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Gene: Pdcd6 (programmed cell death 6) Rattus norvegicus

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Symbol:

Pdcd6

Name:

programmed cell death 6

RGD ID:

1311239

Description:

Predicted to enable several functions, including metal ion binding activity; protein dimerization activity; and ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in several processes, including COPII vesicle coating; mesenchymal cell differentiation; and negative regulation of signal transduction. Predicted to act upstream of or within apoptotic process. Predicted to be located in several cellular components, including cytoplasmic vesicle; endoplasmic reticulum exit site; and perinuclear region of cytoplasm. Predicted to be part of COPII vesicle coat and Cul3-RING ubiquitin ligase complex. Orthologous to human PDCD6 (programmed cell death 6); INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 3-chloropropane-1,2-diol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

ALG-2; apoptosis-linked gene 2 protein homolog; LOC308061; programmed cell death protein 6

RGD Orthologs

Alliance Orthologs

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):	PDCD6 (programmed cell death 6)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, Treefam
Mus musculus (house mouse):	Pdcd6 (programmed cell death 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Pdcd6 (programmed cell death 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PDCD6 (programmed cell death 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PDCD6 (programmed cell death 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pdcd6 (programmed cell death 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	PDCD6 (programmed cell death 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PDCD6 (programmed cell death 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pdcd6 (programmed cell death 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Pdcd6 (programmed cell death 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	PDCD6 (programmed cell death 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	PDCD6 (programmed cell death 6)	Alliance	DIOPT (Ensembl Compara\|HGNC\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Pdcd6 (programmed cell death 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	pdcd6 (programmed cell death 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	pdcd6 (programmed cell death 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Alg-2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Alg-2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	M04F3.4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	M04F3.4	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	PEF1	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	PEF1	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	pdcd6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	pdcd6	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)

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	1	30,795,105 - 30,810,771 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	30,795,040 - 30,810,773 (+)	Ensembl				GRCr8
mRatBN7.2	1	28,966,518 - 28,982,188 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	28,966,518 - 28,982,189 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	28,767,781 - 28,783,445 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	34,767,645 - 34,783,309 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	28,968,411 - 28,984,075 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	31,576,183 - 31,591,852 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	31,576,183 - 31,591,849 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	33,002,331 - 33,017,997 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	29,769,911 - 29,785,577 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	27,618,297 - 27,633,964 (+)	NCBI		Celera
RGSC_v3.1	1	29,772,917 - 29,788,523 (+)	NCBI
Cytogenetic Map	1	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-dexrazoxane (ISO)

(+)-schisandrin B (EXP)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

2,4-dinitrotoluene (EXP)

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

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

amphetamine (EXP)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

benzo[e]pyrene (ISO)

beta-lapachone (ISO)

bis(2-chloroethyl) sulfide (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

CGP 52608 (ISO)

clofibric acid (EXP)

cocaine (ISO)

cyclosporin A (ISO)

deoxynivalenol (ISO)

diazinon (EXP)

dibenzo[a,l]pyrene (ISO)

dibutyl phthalate (EXP,ISO)

dieldrin (EXP)

diethylstilbestrol (ISO)

diuron (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

epoxiconazole (ISO)

ethanol (ISO)

fipronil (EXP)

flutamide (EXP)

folic acid (ISO)

fulvestrant (ISO)

gentamycin (EXP)

glycidyl methacrylate (ISO)

ivermectin (ISO)

leflunomide (EXP)

lithium atom (EXP)

lithium hydride (EXP)

methapyrilene (ISO)

microcystin RR (ISO)

mono(2-ethylhexyl) phthalate (ISO)

N-nitrosodiethylamine (EXP)

nickel dichloride (EXP)

nitrates (ISO)

ouabain (ISO)

ozone (ISO)

p-menthan-3-ol (ISO)

SB 431542 (ISO)

sodium arsenite (ISO)

succimer (ISO)

tetrachloromethane (EXP)

titanium dioxide (ISO)

triphenyl phosphate (ISO)

tungsten (ISO)

valproic acid (ISO)

vanadyl sulfate (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

angiogenesis (IEA)

apoptotic process (IEA,ISO)

cellular response to heat (IEA,ISO)

