Scp2d1 (SCP2 sterol-binding domain containing 1)

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Gene: Scp2d1 (SCP2 sterol-binding domain containing 1) Rattus norvegicus

Analyze

Symbol:

Scp2d1

Name:

SCP2 sterol-binding domain containing 1

RGD ID:

1308385

Description:

Orthologous to human SCP2D1 (SCP2 sterol binding domain containing 1); INTERACTS WITH bisphenol A; 2,2',4,4',5,5'-hexachlorobiphenyl (ortholog); 2,2',5,5'-tetrachlorobiphenyl (ortholog).

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

hypothetical protein LOC311491; LOC311491; RGD1308385; SCP2 sterol-binding domain-containing protein 1; similar to RIKEN cDNA 1700010M22; uncharacterized protein LOC311491

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	3	132,201,979 - 132,202,729 (+)	NCBI
Rnor_6.0 Ensembl	3	138,974,871 - 138,975,621 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	138,973,171 - 138,975,624 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	145,405,170 - 145,405,920 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	133,374,144 - 133,374,894 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	133,279,707 - 133,280,377 (+)	NCBI
Celera	3	131,086,358 - 131,087,108 (+)	NCBI		Celera
Cytogenetic Map	3	q41	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

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

2,2',5,5'-tetrachlorobiphenyl (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

cyclosporin A (ISO)

PCB138 (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

phospholipid transport (IBA)

positive regulation of intracellular cholesterol transport (IBA)

steroid biosynthetic process (IBA)

Molecular Function

sterol binding (IBA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	MGD data from the GO Consortium
3.	RGD automated data pipeline
4.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data

Scp2d1
(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	132,201,979 - 132,202,729 (+)	NCBI
Rnor_6.0 Ensembl	3	138,974,871 - 138,975,621 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	3	138,973,171 - 138,975,624 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	145,405,170 - 145,405,920 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	133,374,144 - 133,374,894 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	3	133,279,707 - 133,280,377 (+)	NCBI
Celera	3	131,086,358 - 131,087,108 (+)	NCBI		Celera
Cytogenetic Map	3	q41	NCBI

SCP2D1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	20	18,813,783 - 18,814,378 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	20	18,813,783 - 18,814,378 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	20	18,794,427 - 18,795,022 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	20	18,742,370 - 18,743,036 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	20	18,742,369 - 18,743,033	NCBI
Celera	20	18,868,645 - 18,869,311 (+)	NCBI
Cytogenetic Map	20	p11.23	NCBI
HuRef	20	18,757,196 - 18,757,862 (+)	NCBI		HuRef
CHM1_1	20	18,795,080 - 18,795,746 (+)	NCBI		CHM1_1

Scp2d1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	144,665,586 - 144,666,335 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	2	144,665,576 - 144,666,335 (+)	Ensembl
GRCm38	2	144,823,666 - 144,824,415 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	144,823,656 - 144,824,415 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	144,649,402 - 144,650,151 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	2	144,515,107 - 144,515,855 (+)	NCBI			mm8
Celera	2	146,019,139 - 146,019,888 (+)	NCBI		Celera
Cytogenetic Map	2	G1	NCBI

Scp2d1
(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	NW_004955415	27,215,991 - 27,229,799 (+)	NCBI	ChiLan1.0	ChiLan1.0

SCP2D1
(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	20	18,746,151 - 18,746,811 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	20	18,746,235 - 18,746,705 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	20	18,775,971 - 18,776,631 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

SCP2D1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	24	4,400,097 - 4,401,447 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	24	4,400,768 - 4,411,013 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Scp2d1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936485	1,464,896 - 1,465,564 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SCP2D1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	17	26,980,152 - 26,984,768 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	17	26,971,791 - 27,128,831 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	17	30,461,522 - 30,473,683 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SCP2D1
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	2	47,855,831 - 47,856,625 (+)	NCBI
ChlSab1.1 Ensembl	2	47,856,061 - 47,856,531 (+)	Ensembl

Scp2d1
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624741	19,425,894 - 19,426,364 (+)	NCBI

Position Markers

BE102219

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	3	138,975,389 - 138,975,568	NCBI	Rnor6.0
Rnor_5.0	3	145,405,688 - 145,405,867	UniSTS	Rnor5.0
RGSC_v3.4	3	133,374,662 - 133,374,841	UniSTS	RGSC3.4
Celera	3	131,086,876 - 131,087,055	UniSTS
RH 3.4 Map	3	1180.2	UniSTS
Cytogenetic Map	3	q41	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
70216	Cm14	Cardiac mass QTL 14	2.1		heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	30846101	172879276	Rat
1358362	Srcrt2	Stress Responsive Cort QTL 2	2.78		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	39248391	140271184	Rat
2301970	Bw81	Body weight QTL 81	5.19		body mass (VT:0001259)	body weight (CMO:0000012)	3	43295930	163640485	Rat
2301971	Cm71	Cardiac mass QTL 71	4.63		heart left ventricle mass (VT:0007031)	heart left ventricle weight (CMO:0000776)	3	43295930	163640485	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	45406058	177699992	Rat
2292591	Esta4	Estrogen-induced thymic atrophy QTL 4			thymus mass (VT:0004954)	thymus wet weight (CMO:0000855)	3	48561928	155263151	Rat
1581568	Rf53	Renal function QTL 53			total urine protein amount (VT:0000032)	urine protein excretion rate to body weight ratio (CMO:0001099)	3	58204463	170534769	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	61241033	165369047	Rat
1581546	Pur13	Proteinuria QTL 13	2.93	0.0335	total urine protein amount (VT:0000032)	urine protein excretion rate (CMO:0000759)	3	81136227	154416635	Rat
631649	Bp123	Blood pressure QTL 123	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	94788365	139788365	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	97009185	142009185	Rat
631841	Niddm39	Non-insulin dependent diabetes mellitus QTL 39	3.36		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	99465522	168732722	Rat
724532	Cm17	Cardiac mass QTL 17	2		heart mass (VT:0007028)	calculated heart weight (CMO:0000073)	3	101058963	146058963	Rat
2293087	Iddm27	Insulin dependent diabetes mellitus QTL 27	2.68		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	3	102152812	155263151	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	102466149	147466149	Rat
2312659	Slep7	Serum leptin concentration QTL 7		0.001	blood leptin amount (VT:0005667)	serum leptin level (CMO:0000780)	3	103141814	176418101	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	103141814	176418101	Rat
2312673	Scl63	Serum cholesterol level QTL 63		0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	103141814	176418101	Rat
2302373	Gluco39	Glucose level QTL 39	5.01		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	3	103141944	170934860	Rat
619618	Rf3	Renal disease susceptibility QTL 3	6.5	0.001	urine albumin amount (VT:0002871)	urine albumin excretion rate to body weight ratio (CMO:0001270)	3	114376250	159376250	Rat
1331758	Bp207	Blood pressure QTL 207	2.848		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	117303473	141971336	Rat
1578754	Stresp16	Stress response QTL 16	4	0.001	blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	3	119471263	164471263	Rat
1358204	Insglur1	Insulin/glucose ratio QTL 1	3.8		blood glucose amount (VT:0000188)	serum glucose level (CMO:0000543)	3	120917788	141971336	Rat
1358204	Insglur1	Insulin/glucose ratio QTL 1	3.8		blood glucose amount (VT:0000188)	serum insulin level (CMO:0000358)	3	120917788	141971336	Rat
1576306	Schws3	Schwannoma susceptibility QTL 3		0.001	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	3	125848628	170848628	Rat
1300173	Rf11	Renal function QTL 11	3.38		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	3	126575595	153412619	Rat
1300159	Kidm4	Kidney mass QTL 4	3.83		kidney mass (VT:0002707)	right kidney wet weight to body weight ratio (CMO:0001953)	3	126575595	165355668	Rat
1598877	Bp285	Blood pressure QTL 285	1.5	0.03	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	128986468	173986468	Rat
631541	Bp81	Blood pressure QTL 81	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	129787213	177699992	Rat
10755461	Coatc16	Coat color QTL 16			coat/hair pigmentation trait (VT:0010463)	pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)	3	130006659	175006659	Rat
2303620	Vencon4	Ventilatory control QTL 4	3.9		respiration trait (VT:0001943)	tidal volume (CMO:0000222)	3	132875075	176418101	Rat
631673	Iddm13	Insulin dependent diabetes mellitus QTL 13	1.3	0.663	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	3	136876155	170935007	Rat
1578653	Vnigr3	Vascular neointimal growth QTL 3	3.1		artery morphology trait (VT:0002191)	artery neointimal hyperplastic lesion area (CMO:0001414)	3	138374177	177699992	Rat
1578656	Vnigr2	Vascular neointimal growth QTL 2	4.2		artery morphology trait (VT:0002191)	lesioned artery residual lumen area (CMO:0001417)	3	138374177	177699992	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	30
Count of miRNA genes:	23
Interacting mature miRNAs:	27
Transcripts:	ENSRNOT00000012524
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.

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
Low			1		1				64	13	22	1
Below cutoff	2	12	21	9	14	9	5	6	8	19	12	6	5

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107785	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH474026	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000119	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000012524 ⟹ ENSRNOP00000012524

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	3	138,974,871 - 138,975,621 (+)	Ensembl

RefSeq Acc Id:

NM_001107785 ⟹ NP_001101255

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	3	132,201,979 - 132,202,729 (+)	NCBI
Rnor_6.0	3	138,974,871 - 138,975,621 (+)	NCBI
Rnor_5.0	3	145,405,170 - 145,405,920 (+)	NCBI
RGSC_v3.4	3	133,374,144 - 133,374,894 (+)	RGD
Celera	3	131,086,358 - 131,087,108 (+)	RGD

Sequence:

show sequence

CACAATCTGGCCTGTAGCCATGAATGTGGCCACAGCTACTCACAGACCAGATGGCCAGGTCTAG
AGGACTACAGTAAGATGTGGAAGAGAACTGATCCTCAAGCCAAGATCAAAGCAGGGGATAGGCC
TCAGACTTGCCATTCTCTGGCTCTGGGATCGGCCACAGAGTCGGCACTGCCCCACCCTCTAGAA
CTGTCAGACTTCCAGAGCTTTTCAGTATTTGAGGACATTAGCCATCACATCAAAGAAGGAGGAG
CCCAACTGGTAAAGAAAGTGAATGCCATCTTTCAGCTTGACATCACCAAAGATGGGAAGACCAT
TCTGCAGTGGACCATTGACCTCAAGAACGGTTCGGGGGACATGTACCTGGGATCAGCCCGGCTT
CCTGCAGACACCATCTTCATCATCCCTGACACGGTCTTCACAGAGTTAGTTGTGGGTAAGATGA
ACCCACAGAAGGCTTTCCTGGCTGGCAAGTTTAAAGTGAGAGGCAAAGTTCTCCTTAGCCAGAA
GCTGGAGAGGATCTTCAGAGAGTGGGCTAAATTTTAAGCATGGGGGAATGCCCAGGAAAGATCA
AGACTTCTGGCGTATTATAACGTTGAGTAGCAATCACGCATTAACTGAAGATTAAAGGAAAAAA
TAGCCAATATTTTTACTCAAATTCTTCCTATTCAAGTTCGATTGATTTCCTGCTGATGTGTACA
TTTGCTGGGAGCTGGGATAGTAAAAAAGTGTTGGAGTGCAACACCTA

hide sequence

RefSeq Acc Id:

XM_017591762 ⟹ XP_017447251

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	138,973,171 - 138,975,624 (+)	NCBI

Sequence:

show sequence

GCCTATCTAGGCTACAGAGTGAGTTCGAGTATAAAGTCAAAAAGGAAGTTTCAGATATACTTTG
TTGGTGAGGCACTTGCCTCATTTGTGTGAACCCTGGGCACAATTCCTAGTACACTAAAAGAGCA
AATAAATAAAAACCCTATTGAAAAATGTTCAGATTAAATGCTTTCTTGGTTTTCATTATATTAT
TCCCTAACTGTGCACTTGTTAATTGTAAACATTAACTGCAGGACACATGAAATGGCTTATATTT
TCAAACCAGTGGGTTTCTAGCAGGTGTGTGAGTGGGCATATGGATCCTTTTCCTTGCCAGGTTT
TATTTTCCCCTATGTCAAGTTTTAACGAGCTGTGGATTCCTTAGAGATCTTGTTAAAGGTAGAC
ACTGTTATAGCAGGCCTTGGGTGTGGCCTTAGATTGTGTATTTCTAACTACTTCCCAGGGATGC
TGCTGCTGGTGGTCAACAAATCCCATTTCCAGGAGCAACTGTGTAAACAAACCTGACTAGGTTT
GTTGCCTGGCCCAGGATTTATTTGACCAATGAGATTGCAGCACACACACCAGCCTCAGCCTGAG
GCCTGAGTCTTACCTTTGATGTCACAATCTGGCCTGTAGCCATGAATGTGGCCACAGCTACTCA
CAGACCAGATGGCCAGGTCTAGAGGACTACAGTAAGATGTGGAAGAGAACTGATCCTCAAGCCA
AGATCAAAGCAGGGGATAGGCCTCAGACTTGCCATTCTCTGGCTCTGGGATCGGCCACAGAGTC
GGCACTGCCCCACCCTCTAGAACTGTCAGACTTCCAGAGCTTTTCAGTATTTGAGGACATTAGC
CATCACATCAAAGAAGGAGGAGCCCAACTGGTAAAGAAAGTGAATGCCATCTTTCAGCTTGACA
TCACCAAAGATGGGAAGACCATTCTGCAGTGGACCATTGACCTCAAGAACGGTTCGGGGGACAT
GTACCTGGGATCAGCCCGGCTTCCTGCAGACACCATCTTCATCATCCCTGACACGGTCTTCACA
GAGTTAGTTGTGGGTAAGATGAACCCACAGAAGGCTTTCCTGGCTGGCAAGTTTAAAGTGAGAG
GCAAAGTTCTCCTTAGCCAGAAGCTGGAGAGGATCTTCAGAGAGTGGGCTAAATTTTAAGCATG
GGGGAATGCCCAGGAAAGATCAAGACTTCTGGCGTATTATAACGTTGAGTAGCAATCACGCATT
AACTGAAGATTAAAGGAAAAAATAGCCAATATTTTTACTCAAATTCTTCCTATTCAAGTTCGAT
TGATTTCCTGCTGATGTGTACATTTGCTGGGAGCTGGGATAGTAAAAAAGTGTTGGAGTGCAAC
ACCTACAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001101255	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL95150	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001101255 ⟸ NM_001107785
- UniProtKB:	D3ZCM8 (UniProtKB/TrEMBL)
- Sequence:	show sequence MWKRTDPQAKIKAGDRPQTCHSLALGSATESALPHPLELSDFQSFSVFEDISHHIKEGGAQLVK KVNAIFQLDITKDGKTILQWTIDLKNGSGDMYLGSARLPADTIFIIPDTVFTELVVGKMNPQKA FLAGKFKVRGKVLLSQKLERIFREWAKF hide sequence

RefSeq Acc Id:	XP_017447251 ⟸ XM_017591762
- Peptide Label:	isoform X1
- Sequence:	show sequence MWKRTDPQAKIKAGDRPQTCHSLALGSATESALPHPLELSDFQSFSVFEDISHHIKEGGAQLVK KVNAIFQLDITKDGKTILQWTIDLKNGSGDMYLGSARLPADTIFIIPDTVFTELVVGKMNPQKA FLAGKFKVRGKVLLSQKLERIFREWAKF hide sequence

RefSeq Acc Id:

ENSRNOP00000012524 ⟸ ENSRNOT00000012524

Protein Domains

SCP2

Transcriptome

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

Promoters

RGD ID:

13692488

Promoter ID:

EPDNEW_R3013

Type:

initiation region

Name:

Scp2d1_1

Description:

SCP2 sterol-binding domain containing 1

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	138,974,919 - 138,974,979	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1308385	AgrOrtholog
Ensembl Genes	ENSRNOG00000009461	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000012524	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000012524	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	3.30.1050.10	UniProtKB/TrEMBL
InterPro	SCP2_sterol-bd_dom	UniProtKB/TrEMBL
	SCP2_sterol-bd_dom_sf	UniProtKB/TrEMBL
KEGG Report	rno:311491	UniProtKB/TrEMBL
NCBI Gene	311491	ENTREZGENE
Pfam	SCP2	UniProtKB/TrEMBL
PhenoGen	Scp2d1	PhenoGen
Superfamily-SCOP	SCP2	UniProtKB/TrEMBL
UniProt	D3ZCM8	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2012-11-07	Scp2d1	SCP2 sterol-binding domain containing 1	RGD1308385	similar to RIKEN cDNA 1700010M22	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-04-30	RGD1308385	similar to RIKEN cDNA 1700010M22	RGD1308385_predicted	similar to RIKEN cDNA 1700010M22 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-20	RGD1308385_predicted	similar to RIKEN cDNA 1700010M22 (predicted)	LOC311491_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC311491_predicted	similar to RIKEN cDNA 1700010M22 (predicted)			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)