Human Gene IL7 (uc003ybg.3) Description and Page Index
  Description: Homo sapiens interleukin 7 (IL7), transcript variant 1, mRNA.
RefSeq Summary (NM_000880): The protein encoded by this gene is a cytokine important for B and T cell development. This cytokine and the hepatocyte growth factor (HGF) form a heterodimer that functions as a pre-pro-B cell growth-stimulating factor. This cytokine is found to be a cofactor for V(D)J rearrangement of the T cell receptor beta (TCRB) during early T cell development. This cytokine can be produced locally by intestinal epithelial and epithelial goblet cells, and may serve as a regulatory factor for intestinal mucosal lymphocytes. Knockout studies in mice suggested that this cytokine plays an essential role in lymphoid cell survival. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Additional splice variants have been described but their presence in normal tissues has not been confirmed.[provided by RefSeq, Dec 2010].
Transcript (Including UTRs)
   Position: hg19 chr8:79,645,007-79,717,758 Size: 72,752 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg19 chr8:79,645,948-79,717,157 Size: 71,210 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:79,645,007-79,717,758)mRNA (may differ from genome)Protein (177 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: IL7_HUMAN
DESCRIPTION: RecName: Full=Interleukin-7; Short=IL-7; Flags: Precursor;
FUNCTION: Hematopoietic growth factor capable of stimulating the proliferation of lymphoid progenitors. It is important for proliferation during certain stages of B-cell maturation.
INTERACTION: P31785:IL2RG; NbExp=2; IntAct=EBI-80516, EBI-80475; P16871:IL7R; NbExp=3; IntAct=EBI-80516, EBI-80490;
SUBCELLULAR LOCATION: Secreted.
SIMILARITY: Belongs to the IL-7/IL-9 family.
WEB RESOURCE: Name=Wikipedia; Note=Interleukin-7 entry; URL="http://en.wikipedia.org/wiki/Interleukin_7";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): IL7
CDC HuGE Published Literature: IL7
Positive Disease Associations: Body Weight , Cholesterol , Creatinine , Creutzfeldt-Jakob Syndrome , Eosinophils , Mortality , Potassium , Stroke
Related Studies:
  1. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  2. Body Weight
    Caroline S Fox et al. BMC medical genetics 2007, Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project., BMC medical genetics. [PubMed 17903300]
    Adiposity traits are associated with SNPs on the Affymetrix 100K SNP GeneChip. Replication of these initial findings is necessary. These data will serve as a resource for replication as more genes become identified with BMI and WC.
  3. Cholesterol
    , , . [PubMed 0]
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: IL7
Diseases sorted by gene-association score: lymphopenia (24), severe combined immunodeficiency, x-linked (16), thyroid lymphoma (15), interleukin-7 receptor alpha deficiency (12), papillary conjunctivitis (9), cutaneous t cell lymphoma (9), giant papillary conjunctivitis (9), severe combined immunodeficiency (8), acute monoblastic leukemia (8), radiculopathy (8), b cell linker protein deficiency (7), natural killer cell leukemia (7), cyclic thrombocytopenia (7), sezary's disease (6), pancreas adenocarcinoma (6), thymic dysplasia (5), leukemia, acute lymphoblastic (5), combined t cell and b cell immunodeficiency (5), leukemia, acute lymphoblastic 3 (3), mycosis fungoides (3), primary immunodeficiency disease (2), chronic lymphocytic leukemia (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 4.67 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 37.84 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -208.22601-0.346 Picture PostScript Text
3' UTR -196.54941-0.209 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001181 - Interleukin-7
IPR018049 - Interleukin-7/-9_CS
IPR000226 - Interleukin_7_9

Pfam Domains:
PF01415 - Interleukin 7/9 family

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1IL7
- Model

3DI2
- X-ray MuPIT

3DI3
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P13232
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0005126 cytokine receptor binding
GO:0005139 interleukin-7 receptor binding
GO:0005515 protein binding
GO:0008083 growth factor activity

Biological Process:
GO:0001961 positive regulation of cytokine-mediated signaling pathway
GO:0002360 T cell lineage commitment
GO:0006955 immune response
GO:0006959 humoral immune response
GO:0007267 cell-cell signaling
GO:0008284 positive regulation of cell proliferation
GO:0009887 animal organ morphogenesis
GO:0010468 regulation of gene expression
GO:0010469 regulation of receptor activity
GO:0019221 cytokine-mediated signaling pathway
GO:0030890 positive regulation of B cell proliferation
GO:0032722 positive regulation of chemokine production
GO:0038111 interleukin-7-mediated signaling pathway
GO:0043066 negative regulation of apoptotic process
GO:0043086 negative regulation of catalytic activity
GO:0045453 bone resorption
GO:0045582 positive regulation of T cell differentiation
GO:0046622 positive regulation of organ growth
GO:0048873 homeostasis of number of cells within a tissue
GO:2001237 negative regulation of extrinsic apoptotic signaling pathway
GO:2001240 negative regulation of extrinsic apoptotic signaling pathway in absence of ligand

