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Gene: Cc2d1b (coiled-coil and C2 domain containing 1B) Rattus norvegicus

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Symbol:

Cc2d1b

Name:

coiled-coil and C2 domain containing 1B

RGD ID:

1306630

Description:

Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in nucleus. Orthologous to human CC2D1B (coiled-coil and C2 domain containing 1B); INTERACTS WITH 17alpha-ethynylestradiol; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

coiled-coil and C2 domain-containing protein 1B; five prime repressor element under dual repression-binding protein 2; FRE under dual repression-binding protein 2; freud-2; LOC313478; MGC109203; RGD1306630; similar to RIKEN cDNA A830039B04 gene

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	128,581,962 - 128,596,045 (+)	NCBI		GRCr8
mRatBN7.2	5	123,353,289 - 123,367,343 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	123,353,292 - 123,367,318 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	125,976,084 - 125,990,134 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	127,699,168 - 127,713,218 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	127,750,462 - 127,764,512 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	128,215,711 - 128,229,762 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	128,215,711 - 128,229,737 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	132,056,222 - 132,070,273 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	129,906,965 - 129,920,984 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	129,913,613 - 129,925,368 (+)	NCBI
Celera	5	122,087,913 - 122,101,964 (+)	NCBI		Celera
Cytogenetic Map	5	q34	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

(-)-epigallocatechin 3-gallate (ISO)

17alpha-ethynylestradiol (EXP)

2,3,7,8-tetrabromodibenzodioxine (ISO)

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

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

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

3,4-methylenedioxymethamphetamine (ISO)

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

acrylamide (EXP)

aristolochic acid A (ISO)

benzo[a]pyrene (ISO)

benzo[e]pyrene (ISO)

beta-lapachone (ISO)

bisphenol A (EXP)

bisphenol F (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

CGP 52608 (ISO)

choline (ISO)

dorsomorphin (ISO)

flutamide (EXP)

folic acid (ISO)

FR900359 (ISO)

gentamycin (EXP)

L-methionine (ISO)

mercury dibromide (ISO)

methamphetamine (EXP)

methapyrilene (ISO)

p-chloromercuribenzoic acid (ISO)

paracetamol (EXP,ISO)

phenylmercury acetate (ISO)

pirinixic acid (ISO)

potassium chromate (ISO)

quercetin (ISO)

SB 431542 (ISO)

SCH 23390 (EXP)

sodium fluoride (ISO)

sunitinib (ISO)

tamoxifen (ISO)

tetrahydropalmatine (ISO)

titanium dioxide (ISO)

triphenyl phosphate (ISO)

trovafloxacin (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

negative regulation of transcription by RNA polymerase II (IEA,ISO)

regulation of Notch signaling pathway (ISO)

regulation of transcription by RNA polymerase II (IBA)

Cellular Component

cytosol (ISO)

endosome membrane (ISO)

intracellular membrane-bounded organelle (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IBA,IDA)

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

DNA-binding transcription repressor activity, RNA polymerase II-specific (IEA,ISO)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,ISO)

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.	Freud-2/CC2D1B mediates dual repression of the serotonin-1A receptor gene.	Hadjighassem MR, etal., Eur J Neurosci. 2011 Jan;33(2):214-23. doi: 10.1111/j.1460-9568.2010.07498.x. Epub 2010 Dec 14.
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:12477932	PMID:27150226

Genomics

Comparative Map Data

Cc2d1b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	5	128,581,962 - 128,596,045 (+)	NCBI		GRCr8
mRatBN7.2	5	123,353,289 - 123,367,343 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	5	123,353,292 - 123,367,318 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	5	125,976,084 - 125,990,134 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	5	127,699,168 - 127,713,218 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	5	127,750,462 - 127,764,512 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	5	128,215,711 - 128,229,762 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	5	128,215,711 - 128,229,737 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	5	132,056,222 - 132,070,273 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	5	129,906,965 - 129,920,984 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	5	129,913,613 - 129,925,368 (+)	NCBI
Celera	5	122,087,913 - 122,101,964 (+)	NCBI		Celera
Cytogenetic Map	5	q34	NCBI

CC2D1B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	52,350,597 - 52,366,205 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	52,345,723 - 52,366,205 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	1	52,816,269 - 52,831,877 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	52,588,855 - 52,604,452 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	1	51,102,961 - 51,118,558 (-)	NCBI		Celera
Cytogenetic Map	1	p32.3	NCBI
HuRef	1	50,932,267 - 50,947,880 (-)	NCBI		HuRef
CHM1_1	1	52,933,642 - 52,949,254 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	1	52,232,062 - 52,247,670 (-)	NCBI		T2T-CHM13v2.0

Cc2d1b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	4	108,477,105 - 108,495,801 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	4	108,477,137 - 108,491,320 (+)	Ensembl		GRCm39 Ensembl
GRCm38	4	108,619,940 - 108,638,604 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	4	108,619,940 - 108,634,123 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	4	108,292,561 - 108,306,727 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	4	108,117,888 - 108,132,054 (+)	NCBI		MGSCv36	mm8
Celera	4	106,964,140 - 106,978,308 (+)	NCBI		Celera
Cytogenetic Map	4	C7	NCBI
cM Map	4	50.64	NCBI

Cc2d1b
(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_004955464	6,794,125 - 6,804,404 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955464	6,792,456 - 6,805,284 (+)	NCBI	ChiLan1.0	ChiLan1.0

CC2D1B
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	1	174,482,926 - 174,501,298 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	173,629,385 - 173,647,381 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	51,608,126 - 51,623,748 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	53,218,432 - 53,231,795 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	53,218,432 - 53,231,795 (-)	Ensembl	panpan1.1		panPan2

CC2D1B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	15	8,998,473 - 9,013,289 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	15	8,999,382 - 9,013,300 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	15	9,150,359 - 9,165,392 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	15	9,121,520 - 9,136,460 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	15	9,121,607 - 9,136,387 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	15	8,934,519 - 8,949,059 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	15	9,023,456 - 9,038,543 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	15	9,041,366 - 9,056,183 (+)	NCBI		UU_Cfam_GSD_1.0

