LOCUS       NM_002996               3285 bp    mRNA    linear   PRI 19-AUG-2024
DEFINITION  Homo sapiens C-X3-C motif chemokine ligand 1 (CX3CL1), transcript
            variant 1, mRNA.
ACCESSION   NM_002996
VERSION     NM_002996.6
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 3285)
  AUTHORS   Watroba,M., Grabowska,A.D. and Szukiewicz,D.
  TITLE     Chemokine CX3CL1 (Fractalkine) Signaling and Diabetic
            Encephalopathy
  JOURNAL   Int J Mol Sci 25 (14), 7527 (2024)
   PUBMED   39062768
  REMARK    GeneRIF: Chemokine CX3CL1 (Fractalkine) Signaling and Diabetic
            Encephalopathy.
            Review article
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3285)
  AUTHORS   Martinez-Flores,R., Lozano-Burgos,C., Niklander,S.E.,
            Fernandez-Cuya,M., Lopes,M.A. and Gonzalez-Arriagada,W.A.
  TITLE     Relationship between aggressive features of oral squamous cell
            carcinoma and the immunoexpression of CX3CR1, CX3CL1 and ITGAV
  JOURNAL   Oral Surg Oral Med Oral Pathol Oral Radiol 138 (1), 79-87 (2024)
   PUBMED   38760287
  REMARK    GeneRIF: Relationship between aggressive features of oral squamous
            cell carcinoma and the immunoexpression of CX3CR1, CX3CL1 and
            ITGAV.
REFERENCE   3  (bases 1 to 3285)
  AUTHORS   Qian,X., Zheng,Y., Xu,L., Liu,Z., Chen,M., Tong,F., Fan,P.,
            Chen,Z., Dong,N., Zhang,C. and Liu,J.
  TITLE     Deciphering the role of CX3CL1-CX3CR1 in aortic aneurysm
            pathogenesis: insights from Mendelian randomization and
            transcriptomic analyses
  JOURNAL   Front Immunol 15, 1383607 (2024)
   PUBMED   38715600
  REMARK    GeneRIF: Deciphering the role of CX3CL1-CX3CR1 in aortic aneurysm
            pathogenesis: insights from Mendelian randomization and
            transcriptomic analyses.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 3285)
  AUTHORS   Liu,W., Jiang,L., Bian,C., Liang,Y., Xing,R., Yishakea,M. and
            Dong,J.
  TITLE     Role of CX3CL1 in Diseases
  JOURNAL   Arch Immunol Ther Exp (Warsz) 64 (5), 371-383 (2016)
   PUBMED   27098399
  REMARK    GeneRIF: CX3CL1 exerts numerous effects on pathophysiological
            conditions that have both negative and positive consequences on
            pathogenesis and outcome [review]
            Review article
REFERENCE   5  (bases 1 to 3285)
  AUTHORS   Mizoue,L.S., Bazan,J.F., Johnson,E.C. and Handel,T.M.
  TITLE     Solution structure and dynamics of the CX3C chemokine domain of
            fractalkine and its interaction with an N-terminal fragment of
            CX3CR1
  JOURNAL   Biochemistry 38 (5), 1402-1414 (1999)
   PUBMED   9931005
REFERENCE   6  (bases 1 to 3285)
  AUTHORS   Combadiere,C., Salzwedel,K., Smith,E.D., Tiffany,H.L., Berger,E.A.
            and Murphy,P.M.
  TITLE     Identification of CX3CR1. A chemotactic receptor for the human CX3C
            chemokine fractalkine and a fusion coreceptor for HIV-1
  JOURNAL   J Biol Chem 273 (37), 23799-23804 (1998)
   PUBMED   9726990
REFERENCE   7  (bases 1 to 3285)
  AUTHORS   Nomiyama,H., Imai,T., Kusuda,J., Miura,R., Callen,D.F. and
            Yoshie,O.
  TITLE     Human chemokines fractalkine (SCYD1), MDC (SCYA22) and TARC
            (SCYA17) are clustered on chromosome 16q13
  JOURNAL   Cytogenet Cell Genet 81 (1), 10-11 (1998)
   PUBMED   9691168
REFERENCE   8  (bases 1 to 3285)
  AUTHORS   Imai,T., Hieshima,K., Haskell,C., Baba,M., Nagira,M., Nishimura,M.,
            Kakizaki,M., Takagi,S., Nomiyama,H., Schall,T.J. and Yoshie,O.
