Human Gene CCL28 (uc003jnu.3)
  Description: Homo sapiens chemokine (C-C motif) ligand 28 (CCL28), mRNA.
RefSeq Summary (NM_148672): This antimicrobial gene belongs to the subfamily of small cytokine CC genes. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The CC cytokines are proteins characterized by two adjacent cysteines. The cytokine encoded by this gene displays chemotactic activity for resting CD4 or CD8 T cells and eosinophils. The product of this gene binds to chemokine receptors CCR3 and CCR10. This chemokine may play a role in the physiology of extracutaneous epithelial tissues, including diverse mucosal organs. Multiple transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Sep 2014].
Transcript (Including UTRs)
   Position: hg19 chr5:43,381,600-43,412,488 Size: 30,889 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr5:43,381,962-43,412,418 Size: 30,457 Coding Exon Count: 3 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:43,381,600-43,412,488)mRNA (may differ from genome)Protein (127 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCLynxMGIneXtProtOMIM
PubMedReactomeTreefamUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CCL28_HUMAN
DESCRIPTION: RecName: Full=C-C motif chemokine 28; AltName: Full=Mucosae-associated epithelial chemokine; Short=MEC; AltName: Full=Protein CCK1; AltName: Full=Small-inducible cytokine A28; Flags: Precursor;
FUNCTION: Chemotactic activity for resting CD4, CD8 T-cells and eosinophils. Binds to CCR3 and CCR10 and induces calcium mobilization in a dose-dependent manner.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Preferentially expressed by epithelial cells of diverse tissues including normal and pathological colon, salivary gland, mammary gland, trachea and rectum. Also found in prostate, spleen, thyroid, psoriasis skin and in lower levels in peripheral blood leukocytes, small intestine, Peyer patches, stomach and normal skin.
SIMILARITY: Belongs to the intercrine beta (chemokine CC) family.
WEB RESOURCE: Name=Wikipedia; Note=CCL28 entry; URL="http://en.wikipedia.org/wiki/CCL28";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CCL28
CDC HuGE Published Literature: CCL28

-  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: 89.78 RPKM in Minor Salivary Gland
Total median expression: 161.25 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 -19.6070-0.280 Picture PostScript Text
3' UTR -88.10362-0.243 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
IPR000827 - Chemokine_CC_CS
IPR001811 - Chemokine_IL8-like_dom

Pfam Domains:
PF00048 - Small cytokines (intecrine/chemokine), interleukin-8 like

SCOP Domains:
54117 - Interleukin 8-like chemokines

ModBase Predicted Comparative 3D Structure on Q9NRJ3
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 orthologNo orthologGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005125 cytokine activity
GO:0005515 protein binding
GO:0008009 chemokine activity

Biological Process:
GO:0001954 positive regulation of cell-matrix adhesion
GO:0006935 chemotaxis
GO:0006955 immune response
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0007584 response to nutrient
GO:0010469 regulation of receptor activity
GO:0031640 killing of cells of other organism
GO:0051715 cytolysis in other organism
GO:0060326 cell chemotaxis
GO:1903237 negative regulation of leukocyte tethering or rolling

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005623 cell
GO:0070062 extracellular exosome
GO:0030141 secretory granule


-  Descriptions from all associated GenBank mRNAs
  AF266504 - Homo sapiens mucosae-associated epithelial chemokine mRNA, complete cds.
AF110384 - Homo sapiens CCK1 protein (CCK1) mRNA, complete cds.
BC069532 - Homo sapiens chemokine (C-C motif) ligand 28, mRNA (cDNA clone MGC:96901 IMAGE:7262110), complete cds.
AK307307 - Homo sapiens cDNA, FLJ97255.
BC062668 - Homo sapiens chemokine (C-C motif) ligand 28, mRNA (cDNA clone MGC:71902 IMAGE:30326117), complete cds.
AF220210 - Homo sapiens CC chemokine CCL28 (SCYA28) mRNA, complete cds.
AK312120 - Homo sapiens cDNA, FLJ92402, Homo sapiens chemokine (C-C motif) ligand 28 (CCL28), transcriptvariant 1, mRNA.
CU686894 - Synthetic construct Homo sapiens gateway clone IMAGE:100022524 5' read CCL28 mRNA.
HQ448455 - Synthetic construct Homo sapiens clone IMAGE:100071883; CCSB013801_01 chemokine (C-C motif) ligand 28 (CCL28) gene, encodes complete protein.
KJ894330 - Synthetic construct Homo sapiens clone ccsbBroadEn_03724 CCL28 gene, encodes complete protein.
AB590493 - Synthetic construct DNA, clone: pFN21AE1616, Homo sapiens CCL28 gene for chemokine (C-C motif) ligand 28, without stop codon, in Flexi system.
HM067700 - Homo sapiens chemokine (C-C motif) ligand 28 splice variant chi (CCL28) mRNA, complete cds, alternatively spliced.
JD533088 - Sequence 514112 from Patent EP1572962.
JD258229 - Sequence 239253 from Patent EP1572962.
JD106743 - Sequence 87767 from Patent EP1572962.
JD375749 - Sequence 356773 from Patent EP1572962.
JD413949 - Sequence 394973 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04062 - Chemokine signaling pathway
hsa04672 - Intestinal immune network for IgA production

Reactome (by CSHL, EBI, and GO)

Protein Q9NRJ3 (Reactome details) participates in the following event(s):

R-HSA-373086 Receptor CCR10 binds CCL27 and 28 ligands
R-HSA-749454 The Ligand:GPCR:Gi complex dissociates
R-HSA-749456 Liganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi
R-HSA-380073 Liganded Gi-activating GPCR acts as a GEF for Gi
R-HSA-380108 Chemokine receptors bind chemokines
R-HSA-418594 G alpha (i) signalling events
R-HSA-375276 Peptide ligand-binding receptors
R-HSA-388396 GPCR downstream signalling
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-372790 Signaling by GPCR
R-HSA-500792 GPCR ligand binding
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: CCL28_HUMAN, NM_148672, NP_683513, Q9NRJ3, SCYA28
UCSC ID: uc003jnu.3
RefSeq Accession: NM_148672
Protein: Q9NRJ3 (aka CCL28_HUMAN)
CCDS: CCDS3944.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_148672.2
exon count: 3CDS single in 3' UTR: no RNA size: 816
ORF size: 384CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 968.00frame shift in genome: no % Coverage: 100.00
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: 303# 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.