Human Gene CXCL5 (ENST00000296027.5_7) from GENCODE V47lift37
  Description: C-X-C motif chemokine ligand 5 (from RefSeq NM_002994.5)
Gencode Transcript: ENST00000296027.5_7
Gencode Gene: ENSG00000163735.7_9
Transcript (Including UTRs)
   Position: hg19 chr4:74,861,359-74,864,394 Size: 3,036 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg19 chr4:74,863,354-74,864,298 Size: 945 Coding Exon Count: 4 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:74,861,359-74,864,394)mRNA (may differ from genome)Protein (114 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MalacardsMGIOMIMPubMedUniProtKBWikipedia
BioGrid CRISPR DB

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: CXCL5
Diseases sorted by gene-association score: pediatric ulcerative colitis (18), acute cervicitis (11), pulmonary sarcoidosis (9), nonspecific interstitial pneumonia (7), gastroduodenitis (7), cerebritis (6), pulmonary fibrosis, idiopathic (5), rheumatoid arthritis (4), asthma (3)

-  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: 40.13 RPKM in Cells - Cultured fibroblasts
Total median expression: 74.34 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 -14.2096-0.148 Picture PostScript Text
3' UTR -493.401995-0.247 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
IPR001089 - Chemokine_CXC
IPR018048 - Chemokine_CXC_CS
IPR002473 - Chemokine_CXCL8/IL8
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 Q6I9S7
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

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

Biological Process:
GO:0006935 chemotaxis
GO:0006952 defense response
GO:0006955 immune response
GO:0010469 regulation of receptor activity
GO:0060326 cell chemotaxis

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


-  Descriptions from all associated GenBank mRNAs
  KJ892114 - Synthetic construct Homo sapiens clone ccsbBroadEn_01508 CXCL5 gene, encodes complete protein.
AK026546 - Homo sapiens cDNA: FLJ22893 fis, clone KAT04792.
LF338347 - JP 2014500723-A/145850: Polycomb-Associated Non-Coding RNAs.
JD206627 - Sequence 187651 from Patent EP1572962.
BC008376 - Homo sapiens chemokine (C-X-C motif) ligand 5, mRNA (cDNA clone MGC:12304 IMAGE:3826939), complete cds.
JD037550 - Sequence 18574 from Patent EP1572962.
X78686 - H.sapiens ENA-78 mRNA.
JD550902 - Sequence 531926 from Patent EP1572962.
JD285052 - Sequence 266076 from Patent EP1572962.
JD074046 - Sequence 55070 from Patent EP1572962.
JD265129 - Sequence 246153 from Patent EP1572962.
JD347942 - Sequence 328966 from Patent EP1572962.
JD297469 - Sequence 278493 from Patent EP1572962.
JD108255 - Sequence 89279 from Patent EP1572962.
JD419048 - Sequence 400072 from Patent EP1572962.
JD168293 - Sequence 149317 from Patent EP1572962.
JD073331 - Sequence 54355 from Patent EP1572962.
AK312128 - Homo sapiens cDNA, FLJ92410, Homo sapiens chemokine (C-X-C motif) ligand 5 (CXCL5), mRNA.
BT006807 - Homo sapiens chemokine (C-X-C motif) ligand 5 mRNA, complete cds.
DQ895547 - Synthetic construct Homo sapiens clone IMAGE:100010007; FLH186877.01L; RZPDo839B0662D chemokine (C-X-C motif) ligand 5 (CXCL5) gene, encodes complete protein.
EU176356 - Synthetic construct Homo sapiens clone IMAGE:100006464; FLH186884.01X; RZPDo839G10251D chemokine (C-X-C motif) ligand 5 (CXCL5) gene, encodes complete protein.
AB590183 - Synthetic construct DNA, clone: pFN21AE1401, Homo sapiens CXCL5 gene for chemokine (C-X-C motif) ligand 5, without stop codon, in Flexi system.
CR457428 - Homo sapiens full open reading frame cDNA clone RZPDo834F0616D for gene CXCL5, chemokine (C-X-C motif) ligand 5; complete cds, incl. stopcodon.
CU678937 - Synthetic construct Homo sapiens gateway clone IMAGE:100018499 5' read CXCL5 mRNA.
JD520458 - Sequence 501482 from Patent EP1572962.
MA573924 - JP 2018138019-A/145850: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: CXCL5 , ENST00000296027.1, ENST00000296027.2, ENST00000296027.3, ENST00000296027.4, hCG_16364 , NM_002994, Q6I9S7, Q6I9S7_HUMAN, uc317lqn.1, uc317lqn.2
UCSC ID: ENST00000296027.5_7
RefSeq Accession: NM_002994.5
Protein: Q6I9S7

-  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.