Pdcd1 (programmed cell death 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pdcd1 (programmed cell death 1) Rattus norvegicus
Analyze
Symbol: Pdcd1
Name: programmed cell death 1
RGD ID: 1311658
Description: Predicted to be involved in negative regulation of immune response and positive regulation of T cell apoptotic process. Predicted to act upstream of or within negative regulation of B cell apoptotic process; negative regulation of tolerance induction; and positive regulation of apoptotic process. Located in plasma membrane. Biomarker of anti-basement membrane glomerulonephritis; periodontitis; and pre-eclampsia. Human ortholog(s) of this gene implicated in autoimmune disease (multiple); hepatitis B; hepatitis C; hepatocellular carcinoma; and lupus nephritis. Orthologous to human PDCD1 (programmed cell death 1); PARTICIPATES IN T cell receptor signaling pathway; INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC102550808; LOC301626; programmed cell death protein 1; programmed cell death protein 1-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2994,418,786 - 94,431,945 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl994,418,791 - 94,431,937 (-)Ensembl
Rnor_6.09101,305,742 - 101,319,937 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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_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
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  (IEP)
asthma  (ISO)
autoimmune hepatitis  (ISO,ISS)
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  (IEP)
cryptococcal meningitis  (ISO)
cystitis  (ISO)
Cytomegalovirus Infections  (ISO)
D-2-hydroxyglutaric aciduria 1  (ISO)
dilated cardiomyopathy  (ISO,ISS)
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,ISS)
hepatitis C  (ISO,ISS)
hepatocellular carcinoma  (ISO,ISS)
hereditary spastic paraplegia 30  (ISO)
histoplasmosis  (ISO)
human immunodeficiency virus infectious disease  (ISO)
hydronephrosis  (ISO)
intellectual disability  (ISO)
Lung Neoplasms  (ISO)
lupus nephritis  (ISO,ISS)
lymphocytic choriomeningitis  (ISO)
melanoma  (ISO)
multiple sclerosis  (ISO)
myocarditis  (ISO)
periodontitis  (IEP)
Pneumovirus Infections  (ISO)
pre-eclampsia  (IEP,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  (IEP)
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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Roles of programmed death-1 (PD-1)/PD-1 ligands pathway in the development of murine acute myocarditis caused by coxsackievirus B3. null
2. Endoplasmic reticulum stress response and inflammatory cytokines in type 2 diabetic nephropathy: role of indoleamine 2,3-dioxygenase and programmed death-1. Baban B, etal., Exp Mol Pathol. 2013 Apr;94(2):343-51. doi: 10.1016/j.yexmp.2012.11.004. Epub 2012 Dec 5.
3. Genetic, immunologic, and immunohistochemical analysis of the programmed death 1/programmed death ligand 1 pathway in human systemic lupus erythematosus. Bertsias GK, etal., Arthritis Rheum. 2009 Jan;60(1):207-18. doi: 10.1002/art.24227.
4. Expression of programmed death 1 and its ligands in the liver of autoimmune hepatitis C57BL/6 mice. Cao J, etal., Chin Med J (Engl). 2009 Aug 20;122(16):1941-6.
5. Blockade of the negative co-stimulatory molecules PD-1 and CTLA-4 improves survival in primary and secondary fungal sepsis. Chang KC, etal., Crit Care. 2013 May 11;17(3):R85. doi: 10.1186/cc12711.
6. In vitro and in vivo effect of PD-1/PD-L1 blockade on microglia/macrophage activation and T cell subset balance in cryptococcal meningitis. Che YM, etal., J Cell Biochem. 2018 Apr;119(4):3044-3057. doi: 10.1002/jcb.26432. Epub 2017 Dec 26.
7. Programmed cell death-1 3'-untranslated region polymorphism is associated with spontaneous clearance of hepatitis B virus infection. Chihab H, etal., J Med Virol. 2018 Nov;90(11):1730-1738. doi: 10.1002/jmv.25265. Epub 2018 Aug 13.
8. Phenotypic Characteristics of PD-1 and CTLA-4 Expression in Symptomatic Acute Hepatitis A. Cho H, etal., Gut Liver. 2016 Mar;10(2):288-94. doi: 10.5009/gnl14368.
9. CD72/CD100 and PD-1/PD-L1 markers are increased on T and B cells in HIV-1+ viremic individuals, and CD72/CD100 axis is correlated with T-cell exhaustion. Correa-Rocha R, etal., PLoS One. 2018 Aug 30;13(8):e0203419. doi: 10.1371/journal.pone.0203419. eCollection 2018.