  TITLE     Identification and molecular characterization of fractalkine
            receptor CX3CR1, which mediates both leukocyte migration and
            adhesion
  JOURNAL   Cell 91 (4), 521-530 (1997)
   PUBMED   9390561
REFERENCE   9  (bases 1 to 3285)
  AUTHORS   Pan,Y., Lloyd,C., Zhou,H., Dolich,S., Deeds,J., Gonzalo,J.A.,
            Vath,J., Gosselin,M., Ma,J., Dussault,B., Woolf,E., Alperin,G.,
            Culpepper,J., Gutierrez-Ramos,J.C. and Gearing,D.
  TITLE     Neurotactin, a membrane-anchored chemokine upregulated in brain
            inflammation
  JOURNAL   Nature 387 (6633), 611-617 (1997)
   PUBMED   9177350
  REMARK    Erratum:[Nature 1997 Sep 4;389(6646):100]
REFERENCE   10 (bases 1 to 3285)
  AUTHORS   Bazan,J.F., Bacon,K.B., Hardiman,G., Wang,W., Soo,K., Rossi,D.,
            Greaves,D.R., Zlotnik,A. and Schall,T.J.
  TITLE     A new class of membrane-bound chemokine with a CX3C motif
  JOURNAL   Nature 385 (6617), 640-644 (1997)
   PUBMED   9024663
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from HY114023.1, BC001163.1 and
            AC009052.8.
            
            On Nov 23, 2018 this sequence version replaced NM_002996.5.
            
            Summary: This gene belongs to the CX3C subgroup of chemokines,
            characterized by the number of amino acids located between the
            conserved cysteine residues. This is the only member of the CX3C
            subgroup, which contains three amino acids between cysteine
            residues, resulting in a Cys-X-X-X-Cys configuration. The encoded
            protein contains an extended mucin-like stalk with a chemokine
            domain on top, and exists in both a membrane-anchored form where it
            acts as a binding molecule, or, in soluble form, as a chemotactic
            cytokine. The mature form of this protein can be cleaved at the
            cell surface, yielding different soluble forms that can interact
            with the G-protein coupled receptor, C-X3-C motif chemokine
            receptor 1 gene product. This gene plays a role in a wide range of
            diseases, including cancer, vasculitis, neuropathies,
            atherosclerosis, inflammatory diseases, and in human
            immunodeficiency virus infections. [provided by RefSeq, Sep 2017].
            
            Transcript Variant: This variant (1) represents the longer
            transcript and encodes the longer isoform (1).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: U84487.1, SRR1803617.180120.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000006053.7/ ENSP00000006053.6
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-12                HY114023.1         31-42
            13-1462             BC001163.1         1-1450
            1463-1463           AC009052.8         80939-80939
            1464-3010           BC001163.1         1452-2998
            3011-3011           AC009052.8         82487-82487
            3012-3053           BC001163.1         3000-3041
            3054-3054           AC009052.8         82530-82530
            3055-3285           BC001163.1         3043-3273
FEATURES             Location/Qualifiers
     source          1..3285
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="16"
                     /map="16q21"
     gene            1..3285
                     /gene="CX3CL1"
                     /gene_synonym="ABCD-3; C3Xkine; CXC3; CXC3C; fractalkine;
                     neurotactin; NTN; NTT; SCYD1"
                     /note="C-X3-C motif chemokine ligand 1"
                     /db_xref="GeneID:6376"
                     /db_xref="HGNC:HGNC:10647"
                     /db_xref="MIM:601880"
     exon            1..149
                     /gene="CX3CL1"
                     /gene_synonym="ABCD-3; C3Xkine; CXC3; CXC3C; fractalkine;
                     neurotactin; NTN; NTT; SCYD1"
                     /inference="alignment:Splign:2.1.0"
     CDS             80..1273
                     /gene="CX3CL1"
                     /gene_synonym="ABCD-3; C3Xkine; CXC3; CXC3C; fractalkine;
                     neurotactin; NTN; NTT; SCYD1"
                     /note="isoform 1 precursor is encoded by transcript
                     variant 1; small inducible cytokine subfamily D
                     (Cys-X3-Cys), member 1 (fractalkine, neurotactin); small
                     inducible cytokine subfamily D (Cys-X3-Cys), member-1;
                     C-X3-C motif chemokine 1; small-inducible cytokine D1;
                     CX3C membrane-anchored chemokine; chemokine (C-X3-C motif)
                     ligand 1"
                     /codon_start=1
                     /product="fractalkine isoform 1 precursor"
                     /protein_id="NP_002987.1"
                     /db_xref="CCDS:CCDS10779.1"
                     /db_xref="GeneID:6376"
                     /db_xref="HGNC:HGNC:10647"
                     /db_xref="MIM:601880"
                     /translation="MAPISLSWLLRLATFCHLTVLLAGQHHGVTKCNITCSKMTSKIP
                     VALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKDAMQHLDRQAAALTRNGGT
                     FEKQIGEVKPRTTPAAGGMDESVVLEPEATGESSSLEPTPSSQEAQRALGTSPELPTG
                     VTGSSGTRLPPTPKAQDGGPVGTELFRVPPVSTAATWQSSAPHQPGPSLWAEAKTSEA
                     PSTQDPSTQASTASSPAPEENAPSEGQRVWGQGQSPRPENSLEREEMGPVPAHTDAFQ
                     DWGPGSMAHVSVVPVSSEGTPSREPVASGSWTPKAEEPIHATMDPQRLGVLITPVPDA
                     QAATRRQAVGLLAFLGLLFCLGVAMFTYQSLQGCPRKMAGEMAEGLRYIPRSCGSNSY
                     VLVPV"
     exon            150..270
                     /gene="CX3CL1"
                     /gene_synonym="ABCD-3; C3Xkine; CXC3; CXC3C; fractalkine;
                     neurotactin; NTN; NTT; SCYD1"
                     /inference="alignment:Splign:2.1.0"
     exon            271..3285
                     /gene="CX3CL1"
                     /gene_synonym="ABCD-3; C3Xkine; CXC3; CXC3C; fractalkine;
                     neurotactin; NTN; NTT; SCYD1"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3262..3267
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CX3CL1"
                     /gene_synonym="ABCD-3; C3Xkine; CXC3; CXC3C; fractalkine;
                     neurotactin; NTN; NTT; SCYD1"
                     /note="hexamer: AATAAA"
     polyA_site      3285
                     /gene="CX3CL1"
                     /gene_synonym="ABCD-3; C3Xkine; CXC3; CXC3C; fractalkine;
                     neurotactin; NTN; NTT; SCYD1"
                     /note="major polyA site"
ORIGIN      
        1 aaggggacag cactgagctc tgccgcctgg ctctagccgc ctgcctggcc cccgccggga
       61 ctcttgccca ccctcagcca tggctccgat atctctgtcg tggctgctcc gcttggccac
      121 cttctgccat ctgactgtcc tgctggctgg acagcaccac ggtgtgacga aatgcaacat
      181 cacgtgcagc aagatgacat caaagatacc tgtagctttg ctcatccact atcaacagaa
      241 ccaggcatca tgcggcaaac gcgcaatcat cttggagacg agacagcaca ggctgttctg
      301 tgccgacccg aaggagcaat gggtcaagga cgcgatgcag catctggacc gccaggctgc
      361 tgccctaact cgaaatggcg gcaccttcga gaagcagatc ggcgaggtga agcccaggac
      421 cacccctgcc gccgggggaa tggacgagtc tgtggtcctg gagcccgaag ccacaggcga
