Pdcd1 (programmed cell death 1) - Rat Genome Database

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Gene: Pdcd1 (programmed cell death 1) Ictidomys tridecemlineatus
Analyze
Symbol: Pdcd1
Name: programmed cell death 1
RGD ID: 12508258
Description: ENCODES a protein that exhibits signaling receptor activity (inferred); INVOLVED IN B cell apoptotic process (ortholog); negative regulation of B cell apoptotic process (ortholog); negative regulation of tolerance induction (ortholog); ASSOCIATED WITH acute myeloid leukemia (ortholog); acute myocarditis (ortholog); anogenital venereal wart (ortholog); FOUND IN plasma membrane (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: programmed cell death protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303193,055,706 - 193,066,914 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936745152,612 - 161,587 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936745152,571 - 163,712 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
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)
Bethlem Myopathy 1A  (ISO)
Burns  (ISO)
cervix uteri carcinoma in situ  (ISO)
Chlamydia pneumonia  (ISO)
chromosome 2q37 deletion syndrome  (ISO)
Chronic Hepatitis B  (ISO)
Colonic Neoplasms  (ISO)
Colorectal Neoplasms  (ISO)
cryptococcal meningitis  (ISO)
cystitis  (ISO)
Cytomegalovirus Infections  (ISO)
D-2-hydroxyglutaric aciduria 1  (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)
hereditary spastic paraplegia 30  (ISO)
histoplasmosis  (ISO)
human immunodeficiency virus infectious disease  (ISO)
hydronephrosis  (ISO)
intellectual disability  (ISO)
Lung Neoplasms  (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:30032202  


Genomics

Comparative Map Data
Pdcd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303193,055,706 - 193,066,914 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936745152,612 - 161,587 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936745152,571 - 163,712 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PDCD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382241,849,884 - 241,858,894 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2241,849,884 - 241,858,894 (-)EnsemblGRCh38hg38GRCh38
GRCh372242,792,036 - 242,801,046 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362242,440,711 - 242,449,731 (-)NCBINCBI36Build 36hg18NCBI36
Celera2236,456,683 - 236,465,707 (-)NCBICelera
Cytogenetic Map2q37.3NCBI
HuRef2234,541,510 - 234,550,535 (-)NCBIHuRef
CHM1_12242,797,131 - 242,806,156 (-)NCBICHM1_1
T2T-CHM13v2.02242,351,431 - 242,360,440 (-)NCBIT2T-CHM13v2.0
Pdcd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39193,966,027 - 93,980,278 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl193,966,027 - 93,980,278 (-)EnsemblGRCm39 Ensembl
GRCm38194,038,305 - 94,052,553 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl194,038,305 - 94,052,553 (-)EnsemblGRCm38mm10GRCm38
MGSCv37195,934,882 - 95,949,130 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36195,868,711 - 95,882,959 (-)NCBIMGSCv36mm8
Celera196,903,284 - 96,917,529 (-)NCBICelera
Cytogenetic Map1DNCBI
cM Map147.47NCBI
Pdcd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr89101,866,124 - 101,879,278 (-)NCBIGRCr8
mRatBN7.2994,418,786 - 94,431,945 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl994,418,791 - 94,431,937 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx9102,854,260 - 102,867,404 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09107,989,476 - 108,002,637 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.09106,346,469 - 106,359,638 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.09101,305,742 - 101,319,937 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9101,307,764 - 101,319,845 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl9101,025,313 - 101,038,625 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09100,676,274 - 100,690,991 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4993,172,543 - 93,185,687 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
NHGRI_mPanPan1-v213144,543,641 - 144,553,063 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B144,558,538 - 144,568,773 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v012130,849,353 - 130,858,776 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02551,809,256 - 51,820,132 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2551,809,263 - 51,823,016 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12551,659,966 - 51,669,894 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02551,399,146 - 51,409,148 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02551,676,302 - 51,686,322 (-)NCBIUU_Cfam_GSD_1.0
PDCD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15140,336,258 - 140,347,478 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.115140,337,353 - 140,347,493 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PDCD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110127,877,383 - 127,886,234 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10127,878,554 - 127,886,088 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604071,433,325 - 71,442,153 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pdcd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248475,732,767 - 5,742,269 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248475,732,922 - 5,741,908 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSSTOT00000021499   ⟹   ENSSTOP00000015985
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
SpeTri2.0 EnsemblNW_004936745152,612 - 161,587 (+)Ensembl
RefSeq Acc Id: XM_005339622   ⟹   XP_005339679
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303193,055,706 - 193,066,914 (-)NCBI
SpeTri2.0NW_004936745152,571 - 163,712 (+)NCBI
Sequence:
RefSeq Acc Id: XM_040268240   ⟹   XP_040124174
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303193,055,706 - 193,066,662 (-)NCBI
RefSeq Acc Id: XM_040268241   ⟹   XP_040124175
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303193,055,706 - 193,066,869 (-)NCBI
RefSeq Acc Id: XM_040268242   ⟹   XP_040124176
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303193,055,706 - 193,066,662 (-)NCBI
RefSeq Acc Id: XM_040268243   ⟹   XP_040124177
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_024405303193,055,706 - 193,066,864 (-)NCBI
Protein Sequences
Protein RefSeqs XP_005339679 (Get FASTA)   NCBI Sequence Viewer  
  XP_040124174 (Get FASTA)   NCBI Sequence Viewer  
  XP_040124175 (Get FASTA)   NCBI Sequence Viewer  
  XP_040124176 (Get FASTA)   NCBI Sequence Viewer  
  XP_040124177 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSTOP00000015985.1
GenBank Protein KAG3275741 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_005339679   ⟸   XM_005339622
- Peptide Label: isoform X2
- UniProtKB: I3MV40 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_040124175   ⟸   XM_040268241
- Peptide Label: isoform X1
RefSeq Acc Id: XP_040124177   ⟸   XM_040268243
- Peptide Label: isoform X1
RefSeq Acc Id: XP_040124176   ⟸   XM_040268242
- Peptide Label: isoform X1
RefSeq Acc Id: XP_040124174   ⟸   XM_040268240
- Peptide Label: isoform X1
Ensembl Acc Id: ENSSTOP00000015985   ⟸   ENSSTOT00000021499
Protein Domains
Ig-like


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000022396 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000021499.1 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
NCBI Gene Pdcd1 ENTREZGENE
PANTHER PROGRAMMED CELL DEATH PROTEIN 1 UniProtKB/TrEMBL
  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 I3MV40 ENTREZGENE, UniProtKB/TrEMBL