10. Gene transfer of programmed death ligand-1.Ig prolongs cardiac allograft survival. Dudler J, etal., Transplantation. 2006 Dec 27;82(12):1733-7.
11. Viral acute lower respiratory infections impair CD8+ T cells through PD-1. Erickson JJ, etal., J Clin Invest. 2012 Aug;122(8):2967-82. doi: 10.1172/JCI62860. Epub 2012 Jul 17.
12. Programmed death-1 impairs secondary effector lung CD8⁺ T cells during respiratory virus reinfection. Erickson JJ, etal., J Immunol. 2014 Nov 15;193(10):5108-17. doi: 10.4049/jimmunol.1302208. Epub 2014 Oct 22.
13. Programmed death 1 protects from fatal circulatory failure during systemic virus infection of mice. Frebel H, etal., J Exp Med. 2012 Dec 17;209(13):2485-99. doi: 10.1084/jem.20121015. Epub 2012 Dec 10.
14. Therapy With Carboplatin and Anti-PD-1 Antibodies Before Surgery Demonstrates Sustainable Anti-Tumor Effects for Secondary Cancers in Mice With Triple-Negative Breast Cancer. Gao M, etal., Front Immunol. 2020 Mar 5;11:366. doi: 10.3389/fimmu.2020.00366. eCollection 2020.
15. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
16. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
17. DUG is a novel homologue of translation initiation factor 4G that binds eIF4A. Goke A, etal., Biochem Biophys Res Commun 2002 Sep 13;297(1):78-82.
18. Regulation of Trypanosoma cruzi-induced myocarditis by programmed death cell receptor 1. Gutierrez FR, etal., Infect Immun. 2011 May;79(5):1873-81. doi: 10.1128/IAI.01047-10. Epub 2011 Feb 28.
19. Immune suppression in premalignant respiratory papillomas: enriched functional CD4+Foxp3+ regulatory T cells and PD-1/PD-L1/L2 expression. Hatam LJ, etal., Clin Cancer Res. 2012 Apr 1;18(7):1925-35. doi: 10.1158/1078-0432.CCR-11-2941. Epub 2012 Feb 9.
20. Dexmedetomidine Mitigates Microglia-Mediated Neuroinflammation through Upregulation of Programmed Cell Death Protein 1 in a Rat Spinal Cord Injury Model. He H, etal., J Neurotrauma. 2018 Nov 1;35(21):2591-2603. doi: 10.1089/neu.2017.5625. Epub 2018 Jun 7.
21. Association between a polymorphism in the human programmed death-1 (PD-1) gene and cytomegalovirus infection after kidney transplantation. Hoffmann TW, etal., J Med Genet. 2010 Jan;47(1):54-8. doi: 10.1136/jmg.2009.068841. Epub 2009 Jul 5.
22. A Programmed Cell Death-1 Haplotype is Associated with Clearance of Hepatitis B Virus. Hou Z, etal., Ann Clin Lab Sci. 2017 May;47(3):334-343.
23. PD-1 expression by macrophages plays a pathologic role in altering microbial clearance and the innate inflammatory response to sepsis. Huang X, etal., Proc Natl Acad Sci U S A. 2009 Apr 14;106(15):6303-8. doi: 10.1073/pnas.0809422106. Epub 2009 Mar 30.
24. Prognostic Significance of PD-1, PD-L1 and CD8 Gene Expression Levels in Gastric Cancer. Ito S, etal., Oncology. 2020;98(7):501-511. doi: 10.1159/000506075. Epub 2020 May 7.
25. Correlation of CpG methylation of the Pdcd1 gene with PD-1 expression on CD8+ T cells and medical laboratory indicators in chronic hepatitis B infection. Jiao L, etal., J Gene Med. 2020 Feb;22(2):e3148. doi: 10.1002/jgm.3148. Epub 2020 Jan 9.
26. Association of a PDCD1 polymorphism with renal manifestations in systemic lupus erythematosus. Johansson M, etal., Arthritis Rheum. 2005 Jun;52(6):1665-9.
27. Chronically inflamed livers up-regulate expression of inhibitory B7 family members. Kassel R, etal., Hepatology. 2009 Nov;50(5):1625-37. doi: 10.1002/hep.23173.
