Homo sapiens gene CCL1, encoding chemokine (C-C motif) ligand 1.
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SUMMARY back to top
RefSeq summary
[CCL1] This gene is one of several cytokine genes clustered on the q-arm of chromosome 17. Cytokines are a family of secreted proteins involved in immunoregulatory and inflammatory processes. The protein encoded by this gene is structurally related to the CXC subfamily of cytokines. Members of this subfamily are characterized by two cysteines separated by a single amino acid. This cytokine is secreted by activated T cells and displays chemotactic activity for monocytes but not for neutrophils. It binds to the chemokine receptor CCR8. [provided by RefSeq].

RefSeq annotates one representative transcript.

AceView synopsis, each blue text links to tables and details
According to AceView, this gene is moderately expressed, only 30.5% of the average gene in this release. The sequence of this gene is defined by 34 GenBank accessions, some from brain, cerebellum, PCR rescued clones (seen 2 times), carcinoid (2), lung (2), tonsils (once).
The gene contains 2 distinct gt-ag introns. Transcription produces one mRNA.
Function: There are 42 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Bronchiolitis, Viral; Chronic Disease; Fibrosis; Infant, Premature, Diseases; Inflammation; Pancreatitis; Respiratory Syncytial Virus Infections; Sarcoma, Kaposi), proposed to participate in pathways (Chemokine signaling pathway, Cytokine-cytokine receptor interaction) and processes (cellular calcium ion homeostasis, signal transduction, viral reproduction, chemotaxis, immune response). Proteins are expected to have molecular functions (chemokine activity, protein binding) and to localize in various compartments (extracellular region, extracellular space). Putative protein interactors have been described (CCR8, HUWE1).
The spliced mRNA putatively encodes a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 17, links to other databases and other names
Map: This gene CCL1 maps on chromosome 17, at 17q12 according to Entrez Gene. In AceView, it covers 2.90 kb, from 32690249 to 32687347 (NCBI 37, August 2010), on the reverse strand.
Links to: , manual annotations from GAD, KEGG_04060, KEGG_04062, the SNP view, gene overviews from Entrez Gene 6346, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC. The previous AceView annotation is here.
Other names: The gene is also known as CCL1, P500, SISe, TCA3, I-309 or SCYA1, LOC6346. It has been described as C-C motif chemokine 1, inflammatory cytokine I-309, small-inducible cytokine A1, T lymphocyte-secreted protein I-309, small inducible cytokine A1 (I-309, homologous to mouse Tca-3).
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
CCL1 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 1.35 0.59 0.48 0.68 0.42 0.55 0.83 0.59 0.55 0.89 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene CCL1 5' 3' encoded on minus strand of chromosome 17 from 32,690,249 to 32,687,347 679 594 a [NM] 500bp 0 145 bp exon 145 bp exon 1189 bp [gt-ag] intron 32 GenBank accessions 647 RNA-seq supporting reads 248 UHR pooled cells 27 Brain 9 Blood 354 Neuroblastoma 9 Other (also 10 Primates bodymap) 112 bp exon 1123 bp [gt-ag] intron 30 GenBank accessions 564 RNA-seq supporting reads 220 UHR pooled cells 22 Brain 15 Blood 296 Neuroblastoma 11 Other (also 7 Primates bodymap) 334 bp exon 34 accessions, NM_002981.1 some from brain, cerebellum PCR rescued clones (seen 2 times) carcinoid (2), lung (2) tonsils (once) capped 5' end, 1 accession Validated 3' end, 3 accessions 334 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 591 bp 96 aa 69 bp 231 bp 2kb including Promoter 2903 bp 1kb

Gene neighbors and Navigator on chromosome 17q12 back to top
CCL2 D I P CCL7 D C I R P CCL11 D I R P CCL8 C I R P CCL13 D I R P TMEM132E D C R P C17orf102 C R C TLK2P1 R D I P CCL1 100kb 0 CCL2, 282 accessions, 3 variants CCL7, 45 accessions, 4 variants CCL11, 31 accessions CCL8, 56 accessions, 2 variants CCL13, 29 accessions, 2 variants TMEM132E, 12 accessions 2 variants sawsley, 1 accession neychey, 1 accession gleysmo, 1 accession glorsmo, 2 accessions korwubu, 1 accession klernee, 1 accession weysley, 1 accession plawnee, 1 accession sporrey, 1 accession sturey, 2 accessions kloysmo, 2 accessions starrey, 4 accessions lywubu, 1 accession sheysley, 1 accession plusmo, 1 accession plosmo, 2 accessions plarsmo, 1 accession pleesmo, 1 accession plersmo, 1 accession tetuma, 1 accession steerey, 2 accessions ploysmo, 1 accession totuma, 4 accessions, 2 variants skusmo, 2 accessions skawsmo, 1 accession satuma, 2 accessions, 2 variants skeesmo, 1 accession satori, 1 accession nerchey, 1 accession glersmo, 1 accession klorlee, 1 accession norchey, 2 accessions kleylee, 1 accession gloysmo, 2 accessions henima, 1 accession sorsley, 1 accession tawsley, 1 accession vysley, 1 accession sitori, 1 accession yutoru, 3 accessions sperrey, 1 accession vawsley, 1 accession warsley, 1 accession zusley, 1 accession zosley, 3 accessions zorsley, 2 accessions gleelee, 1 accession kleysmo, 1 accession klorsmo, 2 accessions plasmo, 1 accession plysmo, 1 accession stawrey, 1 accession pleysmo, 1 accession plorsmo, 1 accession C17orf102, 8 accessions steyrey, 7 accessions skosmo, 1 accession lerwubu, 1 accession ACCN1, 64 accessions, 3 variants gleesmo, 5 accessions 2 variants TLK2P1, 29 accessions gulee, 4 accessions, 3 variants CCL1, 34 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               42 articles in PubMed back to top
? Gene Summary Gene on genome mRNA Expression Tissue Function, regulation, related genes DI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To see the mRNA diagram, sequence and annotation, click the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !