Human Gene CX3CL1 (ENST00000006053.7_10) from GENCODE V47lift37
  Description: C-X3-C motif chemokine ligand 1, transcript variant 1 (from RefSeq NM_002996.6)
Gencode Transcript: ENST00000006053.7_10
Gencode Gene: ENSG00000006210.7_12
Transcript (Including UTRs)
   Position: hg19 chr16:57,406,402-57,418,956 Size: 12,555 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr16:57,406,481-57,416,944 Size: 10,464 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:57,406,402-57,418,956)mRNA (may differ from genome)Protein (397 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: X3CL1_HUMAN
DESCRIPTION: RecName: Full=Fractalkine; AltName: Full=C-X3-C motif chemokine 1; AltName: Full=CX3C membrane-anchored chemokine; AltName: Full=Neurotactin; AltName: Full=Small-inducible cytokine D1; Contains: RecName: Full=Processed fractalkine; Flags: Precursor;
FUNCTION: The soluble form is chemotactic for T-cells and monocytes, but not for neutrophils. The membrane-bound form promotes adhesion of those leukocytes to endothelial cells. May play a role in regulating leukocyte adhesion and migration processes at the endothelium. Binds to CX3CR1.
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane protein.
SUBCELLULAR LOCATION: Processed fractalkine: Secreted.
TISSUE SPECIFICITY: Small intestine, colon, testis, prostate, heart, brain, lung, skeletal muscle, kidney and pancreas.
INDUCTION: By TNF and IL1/interleukin-1 in pulmonary endothelial cells and umbilical vein endothelial cells.
PTM: A soluble short 95 kDa form may be released by proteolytic cleavage from the long membrane-anchored form (By similarity).
PTM: O-glycosylated with core 1 or possibly core 8 glycans.
SIMILARITY: Belongs to the intercrine delta family.
WEB RESOURCE: Name=Wikipedia; Note=CX3CL1 entry; URL="http://en.wikipedia.org/wiki/CX3CL1";

-  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: CX3CL1
Diseases sorted by gene-association score: rheumatoid vasculitis (2), listeria meningitis (1), eye disease (1)

-  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: 33.76 RPKM in Breast - Mammary Tissue
Total median expression: 543.09 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 -25.8079-0.327 Picture PostScript Text
3' UTR -790.002012-0.393 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
IPR008097 - Chemokine_fractalkine_CX3CL1
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
1B2T - NMR MuPIT 1F2L - X-ray MuPIT 3ONA - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P78423
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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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005102 receptor binding
GO:0005125 cytokine activity
GO:0005178 integrin binding
GO:0005515 protein binding
GO:0008009 chemokine activity
GO:0031737 CX3C chemokine receptor binding
GO:0048020 CCR chemokine receptor binding

Biological Process:
GO:0002523 leukocyte migration involved in inflammatory response
GO:0002548 monocyte chemotaxis
GO:0006935 chemotaxis
GO:0006952 defense response
GO:0006955 immune response
GO:0007155 cell adhesion
GO:0007186 G-protein coupled receptor signaling pathway
GO:0010469 regulation of receptor activity
GO:0010976 positive regulation of neuron projection development
GO:0019221 cytokine-mediated signaling pathway
GO:0030336 negative regulation of cell migration
GO:0030593 neutrophil chemotaxis
GO:0030595 leukocyte chemotaxis
GO:0032914 positive regulation of transforming growth factor beta1 production
GO:0033622 integrin activation
GO:0042060 wound healing
GO:0043547 positive regulation of GTPase activity
GO:0045766 positive regulation of angiogenesis
GO:0048246 macrophage chemotaxis
GO:0048247 lymphocyte chemotaxis
GO:0050729 positive regulation of inflammatory response
GO:0050902 leukocyte adhesive activation
GO:0051041 positive regulation of calcium-independent cell-cell adhesion
GO:0060055 angiogenesis involved in wound healing
GO:0060326 cell 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
GO:2001240 negative regulation of extrinsic apoptotic signaling pathway in absence of ligand