28. Non-oncogenic Acute Viral Infections Disrupt Anti-cancer Responses and Lead to Accelerated Cancer-Specific Host Death. Kohlhapp FJ, etal., Cell Rep. 2016 Oct 18;17(4):957-965. doi: 10.1016/j.celrep.2016.09.068.
29. Upregulation of PD-1 on CD4⁺CD25⁺ T cells is associated with immunosuppression in liver of mice infected with Echinococcus multilocularis. La X, etal., Int Immunopharmacol. 2015 Jun;26(2):357-66. doi: 10.1016/j.intimp.2015.04.013. Epub 2015 Apr 20.
30. Anti-programmed death-1 synergizes with granulocyte macrophage colony-stimulating factor--secreting tumor cell immunotherapy providing therapeutic benefit to mice with established tumors. Li B, etal., Clin Cancer Res. 2009 Mar 1;15(5):1623-34. doi: 10.1158/1078-0432.CCR-08-1825. Epub 2009 Feb 10.
31. Genetic polymorphisms of immune checkpoint proteins PD-1 and TIM-3 are associated with survival of patients with hepatitis B virus-related hepatocellular carcinoma. Li Z, etal., Oncotarget. 2016 May 3;7(18):26168-80. doi: 10.18632/oncotarget.8435.
32. Genetic variations in LTA gene and PDCD1 gene and intrauterine infection of hepatitis B virus: a case-control study in China. Liu T, etal., Amino Acids. 2018 Jul;50(7):877-883. doi: 10.1007/s00726-018-2568-9. Epub 2018 May 21.
33. The PD-1/PD-L costimulatory pathway critically affects host resistance to the pathogenic fungus Histoplasma capsulatum. Lázár-Molnár E, etal., Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2658-63. doi: 10.1073/pnas.0711918105. Epub 2008 Feb 11.
34. Programmed Death-Ligand 1 Expression Is Common in Gastric Cancer Associated With Epstein-Barr Virus or Microsatellite Instability. Ma C, etal., Am J Surg Pathol. 2016 Nov;40(11):1496-1506. doi: 10.1097/PAS.0000000000000698.
35. Blockade of the PD-1/PD-1L pathway reverses the protective effect of anti-CD40L therapy in a rat to mouse concordant islet xenotransplantation model. Mai G, etal., Xenotransplantation. 2007 May;14(3):243-8.
36. Anti-programmed cell death-1 antibody as a new serological marker for type 1 autoimmune hepatitis. Matsumoto K, etal., J Gastroenterol Hepatol. 2014 Jan;29(1):110-5. doi: 10.1111/jgh.12340.
37. PD-1 suppresses protective immunity to Streptococcus pneumoniae through a B cell-intrinsic mechanism. McKay JT, etal., J Immunol. 2015 Mar 1;194(5):2289-99. doi: 10.4049/jimmunol.1401673. Epub 2015 Jan 26.
38. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
39. Modulation of expression of Programmed Death-1 by administration of probiotic Dahi in DMH-induced colorectal carcinogenesis in rats. Mohania D, etal., Acta Biomed. 2013 Sep 1;84(2):102-9.
40. A putative regulatory polymorphism in PD-1 is associated with nephropathy in a population-based cohort of systemic lupus erythematosus patients. Nielsen C, etal., Lupus. 2004;13(7):510-6.
41. Hydronephrosis associated with antiurothelial and antinuclear autoantibodies in BALB/c-Fcgr2b-/-Pdcd1-/- mice. Okazaki T, etal., J Exp Med. 2005 Dec 19;202(12):1643-8. Epub 2005 Dec 13.
42. Autoantibodies against cardiac troponin I are responsible for dilated cardiomyopathy in PD-1-deficient mice. Okazaki T, etal., Nat Med. 2003 Dec;9(12):1477-83. Epub 2003 Nov 2.
43. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
44. Notch Signaling Pathway Was Involved in Regulating Programmed Cell Death 1 Expression during Sepsis-Induced Immunosuppression. Pan T, etal., Mediators Inflamm. 2015;2015:539841. doi: 10.1155/2015/539841. Epub 2015 Apr 30.
45. Frontline Science: Anti-PD-L1 protects against infection with common bacterial pathogens after burn injury. Patil NK, etal., J Leukoc Biol. 2018 Jan;103(1):23-33. doi: 10.1002/JLB.5HI0917-360R. Epub 2017 Dec 21.
46. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
47. Stimulation of the PD-1/PDL-1 T-cell co-inhibitory pathway is effective in treatment of experimental autoimmune glomerulonephritis. Reynolds J, etal., Nephrol Dial Transplant. 2012 Apr;27(4):1343-50. doi: 10.1093/ndt/gfr529. Epub 2011 Sep 29.
48. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
49. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
50. Comprehensive gene review and curation RGD comprehensive gene curation
51. Monocyte programmed death ligand-1 expression after 3-4 days of sepsis is associated with risk stratification and mortality in septic patients: a prospective cohort study. Shao R, etal., Crit Care. 2016 May 9;20(1):124. doi: 10.1186/s13054-016-1301-x.
52. The characteristic profiles of PD-1 and PD-L1 expressions and dynamic changes during treatment in active tuberculosis. Shen L, etal., Tuberculosis (Edinb). 2016 Dec;101:146-150. doi: 10.1016/j.tube.2016.10.001. Epub 2016 Oct 1.
53. Immunovirotherapy with vesicular stomatitis virus and PD-L1 blockade enhances therapeutic outcome in murine acute myeloid leukemia. Shen W, etal., Blood. 2016 Mar 17;127(11):1449-58. doi: 10.1182/blood-2015-06-652503. Epub 2015 Dec 28.
54. Mechanistic investigation of immunosuppression in patients with condyloma acuminata. Shi YJ, etal., Mol Med Rep. 2013 Aug;8(2):480-6. doi: 10.3892/mmr.2013.1511. Epub 2013 Jun 6.
55. PD-1 Dynamically Regulates Inflammation and Development of Brain-Resident Memory CD8 T Cells During Persistent Viral Encephalitis. Shwetank, etal., Front Immunol. 2019 Apr 17;10:783. doi: 10.3389/fimmu.2019.00783. eCollection 2019.
56. Inhibiting the programmed death 1 pathway rescues Mycobacterium tuberculosis-specific interferon γ-producing T cells from apoptosis in patients with pulmonary tuberculosis. Singh A, etal., J Infect Dis. 2013 Aug 15;208(4):603-15. doi: 10.1093/infdis/jit206. Epub 2013 May 9.
57. Programmed Death Ligand 1 Promotes Early-Life Chlamydia Respiratory Infection-Induced Severe Allergic Airway Disease. Starkey MR, etal., Am J Respir Cell Mol Biol. 2016 Apr;54(4):493-503. doi: 10.1165/rcmb.2015-0204OC.
58. BALB/c-Fcgr2bPdcd1 mouse expressing anti-urothelial antibody is a novel model of autoimmune cystitis. Sugino Y, etal., Sci Rep. 2012;2:317. doi: 10.1038/srep00317. Epub 2012 Mar 19.
59. PD-1 is expressed by tumor-infiltrating immune cells and is associated with poor outcome for patients with renal cell carcinoma. Thompson RH, etal., Clin Cancer Res. 2007 Mar 15;13(6):1757-61.
60. The PD-1/PD-L1 inhibitory pathway is altered in pre-eclampsia and regulates T cell responses in pre-eclamptic rats. Tian M, etal., Sci Rep. 2016 Jun 9;6:27683. doi: 10.1038/srep27683.
61. Association of PDCD1 polymorphisms with childhood-onset systemic lupus erythematosus. Velazquez-Cruz R, etal., Eur J Hum Genet. 2007 Mar;15(3):336-41. Epub 2007 Jan 17.
62. Aberrant production of soluble inducible T cell co‑stimulator and soluble programmed cell death protein 1 in patients with chronic hepatitis B. Wang D, etal., Mol Med Rep. 2017 Dec;16(6):8556-8562. doi: 10.3892/mmr.2017.7630. Epub 2017 Sep 26.
63. TLR4 signaling improves PD-1 blockade therapy during chronic viral infection. Wang Y, etal., PLoS Pathog. 2019 Feb 6;15(2):e1007583. doi: 10.1371/journal.ppat.1007583. eCollection 2019 Feb.
64. Programmed death 1 mRNA in peripheral blood as biomarker of acute renal allograft rejection. Wang YW, etal., Chin Med J (Engl). 2011 Mar;124(5):674-8.
65. Lymphocyte subset expression and serum concentrations of PD-1/PD-L1 in sepsis - pilot study. Wilson JK, etal., Crit Care. 2018 Apr 17;22(1):95. doi: 10.1186/s13054-018-2020-2.
