	16	19,334,213 - 19,345,096 (+)	NCBI
Celera	16	19,019,524 - 19,030,403 (+)	NCBI		Celera
Cytogenetic Map	16	p14	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

Megalencephaly-Polymicrogyria-Polydactyly-Hydrocephalus Syndrome 1 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

17beta-estradiol (EXP)

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

3,4-methylenedioxymethamphetamine (ISO)

4,4'-sulfonyldiphenol (EXP,ISO)

4-hydroxyphenyl retinamide (ISO)

6-propyl-2-thiouracil (EXP)

acetamide (EXP)

acrylamide (EXP,ISO)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

amitrole (EXP)

antirheumatic drug (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (EXP,ISO)

bisphenol A (EXP,ISO)

bisphenol F (EXP)

cadmium atom (ISO)

carbon nanotube (ISO)

chlorpyrifos (ISO)

choline (ISO)

clofibrate (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

dibutyl phthalate (ISO)

ethanol (ISO)

folic acid (ISO)

gentamycin (EXP)

hydralazine (ISO)

L-methionine (ISO)

methimazole (EXP)

methylmercury chloride (ISO)

miconazole (ISO)

paracetamol (EXP,ISO)

perfluorooctane-1-sulfonic acid (ISO)

perfluorooctanoic acid (ISO)

resveratrol (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

thioacetamide (EXP)

trovafloxacin (ISO)

valproic acid (ISO)

vancomycin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

positive regulation of transcription by RNA polymerase II (IBA)

Cellular Component

nucleus (IBA)

Molecular Function

protein binding (ISO)

single-stranded DNA binding (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.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
4.	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

Ssbp4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	16	18,828,014 - 18,838,941 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	16	18,828,054 - 18,838,947 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	16	18,869,738 - 18,880,637 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	16	20,002,544 - 20,013,421 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	16	18,922,700 - 18,933,599 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	16	20,578,111 - 20,589,295 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	20,578,131 - 20,589,290 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	20,433,829 - 20,445,004 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	19,334,216 - 19,345,098 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	16	19,334,213 - 19,345,096 (+)	NCBI
Celera	16	19,019,524 - 19,030,403 (+)	NCBI		Celera
Cytogenetic Map	16	p14	NCBI

SSBP4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	18,402,725 - 18,434,562 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	19	18,418,864 - 18,434,562 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	19	18,530,208 - 18,545,372 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	18,391,136 - 18,406,459 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	19	18,391,135 - 18,406,459	NCBI
Celera	19	18,432,041 - 18,447,194 (+)	NCBI		Celera
Cytogenetic Map	19	p13.11	NCBI
HuRef	19	18,093,430 - 18,108,673 (+)	NCBI		HuRef
CHM1_1	19	18,530,390 - 18,545,520 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	19	18,536,880 - 18,568,741 (+)	NCBI		T2T-CHM13v2.0

Ssbp4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	71,050,135 - 71,061,084 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	8	71,050,140 - 71,061,522 (-)	Ensembl		GRCm39 Ensembl
GRCm38	8	70,597,485 - 70,608,387 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	70,597,490 - 70,608,872 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	73,121,389 - 73,132,213 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	8	73,526,479 - 73,537,262 (-)	NCBI		MGSCv36	mm8
Celera	8	73,153,605 - 73,164,429 (-)	NCBI		Celera
Cytogenetic Map	8	B3.3	NCBI
cM Map	8	34.15	NCBI

Ssbp4
(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_004955524	3,101,906 - 3,109,178 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955524	3,101,935 - 3,109,178 (-)	NCBI	ChiLan1.0	ChiLan1.0

SSBP4
(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	19	22,287,858 - 22,303,364 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	17,897,548 - 17,913,159 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	18,865,443 - 18,883,849 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	18,877,213 - 18,883,849 (+)	Ensembl	panpan1.1		panPan2

SSBP4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	20	44,599,576 - 44,613,344 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	20	44,598,920 - 44,613,266 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	20	44,513,130 - 44,527,624 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	20	45,084,707 - 45,099,201 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	20	45,084,702 - 45,099,235 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	20	44,322,003 - 44,336,494 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	20	44,732,143 - 44,746,622 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	20	45,007,562 - 45,022,046 (-)	NCBI		UU_Cfam_GSD_1.0