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK222692 - Homo sapiens mRNA for chemokine (C-X3-C motif) ligand 1 variant, clone: CBR07653.
AK313806 - Homo sapiens cDNA, FLJ94424, Homo sapiens chemokine (C-X3-C motif) ligand 1 (CX3CL1), mRNA.
AK223351 - Homo sapiens mRNA for chemokine (C-X3-C motif) ligand 1 variant, clone: TST08069.
LP880262 - Sequence 66 from Patent WO2017181111.
LP882093 - Sequence 35 from Patent WO2017181079.
U91835 - Human CX3C chemokine precursor, mRNA, alternatively spliced, complete cds.
U84487 - Human CX3C chemokine precursor, mRNA, alternatively spliced, complete cds.
BC001163 - Homo sapiens chemokine (C-X3-C motif) ligand 1, mRNA (cDNA clone MGC:1623 IMAGE:3503870), complete cds.
BC016164 - Homo sapiens chemokine (C-X3-C motif) ligand 1, mRNA (cDNA clone MGC:15771 IMAGE:3502121), complete cds.
AB590256 - Synthetic construct DNA, clone: pFN21AE1310, Homo sapiens CX3CL1 gene for chemokine (C-X3-C motif) ligand 1, without stop codon, in Flexi system.
DQ890704 - Synthetic construct clone IMAGE:100003334; FLH165308.01X; RZPDo839A09160D chemokine (C-X3-C motif) ligand 1 (CX3CL1) gene, encodes complete protein.
DQ891871 - Synthetic construct clone IMAGE:100004501; FLH180767.01X; RZPDo839F10134D chemokine (C-X3-C motif) ligand 1 (CX3CL1) gene, encodes complete protein.
DQ893888 - Synthetic construct Homo sapiens clone IMAGE:100008348; FLH165304.01L; RZPDo839A09159D chemokine (C-X3-C motif) ligand 1 (CX3CL1) gene, encodes complete protein.
DQ895059 - Synthetic construct Homo sapiens clone IMAGE:100009519; FLH180763.01L; RZPDo839F10133D chemokine (C-X3-C motif) ligand 1 (CX3CL1) gene, encodes complete protein.
CU674588 - Synthetic construct Homo sapiens gateway clone IMAGE:100017183 5' read CX3CL1 mRNA.
KJ892116 - Synthetic construct Homo sapiens clone ccsbBroadEn_01510 CX3CL1 gene, encodes complete protein.
CR457426 - Homo sapiens full open reading frame cDNA clone RZPDo834B0518D for gene CX3CL1, chemokine (C-X3-C motif) ligand 1; complete cds, incl. stopcodon.
MB143807 - JP 2019515670-A/18: METHODS FOR MONITORING AND TREATING CANCER.
MB423130 - JP 2019521641-A/17: METHODS FOR MONITORING AND TREATING CANCER.
JD459031 - Sequence 440055 from Patent EP1572962.
JD204025 - Sequence 185049 from Patent EP1572962.
AB209037 - Homo sapiens mRNA for chemokine (C-X3-C motif) ligand 1 variant protein.
JD270975 - Sequence 251999 from Patent EP1572962.
JD126244 - Sequence 107268 from Patent EP1572962.
GU047346 - Homo sapiens chemokine (C-X3-C motif) ligand 1 (CX3CL1) mRNA, partial sequence.
JD317745 - Sequence 298769 from Patent EP1572962.
JD371854 - Sequence 352878 from Patent EP1572962.
JD148096 - Sequence 129120 from Patent EP1572962.
JD111674 - Sequence 92698 from Patent EP1572962.
JD121667 - Sequence 102691 from Patent EP1572962.
JD121061 - Sequence 102085 from Patent EP1572962.
JD132387 - Sequence 113411 from Patent EP1572962.
JD071440 - Sequence 52464 from Patent EP1572962.
JD518565 - Sequence 499589 from Patent EP1572962.
JD476852 - Sequence 457876 from Patent EP1572962.
JD383427 - Sequence 364451 from Patent EP1572962.
JD360051 - Sequence 341075 from Patent EP1572962.