Cc2d1b
(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	66,786,975 - 66,802,501 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936522	8,615,459 - 8,645,795 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936522	8,613,766 - 8,644,714 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CC2D1B
(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	159,854,593 - 159,872,015 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	159,854,280 - 159,872,363 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	147,514,731 - 147,525,988 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CC2D1B
(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	80,577,385 - 80,591,018 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	20	80,577,725 - 80,590,046 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666033	36,671,666 - 36,692,878 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Cc2d1b
(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_004624859	866,824 - 877,264 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624859	865,270 - 900,288 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Cc2d1b
35 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	371
Count of miRNA genes:	207
Interacting mature miRNAs:	247
Transcripts:	ENSRNOT00000011670
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1549845	Scl44	Serum cholesterol level QTL 44	6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	40128307	148607290	Rat
8552960	Pigfal15	Plasma insulin-like growth factor 1 level QTL 15			blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	5	111416838	156416838	Rat
1298070	Scl18	Serum cholesterol level QTL 18	3.7		blood LDL cholesterol amount (VT:0000181)	calculated plasma low density lipoprotein cholesterol level (CMO:0001245)	5	79584860	124584860	Rat
61452	Ciaa5	CIA Autoantibody QTL 5	3.5		blood autoantibody amount (VT:0003725)	calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)	5	94858972	143070159	Rat
1582230	Bw78	Body weight QTL 78	3.2	0.0016	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	5	119085612	128034027	Rat
7411582	Foco3	Food consumption QTL 3	7.5	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	5	87468046	132468046	Rat
1598859	Cm66	Cardiac mass QTL 66	2		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	79584860	124584860	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
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
1549838	Bss4	Bone structure and strength QTL 4	9.2		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	5	106906205	151906205	Rat
2317753	Glom24	Glomerulus QTL 24	3.1		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	5	97570330	136479578	Rat
7411564	Bw135	Body weight QTL 135		0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	87468046	132468046	Rat
8657050	Bw146	Body weight QTL 146	19.84	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	5	108938288	153938288	Rat
1641912	Alcrsp18	Alcohol response QTL 18			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	5	35189153	141643988	Rat
2317056	Wbc3	White blood cell count QTL 3	2.51	0.01	leukocyte quantity (VT:0000217)	white blood cell count (CMO:0000027)	5	105999803	150999803	Rat
2293642	Bss37	Bone structure and strength QTL 37	4.64	0.0001	femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	120740824	151018848	Rat
1358909	Kidm25	Kidney mass QTL 25	1.87		kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	5	90067849	128034027	Rat
1578673	Bmd13	Bone mineral density QTL 13	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	5	103689353	148689353	Rat
70189	Mcs5	Mammary carcinoma susceptibility QTL 5	10.51		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	55805606	132207589	Rat
7207488	Bss110	Bone structure and strength QTL 1	8.4		femur strength trait (VT:0010010)	femur stiffness (CMO:0001674)	5	106906205	151906205	Rat
8694441	Bw169	Body weight QTL 169	17.61	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	5	111416838	156416838	Rat
7207491	Bss112	Bone structure and strength QTL 112	7		femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	5	106906205	151906205	Rat
2290448	Scl54	Serum cholesterol level QTL 54	2.93		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	31663789	131345958	Rat
8694198	Abfw3	Abdominal fat weight QTL 3	16.13	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	5	111416838	156416838	Rat
1298086	Bp156	Blood pressure QTL 156			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	84132602	129132602	Rat
2306971	Anxrr21	Anxiety related response QTL 21	9.47		fear/anxiety-related behavior trait (VT:1000241)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	5	66174080	124160948	Rat
1298089	Scl14	Serum cholesterol level QTL 14	5.8	0.0004	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	5	108845856	153845856	Rat
1358895	Bp254	Blood pressure QTL 254	3.6	0.0003	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	58829236	128034027	Rat
1358889	Bp261	Blood pressure QTL 261	2.86		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	5	90067849	128034027	Rat
1331796	Thshl2	Thyroid stimulating hormone level QTL 2	2.3		blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	5	97059760	147465714	Rat
70212	Niddm25	Non-insulin dependent diabetes mellitus QTL 25	3.54		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	5	1	131345958	Rat
7794739	Bp372	Blood pressure QTL 372		0.0058	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	117913688	125222967	Rat
1331801	Rf33	Renal function QTL 33	4.149		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	5	43726656	129132602	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
7207486	Bss109	Bone structure and strength QTL 109			femur strength trait (VT:0010010)	femur total energy absorbed before break (CMO:0001677)	5	106906205	151906205	Rat
7207481	Bss106	Bone structure and strength QTL 106	7.9		femur strength trait (VT:0010010)	femur ultimate force (CMO:0001675)	5	106906205	151906205	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
1581510	Cm54	Cardiac mass QTL 54	3.4	0.05	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	5	120740824	143608494	Rat
1576312	Emca8	Estrogen-induced mammary cancer QTL 8	4.1		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	5	50328551	141643988	Rat
7411601	Foco12	Food consumption QTL 12	19.7	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	5	87468046	132468046	Rat
1576314	Eutr1	Estrogen induced uterine response QTL 1			uterus integrity trait (VT:0010575)	pyometritis severity score (CMO:0002009)	5	2138965	166875058	Rat
1598846	Bp293	Blood pressure QTL 293	3.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	5	79584860	124584860	Rat
1598847	Cm62	Cardiac mass QTL 62	3.4		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	5	108845856	153845856	Rat
631527	Tls1	T-lymphoma susceptibility QTL 1	0	0.001	thymus integrity trait (VT:0010555)	post-insult time to onset of T-cell lymphoma (CMO:0001907)	5	90450144	135450144	Rat
8694389	Bw160	Body weight QTL 160	6.17	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	5	111416838	156416838	Rat
61426	Scl2	Serum cholesterol level QTL 2	7.3	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	5	59793399	143070159	Rat
1354598	Srn6	Serum renin concentration QTL 6	3.8		blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	5	69540295	151018848	Rat
6903316	Bw113	Body weight QTL 113	2	0.0103	body mass (VT:0001259)	body weight (CMO:0000012)	5	87765973	132765973	Rat
1358187	Emca1	Estrogen-induced mammary cancer QTL 1	4.4		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	5	99216724	148607142	Rat

