Human Gene CCL13 (ENST00000225844.7_4) from GENCODE V47lift37
  Description: C-C motif chemokine ligand 13 (from RefSeq NM_005408.3)
Gencode Transcript: ENST00000225844.7_4
Gencode Gene: ENSG00000181374.8_7
Transcript (Including UTRs)
   Position: hg19 chr17:32,683,499-32,685,629 Size: 2,131 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr17:32,683,546-32,685,150 Size: 1,605 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:32,683,499-32,685,629)mRNA (may differ from genome)Protein (98 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CCL13_HUMAN
DESCRIPTION: RecName: Full=C-C motif chemokine 13; AltName: Full=CK-beta-10; AltName: Full=Monocyte chemoattractant protein 4; AltName: Full=Monocyte chemotactic protein 4; Short=MCP-4; AltName: Full=NCC-1; AltName: Full=Small-inducible cytokine A13; Contains: RecName: Full=C-C motif chemokine 13, long chain; Contains: RecName: Full=C-C motif chemokine 13, medium chain; Contains: RecName: Full=C-C motif chemokine 13, short chain; Flags: Precursor;
FUNCTION: Chemotactic factor that attracts monocytes, lymphocytes, basophils and eosinophils, but not neutrophils. Signals through CCR2B and CCR3 receptors. Plays a role in the accumulation of leukocytes at both sides of allergic and non-allergic inflammation. May be involved in the recruitment of monocytes into the arterial wall during the disease process of atherosclerosis. May play a role in the monocyte attraction in tissues chronically exposed to exogenous pathogens.
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Widely expressed. Found in small intestine, thymus, colon, lung, trachea, stomach and lymph node. Low levels seen in the pulmonary artery smooth muscle cells.
INDUCTION: By IL1/interleukin-1 and TNF.
PTM: One major form (form long), and two minor forms (short chain and medium chain) are produced by differential signal peptide cleavage. The medium chain is about 30-fold less active than the long chain.
MASS SPECTROMETRY: Mass=9314; Mass_error=30; Method=MALDI; Range=17-98; Source=PubMed:8642349;
MASS SPECTROMETRY: Mass=8760; Mass_error=30; Method=MALDI; Range=22-98; Source=PubMed:8642349;
MASS SPECTROMETRY: Mass=8575; Mass_error=30; Method=MALDI; Range=24-98; Source=PubMed:8642349;
MISCELLANEOUS: This protein can bind heparin.
SIMILARITY: Belongs to the intercrine beta (chemokine CC) family.
WEB RESOURCE: Name=Wikipedia; Note=CCL13 entry; URL="http://en.wikipedia.org/wiki/CCL13";

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 16.74 RPKM in Nerve - Tibial
Total median expression: 80.25 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.0047-0.106 Picture PostScript Text
3' UTR -117.10479-0.244 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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2RA4 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q99616
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 orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005125 cytokine activity
GO:0008009 chemokine activity
GO:0048020 CCR chemokine receptor binding

Biological Process:
GO:0002548 monocyte chemotaxis
GO:0006874 cellular calcium ion homeostasis
GO:0006935 chemotaxis
GO:0006954 inflammatory response
GO:0006955 immune response
GO:0007010 cytoskeleton organization
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007267 cell-cell signaling
GO:0008360 regulation of cell shape
GO:0010469 regulation of receptor activity
GO:0030593 neutrophil chemotaxis
GO:0031640 killing of cells of other organism
GO:0043547 positive regulation of GTPase activity
GO:0048245 eosinophil chemotaxis
GO:0048247 lymphocyte chemotaxis
GO:0070098 chemokine-mediated signaling pathway
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0071346 cellular response to interferon-gamma
GO:0071347 cellular response to interleukin-1
GO:0071356 cellular response to tumor necrosis factor

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005623 cell


-  Descriptions from all associated GenBank mRNAs
  KJ892106 - Synthetic construct Homo sapiens clone ccsbBroadEn_01500 CCL13 gene, encodes complete protein.
U59808 - Human monocyte chemotactic protein-4 precursor (MCP-4) mRNA, complete cds.
JD064240 - Sequence 45264 from Patent EP1572962.
AJ001634 - Homo sapiens mRNA for CC-chemokine MCP-4.
BC008621 - Homo sapiens chemokine (C-C motif) ligand 13, mRNA (cDNA clone MGC:17134 IMAGE:4184250), complete cds.
U46767 - Homo sapiens monocyte chemoattractant protein-4 precursor (MCP-4) mRNA, complete cds.
JD168239 - Sequence 149263 from Patent EP1572962.
X98306 - H.sapiens mRNA for monocyte chemoattractant protein 4.
JD153746 - Sequence 134770 from Patent EP1572962.
AB463483 - Synthetic construct DNA, clone: pF1KB6741, Homo sapiens CCL13 gene for chemokine (C-C motif) ligand 13, without stop codon, in Flexi system.
CU679005 - Synthetic construct Homo sapiens gateway clone IMAGE:100017898 5' read CCL13 mRNA.
DQ891497 - Synthetic construct clone IMAGE:100004127; FLH177490.01X; RZPDo839A10126D chemokine (C-C motif) ligand 13 (CCL13) gene, encodes complete protein.
DQ894688 - Synthetic construct Homo sapiens clone IMAGE:100009148; FLH177486.01L; RZPDo839A10125D chemokine (C-C motif) ligand 13 (CCL13) gene, encodes complete protein.
CR450337 - Homo sapiens full open reading frame cDNA clone RZPDo834B112D for gene CCL13, chemokine (C-C motif) ligand 13; complete cds; without stopcodon.
BT007385 - Homo sapiens chemokine (C-C motif) ligand 13 mRNA, complete cds.
Z77650 - H.sapiens mRNA for CC-chemokine.
Z77651 - H.sapiens mRNA for CC-chemokine (sequence variant).
JD120051 - Sequence 101075 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q99616 (Reactome details) participates in the following event(s):

R-HSA-8862733 CCR2, CCR3 bind CCL13
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: CCL13_HUMAN, ENST00000225844.1, ENST00000225844.2, ENST00000225844.3, ENST00000225844.4, ENST00000225844.5, ENST00000225844.6, MCP4, NCC1, NM_005408, O95689, Q6ICQ6, Q99616, SCYA13, uc317dkj.1, uc317dkj.2
UCSC ID: ENST00000225844.7_4
RefSeq Accession: NM_005408.3
Protein: Q99616 (aka CCL13_HUMAN)

-  Gene Model Information
  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.