Homo sapiens complex locus CD69, encoding CD69 molecule.
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SUMMARY back to top
RefSeq summary
[CD69] This gene encodes a member of the calcium dependent lectin superfamily of type II transmembrane receptors. Expression of the encoded protein is induced upon activation of T lymphocytes, and may play a role in proliferation. Furthermore, the protein may act to transmit signals in natural killer cells and platelets. Alternative splicing results in multiple transcript variants.

RefSeq annotates 3 representative transcripts (NM included in AceView variants .a, .b and .f), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 7 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at high level, 2.5 times the average gene in this release. The sequence of this gene is defined by 287 GenBank accessions from 272 cDNA clones, some from breast carcinoma (seen 27 times), thymus (14), leukopheresis (8), lung (8), germinal center B cell (7), bone marrow (5), pancreas (5) and 52 other tissues. We annotate structural defects or features in 4 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 6 distinct gt-ag introns. Transcription produces 8 different mRNAs, 7 alternatively spliced variants and 1 unspliced form. There are 2 probable alternative promotors, 2 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 2 cassette exons, overlapping exons with different boundaries, splicing versus retention of 3 introns.
Note that mRNA .dAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Function: There are 46 articles specifically referring to this gene in PubMed. Proteins are expected to have molecular functions (binding, calcium ion binding, sugar binding) and to localize in various compartments (endoplasmic reticulum membrane, external side of plasma membrane). A putative protein interactor has been described (CD69).
Protein coding potential: 7 spliced mRNAs putatively encode good proteins, altogether 6 different isoforms (6 complete), some containing Lectin C-type domain [Pfam], some transmembrane domains [Psort2]. The remaining mRNA variant (unspliced) appears not to encode a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 12, links to other databases and other names
Map: This gene CD69 maps on chromosome 12, at 12p13 according to Entrez Gene. In AceView, it covers 8.42 kb, from 9913505 to 9905082 (NCBI 37, August 2010), on the reverse strand.
Links to: the SNP view, gene overviews from Entrez Gene 969, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as CD69 or CLEC2C, LOC969. It has been described as early activation antigen CD69, AIM, EA1, MLR-3, GP32/28, BL-AC/P26, leukocyte surface antigen Leu-23, early T-cell activation antigen p60, early lymphocyte activation antigen, C-type lectin domain family 2 member C, activation inducer molecule (AIM/CD69), C-type lectin domain family 2, member C, CD69 antigen (p60, early T-cell activation antigen).
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Cd69 (e=3 10-34).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes clec-266 (e=4 10-04), clec-78 (e=8 10-04), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene AT1G52310andAT1G52315 (e=0.36), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
CD69 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 6.65 1.26 0.21 0.96 0.16 4.39 24.8 5.40 2.90 0.96 0.68 0.42 0.89 1.66 21.6 20.2 0.10 1.66 1.66 9.41 3.33 14.3 2.19 12.4 5.04 9.41 0.68 4.71 0.72 0.68 0.48 2.05 0.11 1.91 0.12 0.42 0.32 21.6 9.41 6.65 0.17 1.55 0.39 0.12 5.04 1.35 2.19 0.09 0.39 17.6 0.10 0.21 7.13 0.08 1.35 0.14 21.6 0.96 1.45 0.16 21.6 20.2 35.1 5.40 4.10 0.12 7.64 0.55 0.24 21.6 14.3 2.52 40.3 6.21 0.16 0.72 0.13 0.45 5.04 0.11 0.45 0.45 11.6 30.6 0.89 11.6 20.2 0.29 3.10 0.78 0.17 0.11 2.70 0.22 14.3 0.83 2.05 6.65 2.05 24.8 0.42 0.68 0.26 3.33 9.41 3.10 0.16 23.2 0.32 0.14 0.12 0.13 0.15 0.15 8.19 1.02 15.3 0.17 4.39 15.3 0.59 5.40 2.35 0.13 0.32 1.26 0.83 11.6 0.26 12.4 24.8 0.29 0.48 17.6 5.79 3.57 4.10 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 CD69 5' 3' encoded on minus strand of chromosome 12 from 9,913,505 to 9,905,082 16594 18980 18779 17998 a [NM] 16594 18980 18779 b h-u 41 c 16594 18980 67 17998 d 16594 18980 e 16594 18980 f 16594 g 1kb 0 144 bp exon 144 bp exon 4337 bp [gt-ag] intron 174 GenBank accessions 16420 RNA-seq supporting reads 7222 UHR pooled cells 102 Brain 3375 Blood 5651 Neuroblastoma 70 Other (also 3071 Primates bodymap) 123 bp exon 1035 bp [gt-ag] intron 171 GenBank accessions 18809 RNA-seq supporting reads 8815 UHR pooled cells 118 Brain 2792 Blood 7010 Neuroblastoma 74 Other (also 3023 Primates bodymap) 200 bp exon 371 bp [gt-ag] intron 145 GenBank accessions 18634 RNA-seq supporting reads 8669 UHR pooled cells 114 Brain 3058 Blood 6710 Neuroblastoma 83 Other (also 3307 Primates bodymap) 104 bp exon 997 bp [gt-ag] intron 120 GenBank accessions 17878 RNA-seq supporting reads 8598 UHR pooled cells 143 Brain 2827 Blood 6255 Neuroblastoma 55 Other (also 2379 Primates bodymap) 1104 bp exon 229 accessions, NM_001781.2 some from breast carcinoma (seen 20 times) lung (8), germinal center B cell (6) leukopheresis (6), bone marrow (5) capped 5' end, 5 accessions Validated 3' end, 13 accessions 1104 bp exon 144 bp exon 144 bp exon 4337 bp [gt-ag] intron 174 GenBank accessions 16420 RNA-seq supporting reads 7222 UHR pooled cells 102 Brain 3375 Blood 5651 Neuroblastoma 70 Other (also 3071 Primates bodymap) 123 bp exon 1035 bp [gt-ag] intron 171 GenBank accessions 18809 RNA-seq supporting reads 8815 UHR pooled cells 118 Brain 2792 Blood 7010 Neuroblastoma 74 Other (also 3023 Primates bodymap) 200 bp exon 371 bp [gt-ag] intron 145 GenBank accessions 18634 RNA-seq supporting reads 8669 UHR pooled cells 114 Brain 3058 Blood 6710 Neuroblastoma 83 Other (also 3307 Primates bodymap) 2201 bp exon 8 accessions, some from breast carcinoma (seen 2 times) leukopheresis (once) spleen (once), thalamus (once) thymus (once) Validated 3' end, 1 accession Validated 3' end, 1 accession 2201 bp exon 752 bp exon 752 bp exon 1 accession from placenta from pre-eclamptic placenta 752 bp exon 481 bp exon 481 bp exon 45 bp uORF 481 bp exon 481 bp exon 1472 bp [gt-ag] intron 1 GenBank accession 40 RNA-seq supporting reads 34 UHR pooled cells 6 Neuroblastoma (also 2 Primates bodymap) 393 bp exon 393 bp exon 2 accessions, some from kidney (seen once) 393 bp exon 144 bp exon 144 bp exon 4337 bp [gt-ag] intron 174 GenBank accessions 16420 RNA-seq supporting reads 7222 UHR pooled cells 102 Brain 3375 Blood 5651 Neuroblastoma 70 Other (also 3071 Primates bodymap) 123 bp exon 1035 bp [gt-ag] intron 171 GenBank accessions 18809 RNA-seq supporting reads 8815 UHR pooled cells 118 Brain 2792 Blood 7010 Neuroblastoma 74 Other (also 3023 Primates bodymap) 200 bp exon 393 bp [gt-ag] intron 1 GenBank accession 66 RNA-seq supporting reads 29 UHR pooled cells 14 Blood 23 Neuroblastoma (also 47 Primates bodymap) 82 bp exon 82 bp exon 997 bp [gt-ag] intron 120 GenBank accessions 17878 RNA-seq supporting reads 8598 UHR pooled cells 143 Brain 2827 Blood 6255 Neuroblastoma 55 Other (also 2379 Primates bodymap) 1 accession 113 bp exon 144 bp exon 144 bp exon 4337 bp [gt-ag] intron 174 GenBank accessions 16420 RNA-seq supporting reads 7222 UHR pooled cells 102 Brain 3375 Blood 5651 Neuroblastoma 70 Other (also 3071 Primates bodymap) 123 bp exon 1035 bp [gt-ag] intron 171 GenBank accessions 18809 RNA-seq supporting reads 8815 UHR pooled cells 118 Brain 2792 Blood 7010 Neuroblastoma 74 Other (also 3023 Primates bodymap) 283 bp exon 283 bp exon Sequence gap 1955 bp 2 accessions, some from germinal center B cell (seen once) neuroblastoma (once) 538 bp exon 144 bp exon 144 bp exon 4337 bp [gt-ag] intron 174 GenBank accessions 16420 RNA-seq supporting reads 7222 UHR pooled cells 102 Brain 3375 Blood 5651 Neuroblastoma 70 Other (also 3071 Primates bodymap) 123 bp exon 1035 bp [gt-ag] intron 171 GenBank accessions 18809 RNA-seq supporting reads 8815 UHR pooled cells 118 Brain 2792 Blood 7010 Neuroblastoma 74 Other (also 3023 Primates bodymap) 694 bp exon 22 accessions, some from thymus (seen 9 times) breast carcinoma (5) leukopheresis (once) pooled pancreas and spleen (once) pooled-skin (once) 694 bp exon 144 bp exon 144 bp exon 4337 bp [gt-ag] intron 174 GenBank accessions 16420 RNA-seq supporting reads 7222 UHR pooled cells 102 Brain 3375 Blood 5651 Neuroblastoma 70 Other (also 3071 Primates bodymap) 754 bp exon 6 accessions, some from thymus (seen 3 times) trachea (once), uterus (once) capped 5' end, 5 accessions 754 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 uORF Upstream sequence Transcription
unit
pre-mRNA		 Downstream sequence
aAug10 1675 bp 199 aa 80 bp 995 bp 2kb including Promoter 8415 bp 1kb
bAug10 2668 bp 164 aa 80 bp 2093 bp 2kb probably including promoter 8411 bp 1kb
cAug10 874 bp 139 aa 82 bp 372 bp 42 bp 2kb possibly including promoter 2346 bp 1kb
dAug10 662 bp 137 aa 80 bp 168 bp 2kb probably including promoter 7424 bp 1kb
eAug10 1859 bp 135 aa 80 bp 1371 bp 2kb probably including promoter 8415 bp 1kb
fAug10 961 bp 135 aa 80 bp 473 bp 2kb probably including promoter 6333 bp 1kb
gAug10 898 bp 88 aa 80 bp 551 bp 2kb including Promoter 5235 bp 1kb
hAug10-unspliced 752 bp 55 aa 89 bp 495 bp 2kb probably including promoter 752 bp 1kb

Gene neighbors and Navigator on chromosome 12p13 back to top
G C R R R R R OVOS C R P C CLEC2DandNPM1P16andNPM1P7 D C I R P KLRF1 C R P R KLRF2 C P CLEC12A C R P R CLEC12B C R P CLEC9A C R P C12orf59 C R GABARAPL1 D C I R P GOT2P3 C G R C R P DDX12 D C I R P KLRB1 R D C R P CLECL1 D C I R P CD69 C R P CLEC2B C R P CLEC2A C C R C I R P CLEC1B R C R P CLEC1A D C R P CLEC7A D C I R P OLR1 R 100kb 0 LOC642846, 113 accessions 20 variants seyfy, 3 accessions, 2 variants shychar, 12 accessions 3 variants tofy, 4 accessions, 2 variants foster, 7 accessions, 4 variants OVOS, 55 accessions, 9 variants kleysho, 1 accession CLEC2DandNPM1P16andNPM1P7 425 accessions, 46 variants KLRF1, 16 accessions, 9 variants vuner, 2 accessions KLRF2, 2 accessions CLEC12A, 72 accessions 11 variants shyzeeby, 1 accession CLEC12B, 43 accessions 9 variants CLEC9A, 17 accessions 3 variants C12orf59, 66 accessions 7 variants GABARAPL1, 392 accessions 15 variants KLRD1, 39 accessions, 10 variants cheychar, 1 accession chorchar, 3 accessions retare, 1 accession pawstey, 4 accessions smyforby, 1 accession bleychu, 3 accessions snerzoyby, 1 accession glarblabu, 2 accessions fochaby, 1 accession vustey, 5 accessions shachar, 3 accessions swoyzoyby, 2 accessions barchaby, 1 accession sorfy, 3 accessions smeyforby, 1 accession yuhemi, 1 accession glorblabu, 1 accession smorforby, 1 accession smoyforby, 1 accession yohemi, 1 accession klyblabu, 1 accession swazoyby, 2 accessions speezoyby, 1 accession klosho, 1 accession spyforby, 1 accession