Pdcd2 (programmed cell death 2) - Rat Genome Database

Name: Pdcd2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Pdcd2 (programmed cell death 2) Chinchilla lanigera

Analyze

Symbol:

Pdcd2

Name:

programmed cell death 2

RGD ID:

8877139

Description:

ENCODES a protein that exhibits enzyme binding (ortholog); INVOLVED IN positive regulation of apoptotic process (ortholog); positive regulation of hematopoietic stem cell proliferation (ortholog); programmed cell death (ortholog); ASSOCIATED WITH genetic disease (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

programmed cell death protein 2

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	PDCD2 (programmed cell death 2)	NCBI	Ortholog
Mus musculus (house mouse):	Pdcd2 (programmed cell death 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Pdcd2 (programmed cell death 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PDCD2 (programmed cell death 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	PDCD2 (programmed cell death 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Pdcd2 (programmed cell death 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PDCD2 (programmed cell death 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Pdcd2 (programmed cell death 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

NCBI Annotation Information:

Annotation category: partial on reference assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955411	3,256,690 - 3,262,322 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955411	3,256,612 - 3,262,685 (+)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

positive regulation of apoptotic process (ISO)

positive regulation of hematopoietic stem cell proliferation (ISO)

programmed cell death (ISO)

regulation of hematopoietic progenitor cell differentiation (ISO)

Molecular Function

enzyme binding (ISO)

protein binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Pdcd2
(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_004955411	3,256,690 - 3,262,322 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955411	3,256,612 - 3,262,685 (+)	NCBI	ChiLan1.0	ChiLan1.0

PDCD2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	170,575,295 - 170,584,637 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	6	170,575,295 - 170,584,692 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	170,884,383 - 170,893,725 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	170,728,375 - 170,735,673 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	6	170,808,467 - 170,811,380	NCBI
Celera	6	171,681,705 - 171,689,005 (-)	NCBI		Celera
Cytogenetic Map	6	q27	NCBI
HuRef	6	168,389,709 - 168,398,835 (-)	NCBI		HuRef
CHM1_1	6	171,146,879 - 171,156,004 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	6	171,948,844 - 171,958,191 (-)	NCBI		T2T-CHM13v2.0

Pdcd2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	15,739,472 - 15,747,560 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	15,739,470 - 15,747,563 (-)	Ensembl		GRCm39 Ensembl
GRCm38	17	15,521,575 - 15,527,319 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	15,519,208 - 15,527,301 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	15,658,539 - 15,664,265 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	17	15,226,541 - 15,232,244 (-)	NCBI		MGSCv36	mm8
Celera	17	16,306,864 - 16,312,586 (-)	NCBI		Celera
Cytogenetic Map	17	A2	NCBI
cM Map	17	8.95	NCBI

Pdcd2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	65,158,034 - 65,163,524 (-)	NCBI		GRCr8
mRatBN7.2	1	56,484,947 - 56,490,437 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	56,463,931 - 56,490,437 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	61,334,277 - 61,339,767 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	69,997,832 - 70,003,322 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	63,244,260 - 63,249,750 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	57,512,968 - 57,518,458 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	57,512,968 - 57,518,458 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	58,443,078 - 58,448,568 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	54,412,081 - 54,417,571 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	54,415,029 - 54,420,298 (-)	NCBI
Celera	1	52,690,226 - 52,695,716 (-)	NCBI		Celera
Cytogenetic Map	1	q12	NCBI

PDCD2
(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	5	190,854,001 - 190,867,069 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	6	188,755,656 - 188,767,672 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	168,735,480 - 168,745,897 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	173,821,468 - 173,830,459 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	173,821,474 - 173,830,459 (-)	Ensembl	panpan1.1		panPan2

PDCD2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	12	72,482,635 - 72,488,678 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	12	72,482,886 - 72,489,437 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	12	72,244,947 - 72,250,909 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	12	73,467,974 - 73,473,935 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	12	73,467,974 - 73,474,687 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	12	72,740,466 - 72,746,423 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	12	72,562,886 - 72,568,846 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	12	72,953,917 - 72,959,885 (-)	NCBI		UU_Cfam_GSD_1.0

Pdcd2
(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_024404946	151,196,236 - 151,203,180 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004937098	39,399 - 44,857 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004937098	39,237 - 46,181 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PDCD2
(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	13	97,650,172 - 97,657,673 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	13	97,650,217 - 97,659,186 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666040	69,648,199 - 69,655,694 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Pdcd2
(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_004624850	6,378,161 - 6,383,946 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624850	6,377,702 - 6,383,874 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_013510897	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01011544	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AGCD01011545	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBBH01209693	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCLAT00000013949 ⟹ ENSCLAP00000013793

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955411	3,256,690 - 3,262,322 (+)	Ensembl

RefSeq Acc Id:

XM_013510897 ⟹ XP_013366351

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955411	3,256,612 - 3,262,685 (+)	NCBI

Sequence:

show sequence

CTCTACTCCCGCCTTCCGGGCAGACGCGACTTCCGCATCCGACCCTGCAGTGCGCGGCGTCGGG
TGCCCCGTGCGGTCATGGCAGTCGCTGGGCCCGGGTCCGTGGAGCTGGGCTTCGCCGAGGAGGC
ACCGGCGTGGCGGCTGCGCAGCGAGCAGTTCCCCAGCAAGGTGGGCGGGCGTCCGGCGTGGCTG
AGCGCGGCCGGGCTGCCGGGGCCCGCGGCCCTGGCGTGCTCGCGTTGCGGCCGGCCCCTTGCCT
TCCTGCTGCAGGTGTACGCGCCGCTGCCGGGCCGCGCCGACGCCTTCCACCGCAGCCTCTTCCT
CTTCTGCTGCCGCGAGCCGCCGTGCTGCGCGGGCCTGCGAGTTTTTAGGAATCAGCTGCCCAGG
AAAAATGAGTTTTACTCATTTGAGCCACCTTCTGAGAACCGTCCCCCAGATGCAGGAGAATCTG
TGTGTCTCCAGCTCCAGTCTGGCACTCACCTGTGCAGGGTGTGTGGCTGCCTAGCCCCCAAAAC
ATGCTCCAGATGCCACCAGGCACATTACTGCAGTAAGGAGCATCAGACGATAGACTGGAGGTTG
GTACATAAGCAGACTTGCACACAGGATCAGGTGGACCATACAGTTCCAGACCACAACTTCCTTT
TTCCAGAATTTGAAATTGTAATAGAAACGGAAGATGAGATTATGCCTGAAGTTGTAGAAAAGGA
AGAAGACTCTGACATTGTAGAAAGCATGGGTGAAACACCTGAAGAAGAATTGGATTCCATGGCC
AAGCATGAATCTAGAGAAGATAACATATTCCAGAAGTTTAAAACTCATATAGCCCATGAACCAG
AGCAGATTCTCCGATACGGCAGAGGTATCGAGCCCATCTGGATTTCTGGTAAAAATATTCCTCA
AGACAAGGATATTCCAGATTGTCCCTGTGGTGCCAAGAGAATATTTGAATTCCAGGTCATGCCG
CAGCTGCTGAACCACCTGAAAGCAGACAGACTGGGCAAGAGCGTGGACTGGGGCGTCCTGGCTG
TCTTCACCTGTGCGGAGAGCTGTAGCTTGGGCAGTGGCTACATGGAGGAATTTGTGTGGAAGCA
AGATGTAGCAGATACACCTTAAGGCTTTAAAGTCACTTATGTCGTAACACTTGCAATTCCGTCC
TTAGAACTTGATCTAAGGAAGTAACTTAGAGTAGTTACTTAGTAACTTACAGACATAGATGTAC
AAACATGTTGCTGGAGGCATTGTTTTATAATGTCTAAATTGATAAAACAAAAATGTCCAGTGAC
AGAAAATTTAGTAAATTTTGTTATATCCAAGGAGGAAAAGTAAGTGTTGTATCTATGTGGACAA
CAAATAAGAGATCTAAACACCATTATAGATGGTGTTTATGGTATGGTAGTTTTGTACAAATATT
TATACATGCATATGTACTTAGAAATAAAACTAGAAAGTTATACTGAACTGGTTACCTGCAAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_013366351	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000013793
	ENSCLAP00000013793.1

RefSeq Acc Id:

XP_013366351 ⟸ XM_013510897

- UniProtKB:

A0A8C2VEP9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAVAGPGSVELGFAEEAPAWRLRSEQFPSKVGGRPAWLSAAGLPGPAALACSRCGRPLAFLLQV
YAPLPGRADAFHRSLFLFCCREPPCCAGLRVFRNQLPRKNEFYSFEPPSENRPPDAGESVCLQL
QSGTHLCRVCGCLAPKTCSRCHQAHYCSKEHQTIDWRLVHKQTCTQDQVDHTVPDHNFLFPEFE
IVIETEDEIMPEVVEKEEDSDIVESMGETPEEELDSMAKHESREDNIFQKFKTHIAHEPEQILR
YGRGIEPIWISGKNIPQDKDIPDCPCGAKRIFEFQVMPQLLNHLKADRLGKSVDWGVLAVFTCA
ESCSLGSGYMEEFVWKQDVADTP

hide sequence

RefSeq Acc Id:

ENSCLAP00000013793 ⟸ ENSCLAT00000013949

Protein Domains

MYND-type

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000009531	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000013949	ENTREZGENE
	ENSCLAT00000013949.1	UniProtKB/TrEMBL
Gene3D-CATH	6.10.140.2220	UniProtKB/TrEMBL
InterPro	PDCD2_C	UniProtKB/TrEMBL
	Znf_MYND	UniProtKB/TrEMBL
NCBI Gene	Pdcd2	ENTREZGENE
PANTHER	PCDC2 PROGRAMMED CELL DEATH PROTEIN 2 -RELATED	UniProtKB/TrEMBL
	PROGRAMMED CELL DEATH PROTEIN 2	UniProtKB/TrEMBL
Pfam	PDCD2_C	UniProtKB/TrEMBL
	zf-MYND	UniProtKB/TrEMBL
PROSITE	ZF_MYND_2	UniProtKB/TrEMBL
Superfamily-SCOP	HIT/MYND zinc finger-like	UniProtKB/TrEMBL
UniProt	A0A8C2VEP9	ENTREZGENE, UniProtKB/TrEMBL

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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