Markers in Region

RH141093

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	123,366,930 - 123,367,115 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	128,229,350 - 128,229,534	NCBI	Rnor6.0
Rnor_5.0	5	132,069,861 - 132,070,045	UniSTS	Rnor5.0
RGSC_v3.4	5	129,920,574 - 129,920,758	UniSTS	RGSC3.4
Celera	5	122,101,552 - 122,101,736	UniSTS
RH 3.4 Map	5	809.4	UniSTS
Cytogenetic Map	5	q35	UniSTS

UniSTS:234996

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	5	123,367,012 - 123,367,235 (+)	MAPPER	mRatBN7.2
Rnor_6.0	5	128,229,432 - 128,229,654	NCBI	Rnor6.0
Rnor_5.0	5	132,069,943 - 132,070,165	UniSTS	Rnor5.0
RGSC_v3.4	5	129,920,656 - 129,920,878	UniSTS	RGSC3.4
Celera	5	122,101,634 - 122,101,856	UniSTS
Cytogenetic Map	5	q35	UniSTS

Expression

RNA-SEQ Expression

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

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001270984	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005504443	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC089922	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474008	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212419	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222909	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000005	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000011670 ⟹ ENSRNOP00000011670

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	123,353,292 - 123,367,318 (+)	Ensembl
Rnor_6.0 Ensembl	5	128,215,711 - 128,229,737 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000097235 ⟹ ENSRNOP00000088232

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	5	123,353,292 - 123,367,318 (+)	Ensembl

RefSeq Acc Id:

NM_001270984 ⟹ NP_001257913

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	128,581,994 - 128,596,045 (+)	NCBI
mRatBN7.2	5	123,353,292 - 123,367,343 (+)	NCBI
Rnor_6.0	5	128,215,711 - 128,229,762 (+)	NCBI
Rnor_5.0	5	132,056,222 - 132,070,273 (+)	NCBI
Celera	5	122,087,913 - 122,101,964 (+)	NCBI

Sequence:

