PDCD1 (programmed cell death 1) - Rat Genome Database

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Gene: PDCD1 (programmed cell death 1) Sus scrofa
Analyze
Symbol: PDCD1
Name: programmed cell death 1
RGD ID: 13906369
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 external side of plasma membrane (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: programmed cell death protein 1
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
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
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 DISEASE WITH SUSCEPTIBILITY TO MYCOBACTERIUM TUBERCULOSIS  (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:14681463   PMID:20347491   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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

Variants

.
Variants in PDCD1
100 total Variants

Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
circulatory system
endoderm
hemolymphoid system
mesenchyme
mesoderm
renal system
reproductive system
respiratory system
10 2 2 5 8 8 1 2 3

Sequence


Ensembl Acc Id: ENSSSCT00000050403   ⟹   ENSSSCP00000037522
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl15140,336,258 - 140,347,478 (-)Ensembl
Ensembl Acc Id: ENSSSCT00000076499   ⟹   ENSSSCP00000066637
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl15140,337,359 - 140,347,476 (-)Ensembl
RefSeq Acc Id: NM_001204379   ⟹   NP_001191308
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.115140,337,357 - 140,347,475 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021074630   ⟹   XP_020930289
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.115140,337,353 - 140,347,493 (-)NCBI
Sequence:
RefSeq Acc Id: XP_020930289   ⟸   XM_021074630
- Peptide Label: isoform X1
- UniProtKB: A0A287A1C3 (UniProtKB/TrEMBL),   A0A8D1HLY2 (UniProtKB/TrEMBL),   A0A345BT91 (UniProtKB/TrEMBL),   A0A8D1KLF3 (UniProtKB/TrEMBL),   A0A8D2BYU1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001191308   ⟸   NM_001204379
- Peptide Label: precursor
- UniProtKB: A0A4X1SVI6 (UniProtKB/TrEMBL),   A0A8D0SRN1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSSSCP00000037522   ⟸   ENSSSCT00000050403
Ensembl Acc Id: ENSSSCP00000066637   ⟸   ENSSSCT00000076499
Protein Domains
Ig-like


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000037319 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00015077214 UniProtKB/TrEMBL
  ENSSSCG00025058865 UniProtKB/TrEMBL
  ENSSSCG00030024422 UniProtKB/TrEMBL
  ENSSSCG00035067026 UniProtKB/TrEMBL
  ENSSSCG00040071871 UniProtKB/TrEMBL
  ENSSSCG00045017521 UniProtKB/TrEMBL
  ENSSSCG00050027512 UniProtKB/TrEMBL
  ENSSSCG00055022270 UniProtKB/TrEMBL
  ENSSSCG00060062493 UniProtKB/TrEMBL
  ENSSSCG00065008799 UniProtKB/TrEMBL
  ENSSSCG00070004561 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000050403 ENTREZGENE
  ENSSSCT00000050403.3 UniProtKB/TrEMBL
  ENSSSCT00015104293.1 UniProtKB/TrEMBL
  ENSSSCT00015104364.1 UniProtKB/TrEMBL
  ENSSSCT00025080592.1 UniProtKB/TrEMBL
  ENSSSCT00030034017.1 UniProtKB/TrEMBL
  ENSSSCT00035090366.1 UniProtKB/TrEMBL
  ENSSSCT00040098819.1 UniProtKB/TrEMBL
  ENSSSCT00045029840.1 UniProtKB/TrEMBL
  ENSSSCT00050036993.1 UniProtKB/TrEMBL
  ENSSSCT00055043696.1 UniProtKB/TrEMBL
  ENSSSCT00060085217.1 UniProtKB/TrEMBL
  ENSSSCT00065011746.1 UniProtKB/TrEMBL
  ENSSSCT00070008606.1 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 A0A287A1C3 ENTREZGENE, UniProtKB/TrEMBL
  A0A345BT91 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1SVI6 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D0SRN1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1HLY2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1KLF3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D2BYU1 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:96472 ENTREZGENE