COPII vesicle coating (IEA,ISO,ISS)

endoplasmic reticulum to Golgi vesicle-mediated transport (IEA,ISO,ISS)

intracellular protein transport (IEA,ISO)

negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction (IEA,ISO)

negative regulation of TOR signaling (IEA,ISO)

negative regulation of vascular endothelial growth factor receptor signaling pathway (IEA,ISO)

neural crest cell development (IEA,ISO,ISS)

neural crest formation (IEA,ISO,ISS)

positive regulation of angiogenesis (IEA,ISO)

positive regulation of apoptotic process (IEA,ISO)

positive regulation of endothelial cell migration (IEA,ISO)

positive regulation of endothelial cell proliferation (IEA,ISO)

positive regulation of protein monoubiquitination (IEA,ISO,ISS)

response to calcium ion (IEA,ISO)

vascular endothelial growth factor receptor-2 signaling pathway (IEA,ISO)

Cellular Component

COPII vesicle coat (IEA,ISO,ISS)

Cul3-RING ubiquitin ligase complex (IEA,ISO,ISS)

cytoplasm (IEA,ISO,ISS)

cytoplasmic vesicle (IEA,ISO)

cytosol (IEA,ISO)

endoplasmic reticulum (IEA,ISO)

endoplasmic reticulum exit site (IEA,ISO,ISS)

endoplasmic reticulum membrane (IEA)

endosome (IEA)

ER to Golgi transport vesicle membrane (IEA)

nucleoplasm (IEA,ISO)

nucleus (IEA,ISO,ISS)

perinuclear region of cytoplasm (IEA,ISO)

Molecular Function

calcium ion binding (IEA,ISO,ISS)

calcium-dependent protein binding (IEA,ISO)

identical protein binding (IEA,ISO)

magnesium ion binding (IEA,ISO,ISS)

metal ion binding (IEA)

protein binding (ISO)

protein dimerization activity (IEA,ISO)

protein heterodimerization activity (IEA,ISO)

protein homodimerization activity (IEA,ISO,ISS)

protein-macromolecule adaptor activity (IEA,ISO)

protein-membrane adaptor activity (IEA,ISO)

ubiquitin-like ligase-substrate adaptor activity (IEA,ISO,ISS)

References

References - curated

#	Reference Title	Reference Citation
1.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
2.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:8560270	PMID:10200558	PMID:11883899	PMID:12477932	PMID:14561754	PMID:16132846	PMID:16189514	PMID:16957052	PMID:17196169	PMID:17214967	PMID:18256029	PMID:18940611
PMID:19056867	PMID:19520058	PMID:20458337	PMID:21122810	PMID:21893193	PMID:21988832	PMID:23376485	PMID:23533145	PMID:23924735	PMID:25416956	PMID:25667979	PMID:27541325
PMID:27716508	PMID:27784779	PMID:27813252	PMID:34762908

Genomics

Comparative Map Data

Pdcd6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	30,795,105 - 30,810,771 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	30,795,040 - 30,810,773 (+)	Ensembl				GRCr8
mRatBN7.2	1	28,966,518 - 28,982,188 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	28,966,518 - 28,982,189 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	28,767,781 - 28,783,445 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	34,767,645 - 34,783,309 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	28,968,411 - 28,984,075 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	31,576,183 - 31,591,852 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	31,576,183 - 31,591,849 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	33,002,331 - 33,017,997 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	29,769,911 - 29,785,577 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	27,618,297 - 27,633,964 (+)	NCBI		Celera
RGSC_v3.1	1	29,772,917 - 29,788,523 (+)	NCBI
Cytogenetic Map	1	p11	NCBI

PDCD6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	5	271,646 - 314,974 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	5	271,621 - 314,974 (+)	Ensembl			hg38	GRCh38
GRCh37	5	271,761 - 315,089 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	5	324,736 - 368,089 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	5	324,738 - 368,089	NCBI
Celera	5	370,282 - 413,335 (+)	NCBI		Celera
Cytogenetic Map	5	p15.33	NCBI
HuRef	5	258,986 - 302,543 (+)	NCBI		HuRef
CHM1_1	5	267,028 - 314,783 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	5	261,673 - 305,205 (+)	NCBI		T2T-CHM13v2.0

Pdcd6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	13	74,451,240 - 74,465,445 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	13	74,451,628 - 74,465,699 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	13	74,303,121 - 74,317,326 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	13	74,303,509 - 74,317,580 (-)	Ensembl			mm10	GRCm38
MGSCv37	13	74,440,569 - 74,454,774 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	13	74,769,130 - 74,790,911 (-)	NCBI		MGSCv36	mm8
Celera	13	76,632,567 - 76,646,789 (-)	NCBI		Celera
Cytogenetic Map	13	C1	NCBI
cM Map	13	40.15	NCBI