Ssbp4
(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_024405118	203,270,412 - 203,283,693 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936596	2,819,551 - 2,833,191 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936596	2,819,551 - 2,833,117 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SSBP4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	2	59,367,246 - 59,384,537 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	2	59,367,243 - 59,384,584 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

SSBP4
(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	6	16,891,140 - 16,906,505 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	6	16,891,430 - 16,910,030 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666074	2,435,239 - 2,450,339 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Ssbp4
(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_004624908	1,649,878 - 1,658,374 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624908	1,648,150 - 1,658,374 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Ssbp4
21 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	57
Count of miRNA genes:	57
Interacting mature miRNAs:	57
Transcripts:	ENSRNOT00000026713
Prediction methods:	Miranda, Rnahybrid
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
1600369	Hcas8	Hepatocarcinoma susceptibility QTL 8			liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	16	1	22477621	Rat
631830	Alc7	Alcohol consumption QTL 7	2.9		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	16	1	26727669	Rat
634355	Rends4	Renal damage susceptibility QTL 4		0.05	kidney blood vessel morphology trait (VT:0000530)	organ lesion measurement (CMO:0000677)	16	1	26727669	Rat
1582235	Insul8	Insulin level QTL 8	3.3	0.0063	blood insulin amount (VT:0001560)	calculated serum insulin level (CMO:0000359)	16	1	26727669	Rat
9590151	Scort8	Serum corticosterone level QTL 8	8.45	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	16	1	30836262	Rat
2302380	Slep6	Serum leptin concentration QTL 6	3.36		blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	16	1	32139025	Rat
2307172	Activ4	Activity QTL 4	3.71	0.00023	locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	16	1	33418960	Rat
1354584	Despr6	Despair related QTL 6	3.1	0.0067	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	16	1	39533930	Rat
2303566	Bw90	Body weight QTL 90	2		body mass (VT:0001259)	body weight (CMO:0000012)	16	1	39533930	Rat
631561	Hcuc2	Hepatic copper content QTL 2	2.8		liver copper amount (VT:0003065)	liver total copper weight (CMO:0001507)	16	1	39533949	Rat
6903319	Bw114	Body weight QTL 114	2.7	0.0037	body mass (VT:0001259)	body weight (CMO:0000012)	16	1	43534949	Rat
7411664	Foco30	Food consumption QTL 30	11	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	16	1	44588133	Rat
1354625	Despr7	Despair related QTL 7	3.16	0.016	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	16	1	44977551	Rat
1600378	Arunc4	Aerobic running capacity QTL 4		0.03	exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	16	380245	80345693	Rat
2293343	Glom16	Glomerulus QTL 16	7.4		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	16	832236	46053497	Rat
2312660	Bw95	Body weight QTL 95		0.05	inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	16	832236	59492508	Rat
2312663	Slep9	Serum leptin concentration QTL 9		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	16	832236	59492508	Rat
2312666	Insul16	Insulin level QTL 16		0.01	blood insulin amount (VT:0001560)	serum insulin level (CMO:0000358)	16	832236	59492508	Rat
2312669	Stl23	Serum triglyceride level QTL 23		0.01	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	16	832236	59492508	Rat
1300133	Rf24	Renal function QTL 24	3.64		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	16	3380150	21361552	Rat
2306902	Bp339	Blood pressure QTL 339		0.01	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	16	3380150	43025077	Rat
70183	BpQTLcluster13	Blood pressure QTL cluster 13	3.654		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	16	4227609	43025077	Rat
70183	BpQTLcluster13	Blood pressure QTL cluster 13	3.654		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	16	4227609	43025077	Rat
70183	BpQTLcluster13	Blood pressure QTL cluster 13	3.654		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	16	4227609	43025077	Rat
737819	Hcas4	Hepatocarcinoma susceptibility QTL 4	4.43		liver integrity trait (VT:0010547)	volume of individual liver tumorous lesion (CMO:0001078)	16	4227609	46975965	Rat
61405	Niddm6	Non-insulin dependent diabetes mellitus QTL 6	3.66	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	16	4227609	48972724	Rat
61338	Bp23	Blood pressure QTL 23	4.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	16	4227609	49227609	Rat
737826	Alc11	Alcohol consumption QTL 11	3.2		consumption behavior trait (VT:0002069)	ethanol drink intake rate (CMO:0001407)	16	4227609	60252231	Rat
631517	Scl9	Serum cholesterol level QTL 9	3.3		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	16	15726433	21034895	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor depth of invasion (CMO:0001888)	16	17696791	82635055	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor depth of invasion (CMO:0001888)	16	17696791	82635055	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor diameter (CMO:0001889)	16	17696791	82635055	Rat
70205	Gcr3	Gastric cancer resistance QTL 3	2.3		stomach morphology trait (VT:0000470)	stomach tumor diameter (CMO:0001889)	16	17696791	82635055	Rat