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space


-  Descriptions from all associated GenBank mRNAs
  BC047698 - Homo sapiens interleukin 7, mRNA (cDNA clone MGC:51943 IMAGE:5748841), complete cds.
BC032487 - Homo sapiens interleukin 7, mRNA (cDNA clone IMAGE:5220028), containing frame-shift errors.
J04156 - Human interleukin 7 (IL-7) mRNA, complete cds.
AK226000 - Homo sapiens mRNA for interleukin 7 precursor variant, clone: FCC109E12.
AK291538 - Homo sapiens cDNA FLJ75417 complete cds, highly similar to Homo sapiens interleukin 7, mRNA.
GQ919059 - Homo sapiens interleukin 7 (IL7) mRNA, partial cds.
KX160446 - Homo sapiens interleukin 7 mRNA, partial cds.
AB102879 - Homo sapiens mRNA for IL7 nirs variant 2, complete cds.
AB102893 - Homo sapiens mRNA for IL7 nirs variant 1, complete cds.
KJ891458 - Synthetic construct Homo sapiens clone ccsbBroadEn_00852 IL7 gene, encodes complete protein.
AB587431 - Synthetic construct DNA, clone: pF1KB6851, Homo sapiens IL7 gene for interleukin 7, without stop codon, in Flexi system.
CU690462 - Synthetic construct Homo sapiens gateway clone IMAGE:100021291 5' read IL7 mRNA.
AB102882 - Homo sapiens mRNA for IL7 nirs variant 3, complete cds.
AB102885 - Homo sapiens mRNA for IL7 nirs variant 6, complete cds.
JD305960 - Sequence 286984 from Patent EP1572962.
JD313067 - Sequence 294091 from Patent EP1572962.
JD044085 - Sequence 25109 from Patent EP1572962.
JD296188 - Sequence 277212 from Patent EP1572962.
JD171866 - Sequence 152890 from Patent EP1572962.
AB102883 - Homo sapiens mRNA for IL7 nirs variant 4, complete cds.
AB102880 - Homo sapiens mRNA for IL7 nirs variant 5, complete cds.
JD325352 - Sequence 306376 from Patent EP1572962.
JD336411 - Sequence 317435 from Patent EP1572962.
JD068819 - Sequence 49843 from Patent EP1572962.
JD462835 - Sequence 443859 from Patent EP1572962.
JD559779 - Sequence 540803 from Patent EP1572962.
JD250196 - Sequence 231220 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04630 - Jak-STAT signaling pathway
hsa04640 - Hematopoietic cell lineage

BioCarta from NCI Cancer Genome Anatomy Project
h_il7Pathway - IL-7 Signal Transduction
h_stemPathway - Regulation of hematopoiesis by cytokines
h_inflamPathway - Cytokines and Inflammatory Response

Reactome (by CSHL, EBI, and GO)

Protein P13232 (Reactome details) participates in the following event(s):

R-HSA-449978 IL7 binds IL7R:JAK1
R-HSA-1266684 IL7 binds HGF(495-728) to form PPBSF
R-NUL-1266699 PPBSF is a complex of Il7 and Hgf(495-728)
R-HSA-449958 IL7:IL7R:JAK1 binds IL2RG:JAK3
R-HSA-1295519 IL7R is phosphorylated on Y499
R-HSA-1295516 IL7:p-Y449-IL7R:JAK1:IL2RG:JAK3 binds PI3K regulatory subunits
R-HSA-6785165 p-STAT5A, p-STAT5B dissociate from IL7:p-Y449-IL7R:JAK1:IL2RG:p-JAK3:p-STAT5A,p-STAT5B
R-HSA-1266695 Interleukin-7 signaling
R-HSA-449147 Signaling by Interleukins
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: A0N0L3, IL7_HUMAN, NM_000880, NP_000871, P13232, Q5FBY9
UCSC ID: uc003ybg.3
RefSeq Accession: NM_000880
Protein: P13232 (aka IL7_HUMAN)
CCDS: CCDS6224.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000880.3
exon count: 6CDS single in 3' UTR: no RNA size: 2089
ORF size: 534CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 921.50frame shift in genome: no % Coverage: 99.38
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.