      481 aagcagtagc ctggagccga ctccttcttc ccaggaagca cagagggccc tggggacctc
      541 cccagagctg ccgacgggcg tgactggttc ctcagggacc aggctccccc cgacgccaaa
      601 ggctcaggat ggagggcctg tgggcacgga gcttttccga gtgcctcccg tctccactgc
      661 cgccacgtgg cagagttctg ctccccacca acctgggccc agcctctggg ctgaggcaaa
      721 gacctctgag gccccgtcca cccaggaccc ctccacccag gcctccactg cgtcctcccc
      781 agccccagag gagaatgctc cgtctgaagg ccagcgtgtg tggggtcagg gacagagccc
      841 caggccagag aactctctgg agcgggagga gatgggtccc gtgccagcgc acacggatgc
      901 cttccaggac tgggggcctg gcagcatggc ccacgtctct gtggtccctg tctcctcaga
      961 agggaccccc agcagggagc cagtggcttc aggcagctgg acccctaagg ctgaggaacc
     1021 catccatgcc accatggacc cccagaggct gggcgtcctt atcactcctg tccctgacgc
     1081 ccaggctgcc acccggaggc aggcggtggg gctgctggcc ttccttggcc tcctcttctg
     1141 cctgggggtg gccatgttca cctaccagag cctccagggc tgccctcgaa agatggcagg
     1201 agagatggcg gagggccttc gctacatccc ccggagctgt ggtagtaatt catatgtcct
     1261 ggtgcccgtg tgaactcctc tggcctgtgt ctagttgttt gattcagaca gctgcctggg
     1321 atccctcatc ctcataccca cccccaccca agggcctggc ctgagctggg atgattggag
     1381 gggggaggtg ggatcctcca ggtgcacaag ctccaagctc ccaggcattc cccaggaggc
     1441 cagccttgac cattctccac ctgccaggga cagagggggt ggcctcccaa ctcaccccag
     1501 ccccaaaact ctcctctgct gctggctggt tagaggttcc ctttgacgcc atcccagccc
     1561 caatgaacaa ttatttatta aatgcccagc cccttctgac ccatgctgcc ctgtgagtac
     1621 tacagtcctc ccatctcaca catgagcatc aggccaggcc ctctgcccac tccctgcaac
     1681 ctgattgtgt ctcttggtcc tgctgcagtt gccagtcacc ccggccacct gcggtgctat
     1741 ctcccccagc cccatcctct gtacagagcc cacgccccca ctggtgacat gtcttttctt
     1801 gcatgaggct agtgtggtgt ttcctggcac tgcttccagt gaggctctgc ccttggttag
     1861 gcattgtggg aaggggagat aagggtatct ggtgactttc ctctttggtc tacactgtgc
     1921 tgagtctgaa ggctgggttc tgatcctagt tccaccatca agccaccaac atactcccat
     1981 ctgtgaaagg aaagagggag gtaaggaata cctgtccccc tgacaacact cattgacctg
     2041 aggcccttct ctccagcccc tggatgcagc ctcacagtcc ttaccagcag agcaccttag
     2101 acagtccctg ccaatggact aacttgtctt tggaccctga ggcccagagg gcctgcaagg
     2161 gagtgagttg atagcacaga ccctgccctg tgggccccca aatggaaatg ggcagagcag
     2221 agaccatccc tgaaggcccc gcccaggctt agtcactgag acagcccggg ctctgcctcc
     2281 catcacccgc taagagggag ggagggctcc agacacatgt ccaagaagcc caggaaaggc
     2341 tccaggagca gccacattcc tgatgcttct tcagagactc ctgcaggcag ccaggccaca
     2401 agacccttgt ggtcccaccc cacacacgcc agattctttc ctgaggctgg gctcccttcc
     2461 cacctctctc actccttgaa aacactgttc tctgccctcc aagaccttct ccttcacctt
     2521 tgtccccacc gcagacagga ccagggattt ccatgatgtt ttccatgagt cccctgtttg
     2581 tttctgaaag ggacgctacc cgggaagggg gctgggacat gggaaagggg aagttgtagg
     2641 cataaagtca ggggttccct tttttggctg ctgaaggctc gagcatgcct ggatggggct
     2701 gcaccggctg gcctggcccc tcagggtccc tggtggcagc tcacctctcc cttggattgt
     2761 ccccgaccct tgccgtctac ctgaggggcc tcttatgggc tgggttctac ccaggtgcta
     2821 ggaacactcc ttcacagatg ggtgcttgga ggaaggaaac ccagctctgg tccatagaga
     2881 gcaagacgct gtgctgccct gcccacctgg cctctgcact cccctgctgg gtgtggcgca
     2941 gcatattcag gaagctcagg gcctggctca ggtggggtca ctctggcagc tcagagaggg
     3001 tgggagtggg cccaatgcac tttgttctgg ctcttccagg ctgggagagc cttccagggg
     3061 tgggacaccc tgtgatgggg ccctgcctcc tttgtgagga agccgctggg gccagttggt
     3121 cccccttcca tggactttgt tagtttctcc aagcaggaca tggacaagga tgatctagga
     3181 agactttgga aagagtagga agactttgga aagacttttc caaccctcat caccaacgtc
     3241 tgtgccattt tgtattttac taataaaatt taaaagtctt gtgaa
//