66. Blockade of programmed death-1 in young (New Zealand black x New Zealand white)F1 mice promotes the activity of suppressive CD8+ T cells that protect from lupus-like disease. Wong M, etal., J Immunol. 2010 Dec 1;185(11):6563-71. doi: 10.4049/jimmunol.0903401. Epub 2010 Nov 1.
67. Suppression of furin by interferon-γ and the impact on hepatitis B virus antigen biosynthesis in human hepatocytes. Wu JF, etal., Am J Pathol. 2012 Jul;181(1):19-25. doi: 10.1016/j.ajpath.2012.03.036. Epub 2012 May 24.
68. Expression of CD25(high) regulatory T cells and PD-1 in gastric infiltrating CD4(+) T lymphocytes in patients with Helicobacter pylori infection. Wu YY, etal., Clin Vaccine Immunol. 2011 Jul;18(7):1198-201. doi: 10.1128/CVI.00422-10. Epub 2011 May 11.
69. Immune Checkpoint Receptors Tim-3 and PD-1 Regulate Monocyte and T Lymphocyte Function in Septic Patients. Xia Q, etal., Mediators Inflamm. 2018 Nov 22;2018:1632902. doi: 10.1155/2018/1632902. eCollection 2018.
70. Genetic variations of IL-28B and PD-1 are in association with the susceptibility and outcomes of HCV infection in Southeast China. Xiao W, etal., Infect Genet Evol. 2015 Jun;32:89-96. doi: 10.1016/j.meegid.2015.02.022. Epub 2015 Mar 5.
71. Increased expression of programmed death (PD)-1 and its ligand PD-L1 correlates with impaired cell-mediated immunity in high-risk human papillomavirus-related cervical intraepithelial neoplasia. Yang W, etal., Immunology. 2013 Aug;139(4):513-22. doi: 10.1111/imm.12101.
72. [Temporal expression of PD-1 and PD-L1 during the development of experimental periodontitis in rats and its implications]. Yang X, etal., Shanghai Kou Qiang Yi Xue. 2019 Dec;28(6):591-596.
73. Control of pathogenic effector T-cell activities in situ by PD-L1 expression on respiratory inflammatory dendritic cells during respiratory syncytial virus infection. Yao S, etal., Mucosal Immunol. 2015 Jul;8(4):746-59. doi: 10.1038/mi.2014.106. Epub 2014 Dec 3.
74. Upregulation of circulating PD-L1/PD-1 is associated with poor post-cryoablation prognosis in patients with HBV-related hepatocellular carcinoma. Zeng Z, etal., PLoS One. 2011;6(9):e23621. doi: 10.1371/journal.pone.0023621. Epub 2011 Sep 1.
75. PD-1 deletion restores susceptibility to experimental autoimmune encephalomyelitis in miR-155-deficient mice. Zhang J and Braun MY, Int Immunol. 2014 Jul;26(7):407-15. doi: 10.1093/intimm/dxu043. Epub 2014 Mar 19.
76. Predictive Value of Soluble Programmed Death-1 for Severe Sepsis and Septic Shock During the First Week in an Intensive Care Unit. Zhao Y, etal., Shock. 2019 Mar;51(3):289-297. doi: 10.1097/SHK.0000000000001171.
77. Association between hepatitis B viral burden in chronic infection and a functional single nucleotide polymorphism of the PDCD1 gene. Zheng L, etal., J Clin Immunol. 2010 Nov;30(6):855-60. doi: 10.1007/s10875-010-9450-1. Epub 2010 Aug 11.
78. Blockade of PD-1 Signaling Enhances Th2 Cell Responses and Aggravates Liver Immunopathology in Mice with Schistosomiasis japonica. Zhou S, etal., PLoS Negl Trop Dis. 2016 Oct 28;10(10):e0005094. doi: 10.1371/journal.pntd.0005094. eCollection 2016 Oct.
79. Relationship between programmed cell death-1 polymorphisms and clearance of hepatitis B virus. Ülger Y, etal., Int J Immunogenet. 2015 Jun;42(3):133-9. doi: 10.1111/iji.12187. Epub 2015 Mar 4.