JD466241 - Sequence 447265 from Patent EP1572962.
JD281552 - Sequence 262576 from Patent EP1572962.
LF208236 - JP 2014500723-A/15739: Polycomb-Associated Non-Coding RNAs.
JD116328 - Sequence 97352 from Patent EP1572962.
JD538310 - Sequence 519334 from Patent EP1572962.
LF373727 - JP 2014500723-A/181230: Polycomb-Associated Non-Coding RNAs.
JD298845 - Sequence 279869 from Patent EP1572962.
JD197379 - Sequence 178403 from Patent EP1572962.
JD488783 - Sequence 469807 from Patent EP1572962.
JD282933 - Sequence 263957 from Patent EP1572962.
JD250490 - Sequence 231514 from Patent EP1572962.
JD164733 - Sequence 145757 from Patent EP1572962.
JD383537 - Sequence 364561 from Patent EP1572962.
JD391010 - Sequence 372034 from Patent EP1572962.
JD156761 - Sequence 137785 from Patent EP1572962.
JD055747 - Sequence 36771 from Patent EP1572962.
JD120654 - Sequence 101678 from Patent EP1572962.
JD075702 - Sequence 56726 from Patent EP1572962.
JD389813 - Sequence 370837 from Patent EP1572962.
JD367432 - Sequence 348456 from Patent EP1572962.
JD122492 - Sequence 103516 from Patent EP1572962.
JD445539 - Sequence 426563 from Patent EP1572962.
JD382163 - Sequence 363187 from Patent EP1572962.
JD050707 - Sequence 31731 from Patent EP1572962.
JD310145 - Sequence 291169 from Patent EP1572962.
JD049525 - Sequence 30549 from Patent EP1572962.
JD342045 - Sequence 323069 from Patent EP1572962.
JD218053 - Sequence 199077 from Patent EP1572962.
JD039809 - Sequence 20833 from Patent EP1572962.
JD323710 - Sequence 304734 from Patent EP1572962.
JD404072 - Sequence 385096 from Patent EP1572962.
JD099095 - Sequence 80119 from Patent EP1572962.
JD045681 - Sequence 26705 from Patent EP1572962.
JD289559 - Sequence 270583 from Patent EP1572962.
JD273685 - Sequence 254709 from Patent EP1572962.
JD527252 - Sequence 508276 from Patent EP1572962.
JD055837 - Sequence 36861 from Patent EP1572962.
JD393215 - Sequence 374239 from Patent EP1572962.
JD401152 - Sequence 382176 from Patent EP1572962.
JD550008 - Sequence 531032 from Patent EP1572962.
JD055904 - Sequence 36928 from Patent EP1572962.
JD162258 - Sequence 143282 from Patent EP1572962.
JD229133 - Sequence 210157 from Patent EP1572962.
JD296287 - Sequence 277311 from Patent EP1572962.
JD458785 - Sequence 439809 from Patent EP1572962.
JD499392 - Sequence 480416 from Patent EP1572962.
JD552555 - Sequence 533579 from Patent EP1572962.
MA443813 - JP 2018138019-A/15739: Polycomb-Associated Non-Coding RNAs.
MA609304 - JP 2018138019-A/181230: Polycomb-Associated Non-Coding RNAs.

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

Protein P78423 (Reactome details) participates in the following event(s):

R-HSA-373342 CX3CR1 binds CX3CL1
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: A-152E5.2, CX3CL1 , ENST00000006053.1, ENST00000006053.2, ENST00000006053.3, ENST00000006053.4, ENST00000006053.5, ENST00000006053.6, FKN , NM_002996, NTT , O00672, P78423, SCYD1, uc317bwa.1, uc317bwa.2, X3CL1_HUMAN
UCSC ID: ENST00000006053.7_10
RefSeq Accession: NM_002996.6
Protein: P78423 (aka X3CL1_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.