show sequence

ACGTGCCGGGCGAGAGCCACCGCCTCCTGGGCGGGTGCTTCCTGTGGCTGTCTCCGCCGCCGCC
CGGGGGCCGCGGGAAGCTAGGCGGTTCCGGGCTCGAGAAGGCCCGGTTTTGGTTCGGGTCCGCC
GCGAGGTATCTAGCCTGCCAAGATGCCAGGGCCAAGACCTCGGAAGGGCCCTAAGACCAGTGGC
CAGGGTGCCGAAACTGCCAAGCAGCTGGGGCTTTTTGTGGAGTTCAACCCTGAGGACATGCTCC
TGGGGATGGATGAGACAGAAGATGATGGAGACCTGGAGGCTGAGTTATTGGCACTCACTGGGGA
AACAGGGAGCACAAGCAGGAAGCCAGCACCCAAGGGGCGGGCCCCACTGCCCATGGCCCACATT
GAGAAGTTGGCAGCAGACTGTATGCGAGATGTGGAGGAGGAGGGCGAGGAAGAGGAAGGGCTGG
AGGACGATGCAGACCTTCTGACAGAGCTGCAGGAAGTCCTGGGTGTGGATGAAGAAACTGGGCT
GGTGGATGACAGTGAGGAAACAAGCCCAGACCTGTCTGAGGAGAAGACAAGGGACAACACTGAA
CAACCTGTAGCACCAGCAGCCTTCCAGCAGGCCTTACCTGCAGCAGTGGCTCAGGCTGGAGGGC
CTCGGGGGCTGCAGGCTTTGCTGGAGGAACGGATCCAGAACTACCGGGAGGCTGCGGCCAGTGC
CAAGGAGGCTGGTGAAGCTGCCAAAGCCCGGCGCTGTGAGCGAGGCCTGAAGACTCTGGAGTCC
CAGCTTGCCACTGTGAGGAAAGGCGGCAAGATCTGTGAGGACGAGATTCCACCTCCAGTGGCCT
TGGGCAAAAGGCCCCCAGCCCACCAGGAAAGACCCAGCAAGGACTCTGAGATAGACTCTGCAGG
CTCCTGTGCCATGGACCCAGGTGACCTTTCCCAACCTGAGTCCAGCCTCCCTGCCGTTGCTGCC
TTGCCTGATTCAGACCCAGACCCACAGGCCCTGCTGTTAGCCCGACAAAGAGAGTACAAAGCAG
CTGCTCTCAGTGCCAAGCGGGCCGGAGATCTAGACCGTGCTCGGGAGCTCATGAGGATTGGGAA
GAGATTTGGTACTGTCCTAGAGGCCCTGGAGAAGGGGCAGCCTGTGGATCTGAGTGGCATGCCC
CCAGCACCTGAGGATCTGAAGGCCCTCCCCCAGGCTTCTGAGGCCTCTGCAGCAACCCAAGTCC
TGTCCCCAGCAGTGGAGCAAATGCAGCCAGTGATGTCCTCTGACCTCCCAGCCACCCCAGCGGC
CCCTGCAGAGCCAAAGACAGTGCTGGATGCTTTACAACAAAGGCTGAACAGGTATCGTGAGGCA
GGCATCCAGGCCAGGGCCAGTGGGGATGAGCGCAAAGCCAGGATGCATGACCGAATTGCCAAGC
AATATCAGGATGCTATTCGAGCTCATCAAGCAGGACGGAAAGTTGACTTTGCTGAGTTACCTGT
TCCTCCAGGATTTCCTCCCATCCCTGGCCTGGAGCCCAGAAAAGATACTGAGGAGGATTCAGTG
ACAGCAACTTTGGCAGCTGCCCAAAAACTGGCCTCAGAAGATACAGCCCTGGTAGATGAAGATG
AGGAGAGGGACACCCCAGCACAGGCCCCATTGGCCAAGAAGCCAGCACAGCCTCTGGTCCCTTC