Markers in Region

RH129421

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	16	18,839,160 - 18,839,326 (+)	MAPPER	mRatBN7.2
Rnor_6.0	16	20,589,515 - 20,589,680	NCBI	Rnor6.0
Rnor_5.0	16	20,445,224 - 20,445,389	UniSTS	Rnor5.0
RGSC_v3.4	16	19,345,323 - 19,345,488	UniSTS	RGSC3.4
Celera	16	19,030,628 - 19,030,793	UniSTS
RH 3.4 Map	16	180.5	UniSTS
Cytogenetic Map	16	p14	UniSTS

RH130875

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	16	18,838,677 - 18,838,866 (+)	MAPPER	mRatBN7.2
Rnor_6.0	16	20,589,032 - 20,589,220	NCBI	Rnor6.0
Rnor_5.0	16	20,444,741 - 20,444,929	UniSTS	Rnor5.0
RGSC_v3.4	16	19,344,840 - 19,345,028	UniSTS	RGSC3.4
Celera	16	19,030,145 - 19,030,333	UniSTS
RH 3.4 Map	16	180.3	UniSTS
Cytogenetic Map	16	p14	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	3	35	38	22	19	22		2	74	29	39	11
Low		8	19	19		19	8	9		6	2		8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001014236	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006252912	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008771139	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008771140	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008771141	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_008771142	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039094713	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039094714	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039094715	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039094716	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005494648	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005494649	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC079147	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474031	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000275	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000026713 ⟹ ENSRNOP00000026713

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	18,828,054 - 18,838,947 (+)	Ensembl
Rnor_6.0 Ensembl	16	20,578,131 - 20,589,290 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000113905 ⟹ ENSRNOP00000079858

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	16	18,828,054 - 18,838,936 (+)	Ensembl

RefSeq Acc Id:

NM_001014236 ⟹ NP_001014258

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	18,828,042 - 18,838,941 (+)	NCBI
Rnor_6.0	16	20,578,131 - 20,589,290 (+)	NCBI
Rnor_5.0	16	20,433,829 - 20,445,004 (+)	NCBI
RGSC_v3.4	16	19,334,216 - 19,345,098 (+)	RGD
Celera	16	19,019,524 - 19,030,403 (+)	RGD

Sequence:

show sequence

CGGAGGCGCGCTTCCCGGAACAGCCCGCGGAGGGCAGCGCGGCGAGAACCCACCCGCGGCCGTA
GCTCCCGCGCGGACATGGCCGCGGGGATCGGGGCGCGGGCAGCGATGGCCACGCGCGCCTGACA
GGTGCGGAGCATGTACGGCAAGGCGAGCAAGGGCTGCGCGCCCTCGGACGGCCAGGCGCGCGAG
AAGCTTGCGCTGTATGTATATGAGTATCTACTGCATGTGGGGGCACAGAAGTCAGCACAGACCT
TCCTGTCTGAGATCCGCTGGGAAAAGAACATCACCTTGGGCGAGCCTCCTGGCTTCCTGCACTC
CTGGTGGTGCGTCTTCTGGGACCTGTACTGCGCAGCGCCAGACCGCAGGGAGGCCTGTGAACAC
TCCAGTGAGGCCAAAGTCTTCCAGGACTATAGTGCAGCAGCAGCAGCTCCCAGCCCTGTGATGG
GTACCTTGGCCCCTAACGATGCAATGGCAGCAGGTCCTGTGGCACCAGGCTTCTTTCAGCCCTT
CATATCACCAAGGTTCCCAGGGGGTGCCCGCCCAATCCTGAGGATGCCGGGCCAGCCTCCTGTG
GGCCTCCCTGGCTCCCAGCACCTCATCCCTGGTGCCATGGACCCCTCCCCACGTGCACAGGGGC
ACCCCAGCCTGGGAGGTCCGATGCAGAGGGTGACCCCTCCGAGGGGAATGGCCAGTGTTGGGCC
CCAGGGCTTTGGAACTGGCATGCGTCCCCCACCCAATTCCCTTGCCACCAGCCAGATCCTGCCA
TCCATGAACATGGGTCCGGGAGTGCGTGGCCCGTGGGCCAGTCCCAGCGGTAACTCGATCCCGT
ACTCTTCCTCATCTCCTGGCAGCTACTCGGGACCGACAGGAGGAGGTGGCGCCCCCGGAACACC
CATCATGTCCAGCCCTGGAGACTCCACCAACTCCAGCGAGAACATGTACACCATCATGAATCCC
ATCGGGCCGGGCGCTGGCAGGGCTAACTTCCCGCTCGGCCCCAGCCCGGAGGGCCCAATGGCCT
CAATGAGCACGATGGAGCCGCACCACGTGAACGGATCCCTGGGCTCGGGCGATATGGACGGGCT
GCCGAAGAACTCCCCCGGCGCCGTGGGCGGCCTGAACAACGCCCCGGGGACCCCGCGCGACGAC
GGCGAGATGGCGGCTGCCGGGACCTTCCTGCACCCGTTCCCGAGCGAAAGCTACTCCCCCGGCA
TGACTATGAGCGTGTGATAGCCCCGGGTCCTGCTGGTGAGGTCTCGGGTCGCGGCAGCACCCCT
GCCATCCGGACTCCTGGCTAGCCCGGCCGGCCGGCAGGACCCCCACGAAGGACTTTTCTAAACA
CACATATATACACACACACAAACTCAAAGGACCTCAGAGAAGTGCAGGCCTTCAAACCTGTGAG
CTATCACAGGGCTGGGGGGTAAGGGCAGGGGTTCTGCCAATAAATGCCATTCAGTTTTGTCTTA
GAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

RefSeq Acc Id:

XM_008771140 ⟹ XP_008769362

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	18,828,019 - 18,838,941 (+)	NCBI
Rnor_6.0	16	20,578,112 - 20,589,295 (+)	NCBI

Sequence:

show sequence

CGGCGGTGGCGCGCTGTGGCGGAGGCGCGCTTCCCGGAACAGCCCGCGGAGGGCAGCGCGGCGA
GAACCCACCCGCGGCCGTAGCTCCCGCGCGGACATGGCCGCGGGGATCGGGGCGCGGGCAGCGA
TGGCCACGCGCGCCTGACAGGTGCGGAGCATGTACGGCAAGGCGAGCAAGGGCTGCGCGCCCTC
GGACGGCCAGGCGCGCGAGAAGCTTGCGCTGTATGTATATGAGTATCTACTGCATGTGGGGGCA
CAGAAGTCAGCACAGACCTTCCTGTCTGAGATCCGCTGGGAAAAGAACATCACCTTGGGCGAGC
CTCCTGGCTTCCTGCACTCCTGGTGGTGCGTCTTCTGGGACCTGTACTGCGCAGCGCCAGACCG
CAGGGAGGCCTGTGAACACTCCAGTGAGGCCAAAGTCTTCCAGGACTATAGTGCAGCAGCAGCA
GCTCCCAGCCCTGTGATGGGTACCTTGGCCCCTAACGATGCAATGGCAGCAGGTCCTGTGGCAC
CAGGCTTCTTTCAGCCCTTCATATCACCAAGGTTCCCAGGGGGTGCCCGCCCAATCCTGAGGAT
GCCGGGCCAGCCTCCTGTGGGCCTCCCTGGCTCCCAGCACCTCATCCCTGGTGCCATGGACCCC
TCCCCACGTGCACAGGGGCACCCCAGCCTGGGAGGTCCGATGCAGAGGGTGACCCCTCCGAGGG
GAATGGCCAGTGTTGGGCCCCAGGGCTTTGGAACTGGCATGCGTCCCCCACCCAATTCCCTTGC
CACCAGCCAGATCCTGCCATCCATGAACATGGGTCCGGGAGTGCGTGGCCCGTGGGCCAGTCCC
AGCGGTAACTCGATCCCGTACTCTTCCTCATCTCCTGGCAGCTACTCGGGACCGACAGGAGGAG
GTGGCGCCCCCGGAACACCCATCATGCCCAGCCCTGGAGACTCCACCAACTCCAGCGAGAACAT
GTACACCATCATGAATCCCATCGGGCCGGGCGCTGGCAGGGCTAACGTGAGTGGGGGCCGGTGC
GCCTCACCCGATGGGGACCTCGCGGGGGGCGGCCGGCCCGAGCCCCACGCTGCCCTGTGCCCGC
AGTTCCCGCTCGGCCCCAGCCCGGAGGGCCCAATGGCCTCAATGAGCACGATGGAGCCGCACCA
CGTGAACGGATCCCTGGGCTCGGGCGATATGGACGGGCTGCCGAAGAACTCCCCCGGCGCCGTG
GGCGGCCTGAACAACGCCCCGGGGACCCCGCGCGACGACGGCGAGATGGCGGCTGCCGGGACCT
TCCTGCACCCGTTCCCGAGCGAAAGCGTAAGCGCCTGCGTCGACTCCCCACCCGCGGCCGCGGC
GGGCCGGAGGGGCCTGGCGGGCAGACCCCGGCGGGGCGGCCGCGGGGCCAGAGCAAGACCGTGA
CCGCGGCGGGCCAGTACTCCCCCGGCATGACTATGAGCGTGTGATAGCCCCGGGTCCTGCTGGT
GAGGTCTCGGGTCGCGGCAGCACCCCTGCCATCCGGACTCCTGGCTAGCCCGGCCGGCCGGCAG
GACCCCCACGAAGGACTTTTCTAAACACACATATATACACACACACAAACTCAAAGGACCTCAG
AGAAGTGCAGGCCTTCAAACCTGTGAGCTATCACAGGGCTGGGGGGTAAGGGCAGGGGTTCTGC
CAATAAATGCCATTCAGTTTTGTCTTTGGTA

hide sequence

RefSeq Acc Id:

XM_039094713 ⟹ XP_038950641

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	18,828,019 - 18,838,941 (+)	NCBI

RefSeq Acc Id:

XM_039094714 ⟹ XP_038950642

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	18,828,021 - 18,838,941 (+)	NCBI

RefSeq Acc Id:

XM_039094715 ⟹ XP_038950643

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	18,828,015 - 18,838,941 (+)	NCBI

RefSeq Acc Id:

XM_039094716 ⟹ XP_038950644

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	18,828,021 - 18,838,941 (+)	NCBI

RefSeq Acc Id:

XR_005494648

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	18,828,014 - 18,838,941 (+)	NCBI

RefSeq Acc Id:

XR_005494649

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	16	18,828,019 - 18,838,941 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001014258	(Get FASTA)	NCBI Sequence Viewer
	XP_008769362	(Get FASTA)	NCBI Sequence Viewer
	XP_038950641	(Get FASTA)	NCBI Sequence Viewer
	XP_038950642	(Get FASTA)	NCBI Sequence Viewer
	XP_038950643	(Get FASTA)	NCBI Sequence Viewer
	XP_038950644	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH79147	(Get FASTA)	NCBI Sequence Viewer
	EDL90711	(Get FASTA)	NCBI Sequence Viewer
	EDL90712	(Get FASTA)	NCBI Sequence Viewer
	EDL90713	(Get FASTA)	NCBI Sequence Viewer
	EDL90714	(Get FASTA)	NCBI Sequence Viewer
	EDL90715	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000026713
	ENSRNOP00000026713.4
	ENSRNOP00000079858
	ENSRNOP00000079858.1

RefSeq Acc Id:

NP_001014258 ⟸ NM_001014236

- UniProtKB:

A6KA22 (UniProtKB/TrEMBL), Q6AY89 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MYGKASKGCAPSDGQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPGFLHSWWC
VFWDLYCAAPDRREACEHSSEAKVFQDYSAAAAAPSPVMGTLAPNDAMAAGPVAPGFFQPFISP
RFPGGARPILRMPGQPPVGLPGSQHLIPGAMDPSPRAQGHPSLGGPMQRVTPPRGMASVGPQGF
GTGMRPPPNSLATSQILPSMNMGPGVRGPWASPSGNSIPYSSSSPGSYSGPTGGGGAPGTPIMS
SPGDSTNSSENMYTIMNPIGPGAGRANFPLGPSPEGPMASMSTMEPHHVNGSLGSGDMDGLPKN
SPGAVGGLNNAPGTPRDDGEMAAAGTFLHPFPSESYSPGMTMSV

hide sequence

RefSeq Acc Id:	XP_008769362 ⟸ XM_008771140
- Peptide Label:	isoform X1
- UniProtKB:	Q6AY89 (UniProtKB/TrEMBL)
- Sequence:	show sequence MYGKASKGCAPSDGQAREKLALYVYEYLLHVGAQKSAQTFLSEIRWEKNITLGEPPGFLHSWWC VFWDLYCAAPDRREACEHSSEAKVFQDYSAAAAAPSPVMGTLAPNDAMAAGPVAPGFFQPFISP RFPGGARPILRMPGQPPVGLPGSQHLIPGAMDPSPRAQGHPSLGGPMQRVTPPRGMASVGPQGF GTGMRPPPNSLATSQILPSMNMGPGVRGPWASPSGNSIPYSSSSPGSYSGPTGGGGAPGTPIMP SPGDSTNSSENMYTIMNPIGPGAGRANVSGGRCASPDGDLAGGGRPEPHAALCPQFPLGPSPEG PMASMSTMEPHHVNGSLGSGDMDGLPKNSPGAVGGLNNAPGTPRDDGEMAAAGTFLHPFPSESV SACVDSPPAAAAGRRGLAGRPRRGGRGARARP hide sequence

RefSeq Acc Id:

ENSRNOP00000026713 ⟸ ENSRNOT00000026713

RefSeq Acc Id:	XP_038950643 ⟸ XM_039094715
- Peptide Label:	isoform X3
- UniProtKB:	Q6AY89 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038950641 ⟸ XM_039094713
- Peptide Label:	isoform X1
- UniProtKB:	Q6AY89 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038950642 ⟸ XM_039094714
- Peptide Label:	isoform X2
- UniProtKB:	Q6AY89 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038950644 ⟸ XM_039094716
- Peptide Label:	isoform X4
- UniProtKB:	G3V8L4 (UniProtKB/TrEMBL), Q6AY89 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSRNOP00000079858 ⟸ ENSRNOT00000113905

Protein Domains

LisH

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-G3V8L4-F1-model_v2	AlphaFold	G3V8L4	1-364	view protein structure

Transcriptome

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

Promoters

RGD ID:

13700023

Promoter ID:

EPDNEW_R10546

Type:

initiation region

Name:

Ssbp4_1

Description:

single stranded DNA binding protein 4

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	16	20,578,152 - 20,578,212	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1359619	AgrOrtholog
BioCyc Gene	G2FUF-11789	BioCyc
Ensembl Genes	ENSRNOG00000019698	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000026713	ENTREZGENE
	ENSRNOT00000026713.4	UniProtKB/TrEMBL
	ENSRNOT00000113905	ENTREZGENE
	ENSRNOT00000113905.1	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7128392	IMAGE-MGC_LOAD
InterPro	LisH_dimerisation	UniProtKB/TrEMBL
	SSDP_DNA-bd	UniProtKB/TrEMBL
KEGG Report	rno:364534	UniProtKB/TrEMBL
MGC_CLONE	MGC:94162	IMAGE-MGC_LOAD
NCBI Gene	364534	ENTREZGENE
PANTHER	SINGLE STRANDED DNA BINDING PROTEIN	UniProtKB/TrEMBL
	SINGLE-STRANDED DNA-BINDING PROTEIN 4	UniProtKB/TrEMBL
Pfam	SSDP	UniProtKB/TrEMBL
PhenoGen	Ssbp4	PhenoGen
PRINTS	SSDNABINDING	UniProtKB/TrEMBL
PROSITE	LISH	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000019698	RatGTEx
SMART	LisH	UniProtKB/TrEMBL
UniProt	A0A8I6G3T8_RAT	UniProtKB/TrEMBL
	A6KA22	ENTREZGENE, UniProtKB/TrEMBL
	G3V8L4	ENTREZGENE, UniProtKB/TrEMBL
	Q6AY89	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-05	Ssbp4	single stranded DNA binding protein 4	LOC364534	similar to RIKEN cDNA 1210002E11	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-07-29	LOC364534	similar to RIKEN cDNA 1210002E11			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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