Pdcd6
(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_004955504	74,944 - 98,282 (+)	Ensembl
ChiLan1.0	NW_004955504	75,378 - 94,654 (+)	NCBI	ChiLan1.0	ChiLan1.0

PDCD6
(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	4	490,544 - 533,958 (+)	NCBI		NHGRI_mPanPan1-v2

PDCD6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	34	11,909,657 - 11,929,850 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	34	11,909,934 - 11,929,855 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	34	16,422,880 - 16,443,067 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	34	11,811,327 - 11,831,550 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	34	11,811,327 - 11,831,555 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	34	11,864,243 - 11,884,414 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	34	11,850,310 - 11,870,511 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	34	12,052,312 - 12,072,529 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Pdcd6
(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_024407213	244,968,082 - 244,982,736 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936815	1,129,352 - 1,143,992 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936815	1,129,367 - 1,144,020 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PDCD6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	16	79,818,958 - 79,835,746 (-)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	16	79,818,960 - 79,832,272 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PDCD6
(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	4	1,432,635 - 1,478,000 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	4	200,926 - 214,718 (+)	NCBI		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
ChlSab1.1 Ensembl	4	200,926 - 214,718 (+)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666518	18,887 - 20,478 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Pdcd6
(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_004624751	99,860 - 120,963 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624751	99,835 - 120,963 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Pdcd6
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	2	203,728,410 - 203,737,616 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Pdcd6
109 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	269
Count of miRNA genes:	182
Interacting mature miRNAs:	201
Transcripts:	ENSRNOT00000019735
Prediction methods:	Microtar, Miranda
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
2313090	Bmd69	Bone mineral density QTL 69	4.4	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	5293229	34184556	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	7746118	52746118	Rat
4889451	Eae29	Experimental allergic encephalomyelitis QTL 29	5.51		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	1	7746121	52746121	Rat
1357397	Bw41	Body weight QTL 41	4.19	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	29409279	74409279	Rat
70179	Xhs2	X-ray hypersensitivity QTL 2	3.2		intestine integrity trait (VT:0010554)	post-insult time to onset of moribundity (CMO:0001896)	1	1	43965634	Rat
1558642	Prcr2	Prostate cancer resistance QTL 2	4.3		prostate integrity trait (VT:0010571)	area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)	1	10379492	55379492	Rat
7421626	Bp360	Blood pressure QTL 360		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	6941022	51941022	Rat
2313070	Bss52	Bone structure and strength QTL 52	4.4	0.0001	body length (VT:0001256)	body length (CMO:0000013)	1	5293229	34184556	Rat
1357401	Bw43	Body weight QTL 43	3.75		body mass (VT:0001259)	body weight (CMO:0000012)	1	6909353	51909353	Rat
631494	Bp95	Blood pressure QTL 95	40	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	17315378	51816258	Rat
5684998	Bss101	Bone structure and strength QTL 101	3.6		tibia strength trait (VT:1000284)	tibia ultimate force (CMO:0001734)	1	6909353	51909353	Rat
5684999	Bss102	Bone structure and strength QTL 102	5.5	7e-07	tibia strength trait (VT:1000284)	tibia stiffness (CMO:0001735)	1	6909353	51909353	Rat
2302038	Pia31	Pristane induced arthritis QTL 31	5.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	1	12820494	57820494	Rat
2317755	Glom22	Glomerulus QTL 22	3.8		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	1	1	34184556	Rat
634353	Rends2	Renal damage susceptibility QTL 2		0.05	kidney blood vessel morphology trait (VT:0000530)	organ lesion measurement (CMO:0000677)	1	20656420	65656420	Rat
1578756	Iddm22	Insulin dependent diabetes mellitus QTL 22	2.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	20508326	65508326	Rat
631508	Sald1	Serum aldosterone level QTL 1	3.7		blood aldosterone amount (VT:0005346)	serum aldosterone level (CMO:0000487)	1	11684464	56684464	Rat
1331785	Rf27	Renal function QTL 27	4.643		urine sodium amount (VT:0006274)	urine sodium level (CMO:0000129)	1	30708375	87558729	Rat
2313053	Bss51	Bone structure and strength QTL 51	3.8	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	5293229	34184556	Rat

Markers in Region

RH138676

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	28,981,896 - 28,982,071 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	31,591,561 - 31,591,735	NCBI	Rnor6.0
Rnor_5.0	1	33,017,709 - 33,017,883	UniSTS	Rnor5.0
RGSC_v3.4	1	29,785,289 - 29,785,463	UniSTS	RGSC3.4
Celera	1	27,633,676 - 27,633,850	UniSTS
RH 3.4 Map	1	311.33	UniSTS
Cytogenetic Map	1	p11	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	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	165	91	90	59	92	59	6	356	192	11	144	81	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001107452	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006227784	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC094217	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC168744	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474002	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213638	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ219997	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ231349	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ231760	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ234686	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000019735 ⟹ ENSRNOP00000019735

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	30,795,040 - 30,810,773 (+)	Ensembl
mRatBN7.2 Ensembl	1	28,966,552 - 28,982,189 (+)	Ensembl
Rnor_6.0 Ensembl	1	31,576,183 - 31,591,849 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000098530 ⟹ ENSRNOP00000088944

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	28,966,630 - 28,981,801 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000102729 ⟹ ENSRNOP00000087055

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	30,795,040 - 30,810,773 (+)	Ensembl
mRatBN7.2 Ensembl	1	28,966,552 - 28,982,189 (+)	Ensembl

Ensembl Acc Id:

ENSRNOT00000114407 ⟹ ENSRNOP00000083510

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	28,966,518 - 28,979,105 (+)	Ensembl

RefSeq Acc Id:

NM_001107452 ⟹ NP_001100922

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	30,795,105 - 30,810,771 (+)	NCBI
mRatBN7.2	1	28,966,518 - 28,982,185 (+)	NCBI
Rnor_6.0	1	31,576,183 - 31,591,849 (+)	NCBI
Rnor_5.0	1	33,002,331 - 33,017,997 (+)	NCBI
RGSC_v3.4	1	29,769,911 - 29,785,577 (+)	RGD
Celera	1	27,618,297 - 27,633,964 (+)	RGD

Sequence:

show sequence

AGTGACTCAAAGGCACGCGCTTCCGTTGTTCCCAGGAAGTTGTGGGCTCCTGGTTCTGCCCCTG
ACTTGAGGCGGAAGCACAGCTTTTGGAGCTGGGCCGCGGGACCGCTGTGCATCAGCCCATGGCT
GCCTACTCCTACCGCCCAGGCCCAGGTGCTGGCCCTGGCCCTGCTGCTGGAGCTGCACTGCCAG
ACCAGAGCTTCCTGTGGAACGTCTTCCAGCGGGTTGATAAAGACAGGAGCGGAGTGATTTCAGA
CAATGAACTTCAGCAAGCATTATCCAATGGTACATGGACTCCGTTTAATCCAGTGACTGTGAGG
TCAATCATTTCTATGTTTGACCGAGAAAACAAGGCTGGTGTGAACTTCAGTGAATTCACAGGTG
TGTGGAAGTATATCACAGACTGGCAGAATGTCTTCCGGACCTACGACAGGGACAACTCTGGGAT
GATTGACAAGCATGAGCTCAAACAAGCACTCTCAGGTTTTGGCTACCGGCTCTCTGATCAGTTC
CATGACATCCTCATCCGAAAATTTGACAGGCAAGGACGAGGGCAGATCGCGTTCGATGACTTCA
TCCAGGGCTGCATCGTCTTGCAGAGGTTGACAGACATATTCAGACGCTATGACACGGATCAGGA
TGGCTGGATTCAGGTGTCTTACGAGCAGTATCTCTCCATGGTTTTCAGCATTGTATAACCAGGC
CTTGTGAACATCCAGCACGGCATGCAAAAAACTGAAGATGCCAAATTCCTTACCTGTGCTAGAA
CAGGGCATGGCTGCAGTGAGACGCTGCCCTTCCCGTTGACTGTATAGCTAATTCTTGGGGACCT
GGCTGTACATATGTGAATACTCTGGTCAGTGACTCTGTAGTGGCAATCTAGCTCCACTGTTAGA
ACACAGACGTTGGGGTTGCTGACTGATTGTGCCATGAGGTGAGACCTAATAATGGTTCAGGATT
CTGCTCCCAAACTATCATGTTCTTTTCTAGATGCCTCTAATTCTGTAGTCGAGATGCTCTCCTT
AGCCAATAGAATGTTAATATAATATGGAACTTGCACAGAAGGCTTTTCATGTGCCTTACTTTTT
AAAACGAAATTTTATCCATTGGAATATGTAACATAAGCAATAAAGTAATGATACAGACTGTCTA
GTTTTGGCTGGTTTTTGTTTTGTTTTGTTTTGCTTTAACTAAACAGGTGGAAGAAATGTACCCT
TTGTTACCACTCTAGTTGTTGTGTGAACATGGGAGAGTGGGACCTAAAAATAACGCAGACTGAA
GTCTCACACAATAGCCAATTTTATTTAGAGCATCAGAAAATGTATACTCTTGAGTGTGAAGAAG
AATCACATGCGAGATGTTCAATCACAAAGACATGGCAAAAGCATGTTTTTTCTGTGAAGGCACA
TGAATGACAGCTGCTGCAGTAAACTCCTGTCTGCCATAGCTGGGAAAAGCACAACACCACATCC
AGGACCAAGTCTATGTATGAAGAACAGGTCGTGTAGCATAAACAATAAAGTGTTGATAC

hide sequence

RefSeq Acc Id:

XM_006227784 ⟹ XP_006227846

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	30,795,193 - 30,810,386 (+)	NCBI
mRatBN7.2	1	28,966,533 - 28,982,188 (+)	NCBI
Rnor_6.0	1	31,576,186 - 31,591,852 (+)	NCBI
Rnor_5.0	1	33,002,331 - 33,017,997 (+)	NCBI

Sequence:

show sequence

GACTCAAAGGCACGCGCTTCCGTTGTTCCCAGGAAGTTGTGGGCTCCTGGTTCTGCCCCTGACT
TGAGGCGGAAGCACAGCTTTTGGAGCTGGGCCGCGGGACCGCTGTGCATCAGCCCATGGCTGCC
TACTCCTACCGCCCAGGCCCAGGTGCTGGCCCTGGCCCTGCTGCTGGAGCTGCACTGCCAGACC
AGAGCTTCCTGTGGAACGTCTTCCAGCGGGTTGATAAAGACAGGAGCGGAGTGATTTCAGACAA
TGAACTTCAGCAAGCATTATCCAATGGTACATGGACTCCGTTTAATCCAGTGACTGTGAGGTCA
ATCATTTCTATGTTTGACCGAGAAAACAAGGCTGGTGTGAACTTCAGTGAATTCACAGGTGTGT
GGAAGTATATCACAGACTGGCAGAATGTCTTCCGGACCTACGACAGGGACAACTCTGGGATGAT
TGACAAGCATGAGCTCAAACAAGCACTCTCAGGCTACCGGCTCTCTGATCAGTTCCATGACATC
CTCATCCGAAAATTTGACAGGCAAGGACGAGGGCAGATCGCGTTCGATGACTTCATCCAGGGCT
GCATCGTCTTGCAGAGGTTGACAGACATATTCAGACGCTATGACACGGATCAGGATGGCTGGAT
TCAGGTGTCTTACGAGCAGTATCTCTCCATGGTTTTCAGCATTGTATAACCAGGCCTTGTGAAC
ATCCAGCACGGCATGCAAAAAACTGAAGATGCCAAATTCCTTACCTGTGCTAGAACAGGGCATG
GCTGCAGTGAGACGCTGCCCTTCCCGTTGACTGTATAGCTAATTCTTGGGGACCTGGCTGTACA
TATGTGAATACTCTGGTCAGTGACTCTGTAGTGGCAATCTAGCTCCACTGTTAGAACACAGACG
TTGGGGTTGCTGACTGATTGTGCCATGAGGTGAGACCTAATAATGGTTCAGGATTCTGCTCCCA
AACTATCATGTTCTTTTCTAGATGCCTCTAATTCTGTAGTCGAGATGCTCTCCTTAGCCAATAG
AATGTTAATATAATATGGAACTTGCACAGAAGGCTTTTCATGTGCCTTACTTTTTAAAACGAAA
TTTTATCCATTGGAATATGTAACATAAGCAATAAAGTAATGATACAGACTGTCTAGTTTTGGCT
GGTTTTTGTTTTGTTTTGTTTTGCTTTAACTAAACAGGTGGAAGAAATGTACCCTTTGTTACCA
CTCTAGTTGTTGTGTGAACATGGGAGAGTGGGACCTAAAAATAACGCAGACTGAAGTCTCACAC
AATAGCCAATTTTATTTAGAGCATCAGAAAATGTATACTCTTGAGTGTGAAGAAGAATCACATG
CGAGATGTTCAATCACAAAGACATGGCAAAAGCATGTTTTTTCTGTGAAGGCACATGAATGACA
GCTGCTGCAGTAAACTCCTGTCTGCCATAGCTGGGAAAAGCACAACACCACATCCAGGACCAAG
TCTATGTATGAAGAACAGGTCGTGTAGCATAAACAATAAAGTGTTGATACAGA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001100922	(Get FASTA)	NCBI Sequence Viewer
	XP_006227846	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68744	(Get FASTA)	NCBI Sequence Viewer
	EDL87681	(Get FASTA)	NCBI Sequence Viewer
	EDL87682	(Get FASTA)	NCBI Sequence Viewer
	EDL87683	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000019735
	ENSRNOP00000019735.4
GenBank Protein	G3V7W1	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_001100922 ⟸ NM_001107452
- UniProtKB:	B5DEP1 (UniProtKB/Swiss-Prot), G3V7W1 (UniProtKB/TrEMBL), A0A8I6A7Q9 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAAYSYRPGPGAGPGPAAGAALPDQSFLWNVFQRVDKDRSGVISDNELQQALSNGTWTPFNPVT VRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKHELKQALSGFGYRLSD QFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV hide sequence

RefSeq Acc Id:	XP_006227846 ⟸ XM_006227784
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I6A7Q9 (UniProtKB/TrEMBL)
- Sequence:	show sequence MAAYSYRPGPGAGPGPAAGAALPDQSFLWNVFQRVDKDRSGVISDNELQQALSNGTWTPFNPVT VRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKHELKQALSGYRLSDQF HDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV hide sequence

Ensembl Acc Id:

ENSRNOP00000019735 ⟸ ENSRNOT00000019735

Ensembl Acc Id:

ENSRNOP00000088944 ⟸ ENSRNOT00000098530

Ensembl Acc Id:

ENSRNOP00000087055 ⟸ ENSRNOT00000102729

Ensembl Acc Id:

ENSRNOP00000083510 ⟸ ENSRNOT00000114407

Protein Domains

EF-hand

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-G3V7W1-F1-model_v2	AlphaFold	G3V7W1	1-191	view protein structure

Transcriptome

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

Promoters

RGD ID:

13689555

Promoter ID:

EPDNEW_R80

Type:

initiation region

Name:

Pdcd6_1

Description:

programmed cell death 6

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	1	31,576,262 - 31,576,322	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311239	AgrOrtholog
BioCyc Gene	G2FUF-61944	BioCyc
Ensembl Genes	ENSRNOG00000014485	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000019735	ENTREZGENE
	ENSRNOT00000019735.6	UniProtKB/Swiss-Prot
Gene3D-CATH	EF-hand	UniProtKB/Swiss-Prot
InterPro	EF-hand-dom_pair	UniProtKB/Swiss-Prot
	EF_Hand_1_Ca_BS	UniProtKB/Swiss-Prot
	EF_hand_dom	UniProtKB/Swiss-Prot
	Peflin/Sorcin_CaBP	UniProtKB/Swiss-Prot
KEGG Report	rno:308061	UniProtKB/Swiss-Prot
NCBI Gene	308061	ENTREZGENE
PANTHER	PEFLIN	UniProtKB/Swiss-Prot
	PROGRAMMED CELL DEATH PROTEIN 6	UniProtKB/Swiss-Prot
Pfam	EF-hand_7	UniProtKB/Swiss-Prot
PhenoGen	Pdcd6	PhenoGen
PROSITE	EF_HAND_1	UniProtKB/Swiss-Prot
	EF_HAND_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000014485	RatGTEx
SMART	EFh	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF47473	UniProtKB/Swiss-Prot
UniProt	A0A8I6A7Q9	ENTREZGENE, UniProtKB/TrEMBL
	B5DEP1	ENTREZGENE
	G3V7W1	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	B5DEP1	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-04-30	Pdcd6	programmed cell death 6	Pdcd6_predicted	programmed cell death 6 (predicted)	'predicted' is removed	2292626	APPROVED
2005-01-12	Pdcd6_predicted	programmed cell death 6 (predicted)			Symbol and Name status set to approved	70820	APPROVED

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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