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Table 2 Immune response (GO:0006955) genes with TE-derived HS sites

From: Transposable element derived DNaseI-hypersensitive sites in the human genome

Cluster 1

Name 2

Accn 3

Description 4

HS site 5

TE 6

2

CD97

NM_078481

leukocyte antigen; receptor involved in both cell adhesion and signalling processes early after leukocyte activation

12460_5

SINE/MIR/MIR

2

IGLC2

BC073786

Ig light-chain, partial Ke-Oz- polypeptide, C-term; immunoglobulin lambda constant region 2

13851_3

LTR/ERVL/LTR16A

2

IGLC1

BC070353

constant region of lambda light chains

13851_3

LTR/ERVL/LTR16A

2

MR1

CR602405

major histocompatibility complex, class I-related

1311_2

LINE/L2/L2

2

ADORA2A

NM_000675

adenosine receptor subtype A2a; G-protein coupled receptor; reduces the activation status of inflammatory cells

13875_2

SINE/MIR/MIR3

2

CKLF

NM_016951

chemokine-like factor (cytokine); essential role in the immune and inflammatory responses; potent chemoattractant for neutrophils, monocytes and lymphocytes

10591_2

SINE/Alu/AluSg

2

KLF6

NM_001008490

Kruppel-like factor 6; core promoter guanine-rich element binding protein; transcriptional activator

6794_2

SINE/MIR/MIRb

2

IL16

CR749286

interleukin 16; lymphocyte chemoattractant factor; cytokine; modulator of T cell activation; mediated by CD4

10023_2

DNA/MER1/MER117

2

ST6GAL1

NM_173216

sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase); role in T-cell death; generation of cell-surface carbohydrate determinants and differentiation antigens

3308_3

SINE/MIR/MIR3

2

HLA-E

NM_005516

HLA class I histocompatibility lymphocyte antigen, E alpha chain; immunoregulatory role for cytotoxic T-lymphocytes

4584_2

DNA/MER1/Charlie1

2

IL21R

NM_181078

interleukin 21 receptor; type I cytokine receptor; transduces the growth promoting signal of IL21, and is important for the proliferation and differentiation of T cells, B cells, and natural killer (NK) cells

10408_3

SINE/MIR/MIRb

2

ITGB2

NM_000211

leukocyte cell surface adhesion glycoprotein; complement receptor C3 beta-subunit; integrin beta 2; macrophage antigen 1; facilitates inflammatory cell recruitment

13756_2

LINE/L1/LIME4a

2

FYB

NM_001465

FYN-binding protein; adhesion and degranulation-promoting adaptor protein; adaptor helps form immunological synapse between T cell and antigen-presenting cell; mediates signaling from the T cell antigen receptor to integrins

3896_2

SINE/MIR/MIR3

2

IGHG1

BC024289

immunoglobulin heavy constant region gamma 1; involved in antigen binding and immune response

9667_2

LINE/L1/L1

2

PTPRC

Y00062

protein tyrosine phosphatase receptor; leukocyte-common CD45 antigen; essential regulator of T- and B-cell antigen receptor signaling; regulator of cytokine receptor signaling; involved in hematopoiesis

1347_2

LINE/L1/L1ME

2

LCP2

NM_005565

lymphocyte cytosolic protein 2; adaptor or scaffold protein that promotes T cell development and activation as well as mast cell and platelet function.

4315_2

SINE/Alu/AluSx

2

CD53

NM_000560

glycoprotein leukocyte cell surface antigen; contributes to the transduction of CD2-generated signals in T cells and natural killer cells; role in T cell growth regulation

964_2

LINE/L2/L2

2

DOCK2

NM_004946

dedicator of cytokinesis 2; hematopoietic cell-specific CDM family protein essential for lymphocyte chemotaxis; mediates T cell receptor-induced activation of Rac2 and IL-2

4313_2

SINE/Alu/AluSx SINE/MIR/MIR

2

CD74

BC024272

cell surface antigen; major histocompatibility complex, class II invariant chain; involved in NF-kappaB activation and interleukin-8 production

4254_2

DNA/MER1/Charlie8

2

MX1

NM_002462

myxovirus resistance protein 1; interferon inducible; role in host defense against viruses

13686_3

DNA/MER1/MER5A

25

CD6

U66145

glycoprotein cell surface antigen; involved in lymphocyte activation and thymocyte development; role in maturation of the immunological synapse

 

DNA/MER1/MER113

25

PLA2G4B

NM_005090

phospholipase enzyme secreted by neutrophils; produces arachidonic acid used for the biosynthesis of leukotriene in inflammatory response

9758_2

SINE/MIR/MIRb SINE/Alu/AluY

25

BCL2

NM_000633

B-cell lymphoma protein 2; blocks the apoptotic death of some cells such as lymphocytes

12021_2

LINE/L1/HAL1

25

TRA@

BC063432

T cell antigen receptor alpha locus; involved in thymocyte developement

9169_2 9171_2 9174_4

LINE/L1/L1ME2 SINE/MIR/MIR LINE/L2/L2

25

CCR9

NM_031200

chemokine (C-C motif) G protein coupled receptor; regulator of thymocytes migration and maturation in normal and inflammation conditions; functional specialization of immune responses in different segments of the gastrointestinal tract

2827_2

LINE/L1/L1ME4a

25

TCF7

NM_003202

T cell specific transcription factor; regulates T cell development and peripheral T cell differentiation

4139_4

LINE/CR1/L3

25

CCL5

NM_002985

T cell specific chemokine (C-C motif) ligand; chemoattractant for blood monocytes, memory T helper cells and eosinophils; causes release of histamine from basophils and activates eosinophils;

11206_2

LINE/L1/L1MB3

25

LAT

NM_001014987

linker for activation of T cells; phosphorylated following activation of the T-cell antigen receptor signal transduction pathway; acts as a docking site and recruits multiple adaptor proteins and downstream signaling molecules into multimolecular signaling complexes

10425_2

SINE/Alu/AluJb SINE/MIR/MIR

  1. 1Gene coexpression cluster from which the gene is taken.
  2. 2Official gene name symbol from the HUGO Gene nomenclature committee
  3. 3Representative mRNA Genbank accession taken from USC genome browser knownGene table.
  4. 4Brief description of the gene function
  5. 5NHGRI DNase-I hypersensitive site identifier taken from the UCSC genome browser nhgriDnaseHs table.
  6. 6Class/family/name of the transposable element (TE) sequence colocalized with the HS site