ATCCCATCTTCTGAATGAGCCCAAGGCCTCAAGTTCTAAGGAGTCACTGAGTCCATCTGTTCGG
GAGCAGGTGACACTGCTGGAGGCTCGGAAACTGCAGTACCAGCGAGCAGCTCTGCAAGCCAAGC
GCAGGCAGGATCTGGAGCAGGCCAAATCCCACTTACGAGTAGCTAAAAGTCTTGAGGCTCAGAT
CATCCAGGCCAGAGCTGGTCAACCGATTGACCTCTCTAAGGTGCCTTCACCCTTGACAGATGAA
GAAGGTGACTTCATCCTCATTCACCATGAGGATCTTCGACTCTCCCAGAAGGCTGAGGAGGTGT
ATGCCCAGCTACAGAAAATACTCCTGGAGCAGCACGAGAAGTGCCTGCTGTTCTCCAAGCAGTT
CATGCACCAGGGTAATGTGGCTGAGACTACACGGTTTGAGAAGCTTGCTGAGGACCGAAAGAAA
CAGCTTGAGATCCTGCAGCTGGCCCAAGCCCAGGGCCTGGACCCTCCCAGTCATCACTTTGAAT
TGAAGACATTGCAGACTGTGAGGATCTTCTCAGAACTCAATAGCACAGAAATGCATCTGATCAT
CGTCCGGGGAATGAACCTCCCAGCCCCACCAGGAGTGACTCCGGATGATTTGGATGCTTTCGTA
CGGTTTGAGTTTCACTACCCTAACTCGGACCAGGCTCAAAAAAGCAAAACAGCTGTGGTAAAAA
ATACGAACTCTCCAGAATTTGAACAAGTTTTCAAACTAAACATCAATCGAAATCACCGAGGCTT
TAGGAGGGTGATCCAGAGCAAAGGAATCAAATTTGAGATCTTCCACAAAGGATCCTTTTTTAGA
AGCGACAAGCTGGTTGGCACAGCACACCTGAAACTGGAAAGGCTGGAGAAAGAGTGTGAGATCA
GAGAGATCATGGAGGTTCTGGATGGAAGAAAGCCCACTGGGGGGAAGCTGGAAGTTAAGGTGAG
GCTGCGGGAGCCTTTGAGCAGCCAGGACGTGCAGATGGTCACTGAGAACTGGCTGGTCCTGGAG
CCTAGGGGCCTGTGAAGAGGTGGACATCACTGGTACGAGCTCACTGACCCGGCTTTGCTGGCTG
CAAGAGCCTTTGTACATGGAGATGCTGCTACACAAAGCACCAAAGACTGTTGAACTAACCGTGG
CTCGGGCGCTCCTCGTGCTGCTTCTCCTGGGCCTTCGTGGAAGCTGGCCACATCTTAGGAGCGT
CTCGTAGCCTCCCACCCCACTCTCCAGAATGTGGGTGAAGACAAGGATACCCCCATTGCTCTGT
GCCATTGAGTCCTACTGCCCCGTAACCTCTGCATAGTAATTATGTACAGCTTAACCCAGCCCCC
CACAACCCCTTGCACCATTTCTGGATGTGCCTTTCAAAGATGTAACTGTAAGGGATGGGAGAAC
TTGAGTGTGATCGGAACATCCCCTGCTTAAGGGAGAGACTGGATTCCGTGACTCCAGCTGGCCA
GTGGCAGACTGTCCTGCTCAGCTGTTTGCCCCTCTGCCTGTGCCTTTGTTCCTGACAGCTGCTG
CACTAGCCTTTCTGATCCCCAGAGGACTCGGGAACAGGAAAGTTACTTTGGTACTATTGGTGGG
GAGTAAGGGGAAGGTTCTCTTTGGTTTGGTTCATGTACCTAAGATGAAAGACTATTAATTAAGG
AGAAAAAAAAGAAAGAAAAACTATC

hide sequence

RefSeq Acc Id:

XR_005504443

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	5	128,581,962 - 128,591,935 (+)	NCBI
mRatBN7.2	5	123,353,289 - 123,363,233 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001257913	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH89922	(Get FASTA)	NCBI Sequence Viewer
	EDL90395	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000011670.5
	ENSRNOP00000088232.1
GenBank Protein	Q5FVK6	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001257913 ⟸ NM_001270984

- UniProtKB:

Q5FVK6 (UniProtKB/Swiss-Prot), A0A8I6A5T1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPGPRPRKGPKTSGQGAETAKQLGLFVEFNPEDMLLGMDETEDDGDLEAELLALTGETGSTSRK
PAPKGRAPLPMAHIEKLAADCMRDVEEEGEEEEGLEDDADLLTELQEVLGVDEETGLVDDSEET
SPDLSEEKTRDNTEQPVAPAAFQQALPAAVAQAGGPRGLQALLEERIQNYREAAASAKEAGEAA
KARRCERGLKTLESQLATVRKGGKICEDEIPPPVALGKRPPAHQERPSKDSEIDSAGSCAMDPG
DLSQPESSLPAVAALPDSDPDPQALLLARQREYKAAALSAKRAGDLDRARELMRIGKRFGTVLE
ALEKGQPVDLSGMPPAPEDLKALPQASEASAATQVLSPAVEQMQPVMSSDLPATPAAPAEPKTV
LDALQQRLNRYREAGIQARASGDERKARMHDRIAKQYQDAIRAHQAGRKVDFAELPVPPGFPPI
PGLEPRKDTEEDSVTATLAAAQKLASEDTALVDEDEERDTPAQAPLAKKPAQPLVPSSHLLNEP
KASSSKESLSPSVREQVTLLEARKLQYQRAALQAKRRQDLEQAKSHLRVAKSLEAQIIQARAGQ
PIDLSKVPSPLTDEEGDFILIHHEDLRLSQKAEEVYAQLQKILLEQHEKCLLFSKQFMHQGNVA
ETTRFEKLAEDRKKQLEILQLAQAQGLDPPSHHFELKTLQTVRIFSELNSTEMHLIIVRGMNLP
APPGVTPDDLDAFVRFEFHYPNSDQAQKSKTAVVKNTNSPEFEQVFKLNINRNHRGFRRVIQSK
GIKFEIFHKGSFFRSDKLVGTAHLKLERLEKECEIREIMEVLDGRKPTGGKLEVKVRLREPLSS
QDVQMVTENWLVLEPRGL

hide sequence

Ensembl Acc Id:

ENSRNOP00000011670 ⟸ ENSRNOT00000011670

Ensembl Acc Id:

ENSRNOP00000088232 ⟸ ENSRNOT00000097235

Protein Domains

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q5FVK6-F1-model_v2	AlphaFold	Q5FVK6	1-850	view protein structure

Transcriptome

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

Promoters

RGD ID:

13693904

Promoter ID:

EPDNEW_R4428

Type:

multiple initiation site

Name:

Cc2d1b_1

Description:

coiled-coil and C2 domain containing 1B

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	128,215,760 - 128,215,820	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1306630	AgrOrtholog
BioCyc Gene	G2FUF-40377	BioCyc
Ensembl Genes	ENSRNOG00000008634	Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000011670.8	UniProtKB/Swiss-Prot
	ENSRNOT00000097235.1	UniProtKB/TrEMBL
Gene3D-CATH	2.60.40.150	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro	C2_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	C2_domain_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	C2_Freud	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CC2D1A/B	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	DM14	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:313478	UniProtKB/Swiss-Prot
NCBI Gene	313478	ENTREZGENE
PANTHER	COILED-COIL AND C2 DOMAIN-CONTAINING PROTEIN 1B	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PTHR13076	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	CC2D1A-B_DM14	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PF00168	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Cc2d1b	PhenoGen
PROSITE	PS50004	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000008634	RatGTEx
SMART	DM14	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SM00239	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF49562	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8I6A5T1	ENTREZGENE, UniProtKB/TrEMBL
	A6JYV8_RAT	UniProtKB/TrEMBL
	C2D1B_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2006-03-30	Cc2d1b	coiled-coil and C2 domain containing 1B	RGD1306630	similar to RIKEN cDNA A830039B04 gene	Symbol and Name updated	1299863	APPROVED
2005-12-06	RGD1306630	similar to RIKEN cDNA A830039B04 gene	RGD1306630_predicted	similar to RIKEN cDNA A830039B04 gene (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-20	RGD1306630_predicted	similar to RIKEN cDNA A830039B04 gene (predicted)	LOC313478_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC313478_predicted	similar to RIKEN cDNA A830039B04 gene (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)

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