spuforby, 1 accession mahemi, 2 accessions, 2 variants klawblabu, 1 accession sparforby, 1 accession klerblabu, 1 accession speeforby, 1 accession sperforby, 1 accession jachaby, 4 accessions speyforby, 2 accessions verstey, 3 accessions mitare, 1 accession GOT2P3, 2 accessions plablabu, 3 accessions plasho, 1 accession plyblabu, 2 accessions plawsho, 1 accession ploblabu, 1 accession plarblabu, 1 accession plawblabu, 3 accessions plorblabu, 1 accession styforby, 1 accession smoysho, 1 accession kohire, 2 accessions, 2 variants skablabu, 1 accession skyblabu, 1 accession skarblabu, 2 accessions snosho, 1 accession steyforby, 1 accession flarchu, 1 accession storforby, 1 accession lychaby, 1 accession slyblabu, 3 accessions mutare, 1 accession larchaby, 5 accessions loychaby, 1 accession mochaby, 1 accession swuforby, 1 accession snawsho, 2 accessions slawblabu, 1 accession sarchaby, 3 accessions smarstey, 1 accession sweyforby, 1 accession bafoyby, 1 accession spoysho, 1 accession bufoyby, 1 accession slorblabu, 1 accession woychaby, 1 accession bawfoyby, 1 accession smyblabu, 2 accessions berfoyby, 1 accession beyfoyby, 1 accession dafoyby, 1 accession dyfoyby, 2 accessions dufoyby, 4 accessions darfoyby, 1 accession smoblabu, 1 accession glosho, 1 accession fawchaby, 2 accessions snerforby, 1 accession swarzoyby, 1 accession smawforby, 1 accession baforby, 3 accessions sihimi, 4 accessions, 3 variants smeeforby, 4 accessions smerforby, 3 accessions rornar, 1 accession glerblabu, 1 accession roynar, 2 accessions yatare, 3 accessions tyfy, 2 accessions gleesho, 1 accession gloyblabu, 1 accession sanar, 2 accessions snaforby, 1 accession klablabu, 1 accession snuforby, 1 accession dawchaby, 1 accession gloysho, 6 accessions deechaby, 1 accession smuforby, 1 accession kloblabu, 3 accessions sneyforby, 1 accession klarblabu, 2 accessions snoyforby, 1 accession pushuby, 1 accession chargoby, 2 accessions spawforby, 1 accession sporforby, 1 accession pleeblabu, 1 accession plorsho, 1 accession jeychaby, 1 accession cheystey, 4 accessions stoforby, 1 accession fluchu, 13 accessions skublabu, 2 accessions skoblabu, 1 accession flochu, 1 accession fleystey, 1 accession klustey, 1 accession skerblabu, 1 accession flawchu, 6 accessions lachaby, 1 accession slablabu, 1 accession swyforby, 1 accession porchaby, 1 accession swawforby, 11 accessions 2 variants swerforby, 2 accessions swoyforby, 1 accession sleyblabu, 1 accession seychaby, 1 accession flerchu, 4 accessions vuchaby, 1 accession beefoyby, 1 accession smablabu, 1 accession charchaby, 2 accessions smublabu, 1 accession borfoyby, 2 accessions florchu, 3 accessions swersho, 1 accession sharchaby, 1 accession gleechaby, 1 accession pleechaby, 1 accession deefoyby, 1 accession A2MP1, 10 accessions, 3 variants spysha, 3 accessions LOC100287838, 85 accessions 15 variants DDX12, 109 accessions 15 variants KLRB1, 36 accessions tawner, 12 accessions 2 variants CLECL1, 29 accessions 4 variants CD69, 275 accessions, 8 variants CLEC2B, 192 accessions 10 variants CLEC2A, 14 accessions 3 variants swoforby, 3 accessions spasho, 1 accession suhimi, 2 accessions CLEC1B, 22 accessions 4 variants fleychu, 2 accessions CLEC1A, 89 accessions 8 variants CLEC7A, 147 accessions 18 variants OLR1, 256 accessions, 14 variants veener, 1 accession ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               46 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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 compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

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