PDCD1 (programmed cell death 1) - Rat Genome Database

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Gene: PDCD1 (programmed cell death 1) Canis lupus familiaris
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Symbol: PDCD1
Name: programmed cell death 1
RGD ID: 12157317
Description: INVOLVED IN negative regulation of apoptotic process (ortholog); negative regulation of tolerance induction (ortholog); positive regulation of apoptotic process (ortholog); ASSOCIATED WITH acute myeloid leukemia (ortholog); acute myocarditis (ortholog); anogenital venereal wart (ortholog); FOUND IN external side of plasma membrane (ortholog); plasma membrane (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: PD-1; programmed cell death protein 1; programmed death 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12551,606,559 - 51,618,903 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2551,608,173 - 51,618,723 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2551,830,362 - 51,840,346 (-)NCBI
ROS_Cfam_1.02551,809,256 - 51,820,132 (-)NCBI
UMICH_Zoey_3.12551,659,966 - 51,669,894 (-)NCBI
UNSW_CanFamBas_1.02551,399,146 - 51,409,148 (-)NCBI
UU_Cfam_GSD_1.02551,676,302 - 51,686,322 (-)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
acute myeloid leukemia  (ISO)
acute myocarditis  (ISO)
anogenital venereal wart  (ISO)
anti-basement membrane glomerulonephritis  (ISO)
asthma  (ISO)
autoimmune hepatitis  (ISO)
Burns  (ISO)
cervix uteri carcinoma in situ  (ISO)
Chlamydia pneumonia  (ISO)
Chronic Hepatitis B  (ISO)
Colonic Neoplasms  (ISO)
Colorectal Neoplasms  (ISO)
cryptococcal meningitis  (ISO)
cystitis  (ISO)
Cytomegalovirus Infections  (ISO)
dilated cardiomyopathy  (ISO)
Experimental Autoimmune Encephalomyelitis  (ISO)
Experimental Melanoma  (ISO)
Fungemia  (ISO)
Graves' disease  (ISO)
Helicobacter Infections  (ISO)
Hepatic Echinococcosis  (ISO)
hepatitis  (ISO)
hepatitis A  (ISO)
hepatitis B  (ISO)
hepatitis C  (ISO)
hepatocellular carcinoma  (ISO)
histoplasmosis  (ISO)
human immunodeficiency virus infectious disease  (ISO)
hydronephrosis  (ISO)
intellectual disability  (ISO)
lupus nephritis  (ISO)
lymphocytic choriomeningitis  (ISO)
melanoma  (ISO)
multiple sclerosis  (ISO)
myocarditis  (ISO)
periodontitis  (ISO)
Pneumovirus Infections  (ISO)
pre-eclampsia  (ISO)
pulmonary tuberculosis  (ISO)
Recurrent Respiratory Papillomatosis  (ISO)
renal cell carcinoma  (ISO)
respiratory syncytial virus infectious disease  (ISO)
Schistosomiasis Japonica  (ISO)
Sepsis  (ISO)
Spinal Cord Injuries  (ISO)
stomach cancer  (ISO)
Streptococcus pneumonia  (ISO)
systemic lupus erythematosus  (ISO)
toxic shock syndrome  (ISO)
Transplant Rejection  (ISO)
triple-receptor negative breast cancer  (ISO)
tuberculosis  (ISO)
type 2 diabetes mellitus  (ISO)
Viral Bronchiolitis  (ISO)
viral encephalitis  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:24154626   PMID:27016050   PMID:27107075   PMID:27276060   PMID:31733502  


Genomics

Comparative Map Data
PDCD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12551,606,559 - 51,618,903 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2551,608,173 - 51,618,723 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2551,830,362 - 51,840,346 (-)NCBI
ROS_Cfam_1.02551,809,256 - 51,820,132 (-)NCBI
UMICH_Zoey_3.12551,659,966 - 51,669,894 (-)NCBI
UNSW_CanFamBas_1.02551,399,146 - 51,409,148 (-)NCBI
UU_Cfam_GSD_1.02551,676,302 - 51,686,322 (-)NCBI
PDCD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2241,849,884 - 241,858,894 (-)EnsemblGRCh38hg38GRCh38
GRCh382241,849,881 - 241,858,908 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372242,792,036 - 242,801,046 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362242,440,711 - 242,449,731 (-)NCBINCBI36hg18NCBI36
Celera2236,456,683 - 236,465,707 (-)NCBI
Cytogenetic Map2q37.3NCBI
HuRef2234,541,510 - 234,550,535 (-)NCBIHuRef
CHM1_12242,797,131 - 242,806,156 (-)NCBICHM1_1
Pdcd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39193,966,027 - 93,980,278 (-)NCBIGRCm39mm39
GRCm39 Ensembl193,966,027 - 93,980,278 (-)Ensembl
GRCm38194,038,305 - 94,052,553 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl194,038,305 - 94,052,553 (-)EnsemblGRCm38mm10GRCm38
MGSCv37195,934,882 - 95,949,130 (-)NCBIGRCm37mm9NCBIm37
MGSCv36195,868,711 - 95,882,959 (-)NCBImm8
Celera196,903,284 - 96,917,529 (-)NCBICelera
Cytogenetic Map1DNCBI
Pdcd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2994,418,786 - 94,431,945 (-)NCBI
Rnor_6.0 Ensembl9101,025,313 - 101,038,625 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl9101,307,764 - 101,319,845 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.09101,305,742 - 101,319,937 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.09100,676,274 - 100,690,991 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4993,172,543 - 93,185,687 (-)NCBIRGSC3.4rn4RGSC3.4
Celera991,952,891 - 91,966,035 (-)NCBICelera
Cytogenetic Map9q36NCBI
Pdcd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495554249,259 - 58,823 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495554249,290 - 57,747 (+)NCBIChiLan1.0ChiLan1.0
PDCD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v02B129,111,509 - 129,121,127 (-)NCBIMhudiblu_PPA_v0panPan3
Pdcd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303193,055,706 - 193,066,914 (-)NCBI
SpeTri2.0NW_004936745152,571 - 163,712 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDCD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15140,336,210 - 140,347,478 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115140,337,353 - 140,347,493 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PDCD1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110127,877,383 - 127,886,234 (-)NCBI
ChlSab1.1 Ensembl10127,878,554 - 127,886,088 (-)Ensembl
Vero_WHO_p1.0NW_02366604071,433,325 - 71,442,153 (+)NCBI
Pdcd1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248475,732,922 - 5,741,908 (-)NCBI


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 reproductive system respiratory system adipose tissue
High
Medium
Low 4 15 6 6 6 2 9 8 6 2
Below cutoff 1 5 7 4 3 3 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000020931   ⟹   ENSCAFP00000019435
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl2551,608,173 - 51,618,723 (-)Ensembl
RefSeq Acc Id: NM_001314097   ⟹   NP_001301026
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12551,608,987 - 51,618,715 (-)NCBI
Dog10K_Boxer_Tasha2551,830,362 - 51,840,346 (-)NCBI
ROS_Cfam_1.02551,810,077 - 51,820,012 (-)NCBI
UMICH_Zoey_3.12551,659,966 - 51,669,894 (-)NCBI
UNSW_CanFamBas_1.02551,399,146 - 51,409,148 (-)NCBI
UU_Cfam_GSD_1.02551,676,302 - 51,686,322 (-)NCBI
Sequence:
RefSeq Acc Id: XM_022409577   ⟹   XP_022265285
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12551,606,559 - 51,618,903 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038434570   ⟹   XP_038290498
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.02551,809,256 - 51,820,132 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001301026 (Get FASTA)   NCBI Sequence Viewer  
  XP_038290498 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAO74171 (Get FASTA)   NCBI Sequence Viewer  
  BAP46805 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_022265285   ⟸   XM_022409577
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001301026   ⟸   NM_001314097
- Peptide Label: precursor
- UniProtKB: A0A090BAM7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000019435   ⟸   ENSCAFT00000020931
RefSeq Acc Id: XP_038290498   ⟸   XM_038434570
- Peptide Label: isoform X1
Protein Domains
Ig-like

Promoters
RGD ID:13687852
Promoter ID:EPDNEW_C5920
Type:single initiation site
Name:PDCD1_1
Description:programmed cell death 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12551,618,723 - 51,618,783EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000013184 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSCAFP00000019435 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000020931 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like_dom UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Ig_V-set UniProtKB/TrEMBL
  PDCD1 UniProtKB/TrEMBL
KEGG Report cfa:486213 UniProtKB/TrEMBL
NCBI Gene PDCD1 ENTREZGENE
PANTHER PTHR15264 UniProtKB/TrEMBL
Pfam V-set UniProtKB/TrEMBL
PROSITE IG_LIKE UniProtKB/TrEMBL
SMART IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt A0A090BAM7 ENTREZGENE, UniProtKB/TrEMBL
  E2RPS2_CANLF UniProtKB/TrEMBL
VGNC ID VGNC:44334 ENTREZGENE