Additional References at PubMed
PMID:10485649   PMID:11209085   PMID:15568026   PMID:23583643   PMID:23636058   PMID:25281059   PMID:25902191   PMID:28196545   PMID:28892130   PMID:30695785   PMID:34170847   PMID:34847253  


Genomics

Comparative Map Data
Pdcd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2994,418,786 - 94,431,945 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl994,418,791 - 94,431,937 (-)Ensembl
Rnor_6.09101,305,742 - 101,319,937 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
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_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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382241,849,884 - 241,858,894 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2241,849,884 - 241,858,894 (-)EnsemblGRCh38hg38GRCh38
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
T2T-CHM13v2.02242,351,431 - 242,360,440 (-)NCBI
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
(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
(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
ROS_Cfam_1.0 Ensembl2551,809,263 - 51,823,016 (-)Ensembl
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
(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 Ensembl15140,336,258 - 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 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl10127,878,554 - 127,886,088 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604071,433,325 - 71,442,153 (+)NCBIVero_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_1.0hetGla2
HetGla 1.0NW_0046248475,732,922 - 5,741,908 (-)NCBIHetGla_female_1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)925268044114175309Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)925661188100929786Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)93696235995410867Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)956771635101771635Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)958163035100929646Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)961381434104821652Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)96207227596470995Rat
1578757Pur6Proteinuria QTL 63.30.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)96207227596470995Rat
61385Edpm9Estrogen-dependent pituitary mass QTL 93.430.05pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)963869687108869687Rat
731171Glom6Glomerulus QTL 62.80.0003kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)964573531109573531Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)975712843111552878Rat
4889852Pur26Proteinuria QTL 26150.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)977813894101597663Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)977813894111552878Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)979271511102910209Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)992491589100929786Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:167
Count of miRNA genes:119
Interacting mature miRNAs:132
Transcripts:ENSRNOT00000025743, ENSRNOT00000074915
Prediction methods:Miranda, Rnahybrid
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.


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 renal system reproductive system respiratory system appendage
High
Medium
Low 2 8 17 1 1 5
Below cutoff 1 3 5 2 2 2 2 2 4 15 17 6 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025743   ⟹   ENSRNOP00000025743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl994,418,791 - 94,431,937 (-)Ensembl
Rnor_6.0 Ensembl9101,025,313 - 101,038,625 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000074915   ⟹   ENSRNOP00000067189
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9101,307,764 - 101,319,845 (-)Ensembl
RefSeq Acc Id: NM_001106927   ⟹   NP_001100397
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2994,418,791 - 94,431,937 (-)NCBI
Rnor_6.09101,306,765 - 101,319,909 (-)NCBI
Rnor_5.09100,676,274 - 100,690,991 (-)NCBI
RGSC_v3.4993,172,543 - 93,185,687 (-)RGD
Celera991,952,891 - 91,966,035 (-)RGD
Sequence:
RefSeq Acc Id: XM_006245524   ⟹   XP_006245586
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2994,418,786 - 94,431,945 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008767396   ⟹   XP_008765618
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2994,418,786 - 94,431,945 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596858   ⟹   XP_017452347
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2994,418,786 - 94,431,945 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100397 (Get FASTA)   NCBI Sequence Viewer  
  XP_006245586 (Get FASTA)   NCBI Sequence Viewer  
  XP_008765618 (Get FASTA)   NCBI Sequence Viewer  
  XP_017452347 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL91893 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100397   ⟸   NM_001106927
- Peptide Label: precursor
- UniProtKB: D3ZIN8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000067189   ⟸   ENSRNOT00000074915
RefSeq Acc Id: XP_017452347   ⟸   XM_017596858
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008765618   ⟸   XM_008767396
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006245586   ⟸   XM_006245524
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000025743   ⟸   ENSRNOT00000025743
Protein Domains
Ig-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZIN8-F1-model_v2 AlphaFold D3ZIN8 1-287 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311658 AgrOrtholog
BioCyc Gene G2FUF-26625 BioCyc
Ensembl Genes ENSRNOG00000019043 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000049797 Ensembl
Ensembl Protein ENSRNOP00000025743 ENTREZGENE
  ENSRNOP00000025743.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025743 ENTREZGENE
  ENSRNOT00000025743.5 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like 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 rno:301626 UniProtKB/TrEMBL
NCBI Gene 301626 ENTREZGENE
PANTHER PTHR15264 UniProtKB/TrEMBL
Pfam V-set UniProtKB/TrEMBL
PhenoGen Pdcd1 PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
SMART IGv UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/TrEMBL
UniProt D3ZIN8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-11-05 Pdcd1  programmed cell death 1  LOC102550808  programmed cell death protein 1-like  Data Merged 737654 APPROVED
2013-12-18 LOC102550808  programmed cell death protein 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Pdcd1  programmed cell death 1   Pdcd1_predicted  programmed cell death 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Pdcd1_predicted  programmed cell death 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED