Homo sapiens complex locus ACAN, encoding aggrecan.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
SUMMARY back to top
RefSeq summary
[ACAN] This gene is a member of the aggrecan/versican proteoglycan family. The encoded protein is an integral part of the extracellular matrix in cartilagenous tissue and it withstands compression in cartilage. Mutations in this gene may be involved in skeletal dysplasia and spinal degeneration. Multiple alternatively spliced transcript variants that encode different protein isoforms have been observed in this gene. [provided by RefSeq].

RefSeq annotates 2 representative transcripts (NM included in AceView variants .a and .b), 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 10 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, 2.8 times the average gene in this release. The sequence of this gene is defined by 309 GenBank accessions from 260 cDNA clones, some from cartilage (seen 69 times), knee (47), osteoarthritic cartilage (47), left pelvis (32), chondrosarcoma (22), bone (12), chondrosarcoma grade II (10) and 36 other tissues. We annotate structural defects or features in 15 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 25 distinct gt-ag introns. Transcription produces 14 different mRNAs, 10 alternatively spliced variants and 4 unspliced forms. There are 3 probable alternative promotors, 2 non overlapping alternative last exons and 10 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 4 cassette exons, overlapping exons with different boundaries.
Function: There are 69 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: Osteochondritis dissecans, short stature, and early-onset osteoarthritis; Spondyloepimetaphyseal dysplasia, aggrecan type; Spondyloepiphyseal dysplasia, Kimberley type; Other sources: Disease Models, Animal; Genetic Predisposition to Disease; Inflammation; Osteoarthritis; Osteochondritis Dissecans; Osteochondrodysplasias; Progeria; Scoliosis; Spinal Diseases) and proposed to participate in processes (proteolysis, skeletal system development, cell adhesion). Proteins are expected to have molecular functions (extracellular matrix structural constituent, protein binding, hyaluronic acid binding, sugar binding) and to localize in various compartments (extracellular space, mitochondrion, nucleus, extracellular matrix, extracellular region, proteinaceous extracellular matrix). Putative protein interactors have been described (ADAMTS1, ADAMTS4, ADAMTS5, CTSB, FBLN1, FBLN2, HAPLN1, LUM, MMP1, MMP2, MMP3, MMP8, MMP14, MMP19, MMP20, TNFAIP6, TNR, VCAN).
Protein coding potential: 10 spliced and the unspliced mRNAs putatively encode good proteins, altogether 11 different isoforms (5 complete, 2 COOH complete, 4 partial), some containing domains EGF-like domain, EGF-like domain, Lectin C-type domain, sushi domain (SCR repeat), Immunoglobulin V-set domain, Extracellular link domain [Pfam]; 3 of the 5 complete proteins appear to be secreted. The remaining 3 mRNA variants (3 unspliced; 3 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by phosphorylation, as detailed at PhosphoSite.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 15, links to other databases and other names
Map: This gene ACAN maps on chromosome 15, at 15q26.1 according to Entrez Gene. In AceView, it covers 71.92 kb, from 89346675 to 89418593 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from OMIM_165800, OMIM_608361, OMIM_612813, PhosphoSite, the SNP view, gene overviews from Entrez Gene 176, GeneCards, expression data from ECgene, UniGene Hs.2159, Hs.616395, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as ACAN, AGC1, SEDK, AGCAN, CSPG1, MSK16 or CSPGCP, LOC176. It has been described as aggrecan core protein, large aggregating proteoglycan, cartilage-specific proteoglycan core protein, chondroitin sulfate proteoglycan core protein 1.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Acan (e=0.0).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes clec-178 (e=2 10-12), clec-50 (e=3 10-12), which may contain interesting functional annotation.
The closest A.thaliana gene, according to BlastP, is the AceView gene AT1G52310andAT1G52315 (e=0.005), 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
ACAN 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 0.34 0.89 0.72 0.22 7.64 5.40 3.10 0.59 1.45 4.71 0.34 0.21 0.06 0.10 0.07 0.08 0.09 0.51 0.06 0.05 0.07 0.06 0.06 0.42 0.55 0.06 0.36 0.21 0.14 1.91 0.16 0.45 0.96 0.18 0.05 0.07 0.13 0.18 0.59 0.42 0.08 0.08 0.04 0.04 0.10 0.34 0.04 0.06 0.68 0.08 0.04 0.06 0.42 0.39 0.05 0.36 0.55 0.14 0.11 0.04 0.05 0.06 0.09 0.07 0.07 1.10 0.09 0.07 0.07 0.13 7.13 0.12 0.11 0.24 0.39 0.06 0.10 0.06 0.14 0.04 0.10 0.21 0.09 0.15 0.07 0.48 0.13 0.39 0.04 0.32 0.10 0.51 0.06 0.34 0.06 0.21 0.78 0.39 0.10 0.05 0.07 0.27 0.05 0.14 0.07 0.04 0.29 0.16 1.35 0.27 0.42 0.39 4.39 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!.
Read more...
          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 ACAN 5' 3' encoded on plus strand of chromosome 15 from 89,346,675 to 89,418,593 902 1281 1499 1661 1562 1722 1494 1569 1428 1664 2050 1080 891 6766 7964 4261 6861 a [NM] 902 1281 1499 1661 1562 1722 1494 1569 1428 1664 2050 3439 6766 7964 312 b [NM] 902 1281 1499 1661 1562 1722 1494 1569 1428 c 3439 6766 7964 4261 6861 d 4 1661 1562 1722 e i-u 4261 227 h 1 1661 1562 g 1080 294 1523 6766 7964 f m-u 6861 j 813 1523 k n-u l-u 5kb 0 366 bp exon 32390 bp [gt-ag] intron 12 GenBank accessions 890 RNA-seq supporting reads 14 UHR pooled cells 64 Brain 802 Neuroblastoma 10 Other (also 59 Primates bodymap) 77 bp exon 77 bp exon 2386 bp [gt-ag] intron 11 GenBank accessions 1270 RNA-seq supporting reads 20 UHR pooled cells 102 Brain 1 Blood 1132 Neuroblastoma 15 Other (also 55 Primates bodymap) 384 bp exon 965 bp [gt-ag] intron 7 GenBank accessions 1492 RNA-seq supporting reads 22 UHR pooled cells 112 Brain 2 Blood 1350 Neuroblastoma 6 Other (also 82 Primates bodymap) 175 bp exon 1553 bp [gt-ag] intron 11 GenBank accessions 1650 RNA-seq supporting reads 21 UHR pooled cells 120 Brain 1 Blood 1494 Neuroblastoma 14 Other (also 149 Primates bodymap) 128 bp exon 1487 bp [gt-ag] intron 11 GenBank accessions 1551 RNA-seq supporting reads 12 UHR pooled cells 89 Brain 1439 Neuroblastoma 11 Other (also 120 Primates bodymap) 294 bp exon 1856 bp [gt-ag] intron 12 GenBank accessions 1710 RNA-seq supporting reads 21 UHR pooled cells 128 Brain 1551 Neuroblastoma 10 Other (also 138 Primates bodymap) 378 bp exon 1360 bp [gt-ag] intron 15 GenBank accessions 1479 RNA-seq supporting reads 23 UHR pooled cells 113 Brain 1 Blood 1335 Neuroblastoma 7 Other (also 81 Primates bodymap) 175 bp exon 493 bp [gt-ag] intron 18 GenBank accessions 1551 RNA-seq supporting reads 25 UHR pooled cells 132 Brain 1 Blood 1387 Neuroblastoma 6 Other (also 157 Primates bodymap) 128 bp exon 1399 bp [gt-ag] intron 18 GenBank accessions 1410 RNA-seq supporting reads 17 UHR pooled cells 128 Brain 1 Blood 1257 Neuroblastoma 7 Other (also 81 Primates bodymap) 294 bp exon 2062 bp [gt-ag] intron 16 GenBank accessions 1648 RNA-seq supporting reads 16 UHR pooled cells 143 Brain 1480 Neuroblastoma 9 Other (also 55 Primates bodymap) 240 bp exon 2818 bp [gt-ag] intron 13 GenBank accessions 2037 RNA-seq supporting reads 32 UHR pooled cells 147 Brain 3 Blood 1841 Neuroblastoma 14 Other (also 182 Primates bodymap) 4566 bp exon 908 bp [gt-ag] intron 13 GenBank accessions 1067 RNA-seq supporting reads 9 UHR pooled cells 47 Brain 1010 Neuroblastoma 1 Other (also 33 Primates bodymap) 114 bp exon 10942 bp [gt-ag] intron 11 GenBank accessions 880 RNA-seq supporting reads 13 UHR pooled cells 26 Brain 838 Neuroblastoma 3 Other (also 39 Primates bodymap) 159 bp exon 462 bp [gt-ag] intron 57 GenBank accessions 6709 RNA-seq supporting reads 91 UHR pooled cells 452 Brain 6115 Neuroblastoma 51 Other (also 176 Primates bodymap) 83 bp exon 795 bp [gt-ag] intron 67 GenBank accessions 7897 RNA-seq supporting reads 108 UHR pooled cells 536 Brain 7191 Neuroblastoma 62 Other (also 189 Primates bodymap) 145 bp exon 816 bp [gt-ag] intron 92 GenBank accessions 4169 RNA-seq supporting reads 59 UHR pooled cells 295 Brain 3795 Neuroblastoma 20 Other (also 124 Primates bodymap) 183 bp exon 380 bp [gt-ag] intron 108 GenBank accessions 6753 RNA-seq supporting reads 96 UHR pooled cells 480 Brain 6149 Neuroblastoma 28 Other (also 128 Primates bodymap) 953 bp exon 248 accessions, NM_013227.3 some from cartilage (seen 50 times) knee (45), osteoarthritic cartilage (45) left pelvis (29), chondrosarcoma (19) Validated 3' end, 15 accessions Validated 3' end, 5 accessions Validated 3' end, 36 accessions Validated 3' end, 31 accessions 953 bp exon 366 bp exon 32390 bp [gt-ag] intron 12 GenBank accessions 890 RNA-seq supporting reads 14 UHR pooled cells 64 Brain 802 Neuroblastoma 10 Other (also 59 Primates bodymap) 77 bp exon 77 bp exon 2386 bp [gt-ag] intron 11 GenBank accessions 1270 RNA-seq supporting reads 20 UHR pooled cells 102 Brain 1 Blood 1132 Neuroblastoma 15 Other (also 55 Primates bodymap) 384 bp exon 965 bp [gt-ag] intron 7 GenBank accessions 1492 RNA-seq supporting reads 22 UHR pooled cells 112 Brain 2 Blood 1350 Neuroblastoma 6 Other (also 82 Primates bodymap) 175 bp exon 1553 bp [gt-ag] intron 11 GenBank accessions 1650 RNA-seq supporting reads 21 UHR pooled cells 120 Brain 1 Blood 1494 Neuroblastoma 14 Other (also 149 Primates bodymap) 128 bp exon 1487 bp [gt-ag] intron 11 GenBank accessions 1551 RNA-seq supporting reads 12 UHR pooled cells 89 Brain 1439 Neuroblastoma 11 Other (also 120 Primates bodymap) 294 bp exon 1856 bp [gt-ag] intron 12 GenBank accessions 1710 RNA-seq supporting reads 21 UHR pooled cells 128 Brain 1551 Neuroblastoma 10 Other (also 138 Primates bodymap) 378 bp exon 1360 bp [gt-ag] intron 15 GenBank accessions 1479 RNA-seq supporting reads 23 UHR pooled cells 113 Brain 1 Blood 1335 Neuroblastoma 7 Other (also 81 Primates bodymap) 175 bp exon 493 bp [gt-ag] intron 18 GenBank accessions 1551 RNA-seq supporting reads 25 UHR pooled cells 132 Brain 1 Blood 1387 Neuroblastoma 6 Other (also 157 Primates bodymap) 128 bp exon 1399 bp [gt-ag] intron 18 GenBank accessions 1410 RNA-seq supporting reads 17 UHR pooled cells 128 Brain 1 Blood 1257 Neuroblastoma 7 Other (also 81 Primates bodymap) 294 bp exon 2062 bp [gt-ag] intron 16 GenBank accessions 1648 RNA-seq supporting reads 16 UHR pooled cells 143 Brain 1480 Neuroblastoma 9 Other (also 55 Primates bodymap) 240 bp exon 2818 bp [gt-ag] intron 13 GenBank accessions 2037 RNA-seq supporting reads 32 UHR pooled cells 147 Brain 3 Blood 1841 Neuroblastoma 14 Other (also 182 Primates bodymap) 4566 bp exon 11964 bp [gt-ag] intron 19 GenBank accessions 3420 RNA-seq supporting reads 64 UHR pooled cells 189 Brain 3149 Neuroblastoma 18 Other (also 42 Primates bodymap) 159 bp exon 462 bp [gt-ag] intron 57 GenBank accessions 6709 RNA-seq supporting reads 91 UHR pooled cells 452 Brain 6115 Neuroblastoma 51 Other (also 176 Primates bodymap) 83 bp exon 795 bp [gt-ag] intron 67 GenBank accessions 7897 RNA-seq supporting reads 108 UHR pooled cells 536 Brain 7191 Neuroblastoma 62 Other (also 189 Primates bodymap) 145 bp exon 1379 bp [gt-ag] intron 3 GenBank accessions 309 RNA-seq supporting reads 2 UHR pooled cells 10 Brain 296 Neuroblastoma 1 Other 950 bp exon 7 accessions, NM_001135.3 some from cartilage (seen 5 times) chondrosarcoma (once) left pelvis (once) 950 bp exon 366 bp exon 32390 bp [gt-ag] intron 12 GenBank accessions 890 RNA-seq supporting reads 14 UHR pooled cells 64 Brain 802 Neuroblastoma 10 Other (also 59 Primates bodymap) 77 bp exon 77 bp exon 2386 bp [gt-ag] intron 11 GenBank accessions 1270 RNA-seq supporting reads 20 UHR pooled cells 102 Brain 1 Blood 1132 Neuroblastoma 15 Other (also 55 Primates bodymap) 384 bp exon 965 bp [gt-ag] intron 7 GenBank accessions 1492 RNA-seq supporting reads 22 UHR pooled cells 112 Brain 2 Blood 1350 Neuroblastoma 6 Other (also 82 Primates bodymap) 175 bp exon 1553 bp [gt-ag] intron 11 GenBank accessions 1650 RNA-seq supporting reads 21 UHR pooled cells 120 Brain 1 Blood 1494 Neuroblastoma 14 Other (also 149 Primates bodymap) 128 bp exon 1487 bp [gt-ag] intron 11 GenBank accessions 1551 RNA-seq supporting reads 12 UHR pooled cells 89 Brain 1439 Neuroblastoma 11 Other (also 120 Primates bodymap) 294 bp exon 1856 bp [gt-ag] intron 12 GenBank accessions 1710 RNA-seq supporting reads 21 UHR pooled cells 128 Brain 1551 Neuroblastoma 10 Other (also 138 Primates bodymap) 378 bp exon 1360 bp [gt-ag] intron 15 GenBank accessions 1479 RNA-seq supporting reads 23 UHR pooled cells 113 Brain 1 Blood 1335 Neuroblastoma 7 Other (also 81 Primates bodymap) 175 bp exon 493 bp [gt-ag] intron 18 GenBank accessions 1551 RNA-seq supporting reads 25 UHR pooled cells 132 Brain 1 Blood 1387 Neuroblastoma 6 Other (also 157 Primates bodymap) 128 bp exon 1399 bp [gt-ag] intron 18 GenBank accessions 1410 RNA-seq supporting reads 17 UHR pooled cells 128 Brain 1 Blood 1257 Neuroblastoma 7 Other (also 81 Primates bodymap) 2086 bp exon 3 accessions, some from testis (seen once) capped 5' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 1 accession 2086 bp exon 1156 bp exon 11964 bp [gt-ag] intron 19 GenBank accessions 3420 RNA-seq supporting reads 64 UHR pooled cells 189 Brain 3149 Neuroblastoma 18 Other (also 42 Primates bodymap) 159 bp exon 462 bp [gt-ag] intron 57 GenBank accessions 6709 RNA-seq supporting reads 91 UHR pooled cells 452 Brain 6115 Neuroblastoma 51 Other (also 176 Primates bodymap) 83 bp exon 795 bp [gt-ag] intron 67 GenBank accessions 7897 RNA-seq supporting reads 108 UHR pooled cells 536 Brain 7191 Neuroblastoma 62 Other (also 189 Primates bodymap) 145 bp exon 816 bp [gt-ag] intron 92 GenBank accessions 4169 RNA-seq supporting reads 59 UHR pooled cells 295 Brain 3795 Neuroblastoma 20 Other (also 124 Primates bodymap) 183 bp exon 380 bp [gt-ag] intron 108 GenBank accessions 6753 RNA-seq supporting reads 96 UHR pooled cells 480 Brain 6149 Neuroblastoma 28 Other (also 128 Primates bodymap) 436 bp exon 12 accessions, some from cartilage (seen 4 times) brain (2), anaplastic oligodendroglioma with 1p/19qloss (once) total brain (once) Validated 3' end, 2 accessions Validated 3' end, 1 accession 436 bp exon 60 bp exon 60 bp exon 491 bp [gt-ag] intron 4 GenBank accessions 175 bp exon 1553 bp [gt-ag] intron 11 GenBank accessions 1650 RNA-seq supporting reads 21 UHR pooled cells 120 Brain 1 Blood 1494 Neuroblastoma 14 Other (also 149 Primates bodymap) 128 bp exon 1487 bp [gt-ag] intron 11 GenBank accessions 1551 RNA-seq supporting reads 12 UHR pooled cells 89 Brain 1439 Neuroblastoma 11 Other (also 120 Primates bodymap) 294 bp exon 1856 bp [gt-ag] intron 12 GenBank accessions 1710 RNA-seq supporting reads 21 UHR pooled cells 128 Brain 1551 Neuroblastoma 10 Other (also 138 Primates bodymap) 199 bp exon 4 accessions, some from melanotic melanoma high MDR (cell line) (seen 4 times) skin (4) 199 bp exon 891 bp exon 891 bp exon 8 accessions, some from cartilage (seen 4 times) colon (once), embryo (once) capped 5' end, 1 accession 891 bp exon 57 bp exon 57 bp exon 816 bp [gt-ag] intron 92 GenBank accessions 4169 RNA-seq supporting reads 59 UHR pooled cells 295 Brain 3795 Neuroblastoma 20 Other (also 124 Primates bodymap) 218 bp exon 345 bp [gt-ag] intron 2 GenBank accessions 225 RNA-seq supporting reads 3 UHR pooled cells 6 Brain 215 Neuroblastoma 1 Other 436 bp exon 2 accessions, some from knee (seen 2 times) osteoarthritic cartilage (2) Validated 3' end, 2 accessions 436 bp exon 58 bp exon 484 bp [gt-ag] intron 1 GenBank accession 175 bp exon 1553 bp [gt-ag] intron 11 GenBank accessions 1650 RNA-seq supporting reads 21 UHR pooled cells 120 Brain 1 Blood 1494 Neuroblastoma 14 Other (also 149 Primates bodymap) 128 bp exon 1487 bp [gt-ag] intron 11 GenBank accessions 1551 RNA-seq supporting reads 12 UHR pooled cells 89 Brain 1439 Neuroblastoma 11 Other (also 120 Primates bodymap) 289 bp exon 1 accession from melanotic melanoma high MDR (cell line) from skin 289 bp exon 273 bp exon 273 bp exon 908 bp [gt-ag] intron 13 GenBank accessions 1067 RNA-seq supporting reads 9 UHR pooled cells 47 Brain 1010 Neuroblastoma 1 Other (also 33 Primates bodymap) 114 bp exon 7776 bp [gt-ag] intron 2 GenBank accessions 292 RNA-seq supporting reads 6 UHR pooled cells 18 Brain 266 Neuroblastoma 2 Other 114 bp exon 3052 bp [gt-ag] intron 4 GenBank accessions 1519 RNA-seq supporting reads 42 UHR pooled cells 132 Brain 1 Blood 1336 Neuroblastoma 8 Other (also 35 Primates bodymap) 159 bp exon 462 bp [gt-ag] intron 57 GenBank accessions 6709 RNA-seq supporting reads 91 UHR pooled cells 452 Brain 6115 Neuroblastoma 51 Other (also 176 Primates bodymap) 83 bp exon 795 bp [gt-ag] intron 67 GenBank accessions 7897 RNA-seq supporting reads 108 UHR pooled cells 536 Brain 7191 Neuroblastoma 62 Other (also 189 Primates bodymap) 3 accessions, some from cartilage (seen 2 times) breast (once) 21 bp exon 499 bp exon 499 bp exon 1 accession 499 bp exon 526 bp exon 526 bp exon 123 bp uORF 526 bp exon 526 bp exon 380 bp [gt-ag] intron 108 GenBank accessions 6753 RNA-seq supporting reads 96 UHR pooled cells 480 Brain 6149 Neuroblastoma 28 Other (also 128 Primates bodymap) 436 bp exon 436 bp exon 2 accessions, some from chondrosarcoma (seen once) left pelvis (once) Validated 3' end, 2 accessions 436 bp exon 76 bp exon 8798 bp [gt-ag] intron 1 GenBank accession 812 RNA-seq supporting reads 23 UHR pooled cells 104 Brain 1 Blood 678 Neuroblastoma 6 Other (also 5 Primates bodymap) 114 bp exon 3052 bp [gt-ag] intron 4 GenBank accessions 1519 RNA-seq supporting reads 42 UHR pooled cells 132 Brain 1 Blood 1336 Neuroblastoma 8 Other (also 35 Primates bodymap) 118 bp exon 1 accession from cartilage 118 bp exon 328 bp exon 328 bp exon 1 accession from cartilage 328 bp exon 627 bp exon 627 bp exon 1 accession from cartilage 627 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.
Read more...
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 8842 bp 2530 aa 373 bp 876 bp 2kb possibly including promoter 71914 bp 1kb
bAug10 8542 bp 2431 aa 373 bp 873 bp 2kb possibly including promoter 71911 bp 1kb
cAug10 4191 bp 721 aa 373 bp 1652 bp 2kb including Promoter 48080 bp 1kb
dAug10 2162 bp 600 aa 359 bp 2kb 16579 bp 1kb
eAug10 856 bp 272 aa 38 bp 2kb possibly including promoter 6243 bp 1kb
fAug10 764 bp 254 aa 2kb 13757 bp 1kb
gAug10 650 bp 216 aa 2kb 4174 bp 1kb
hAug10 711 bp 155 aa 241 bp 2kb 1872 bp 1kb
iAug10-unspliced 891 bp 135 aa 312 bp 171 bp 2kb including Promoter 891 bp 1kb
jAug10 962 bp 115 aa 373 bp 241 bp 120 bp 2kb possibly including promoter 1342 bp 1kb
kAug10 308 bp 102 aa 2kb 12158 bp 1kb
lAug10-unspliced 627 bp 78 aa 391 bp 2kb 627 bp 1kb
mAug10-unspliced 499 bp 27 aa 413 bp 2kb 499 bp 1kb
nAug10-unspliced 328 bp 59 aa 147 bp 2kb 328 bp 1kb

Gene neighbors and Navigator on chromosome 15q26.1 back to top
MRPS11 C R P R R R MIR7-2 P AEN C R P ISG20 C R P C ACAN D C I R P ABHD2 C R P C FANCI D C I R P C I R P DET1andMRPL46 R R C R P HAPLN3 D C R P MFGE8 G R D C I R P RLBP1 100kb 0 MRPS11, 348 accessions 14 variants forsky, 1 accession keyswy, 3 accessions rapoy, 1 accession MIR7-2, 2 accessions AEN, 392 accessions, 7 variants ISG20, 160 accessions 19 variants mamoru, 2 accessions ACAN, 303 accessions, 14 variants ABHD2, 420 accessions 20 variants noswy, 3 accessions FANCI, 331 accessions 30 variants florchabu, 1 accession glachabu, 1 accession yumoru, 3 accessions jeyswy, 2 accessions kyswy, 4 accessions koswy, 3 accessions chartar, 1 accession glorree, 1 accession blutar, 1 accession koyswy, 1 accession poypoy, 2 accessions yomoru, 1 accession laswy, 1 accession glorchabu, 1 accession flartar, 1 accession luswy, 3 accessions leeswy, 1 accession lorswy, 2 accessions pleezaw, 3 accessions loyswy, 1 accession flawtar, 1 accession klerchabu, 1 accession mawswy, 1 accession swawkoby, 1 accession meyswy, 1 accession lersky, 3 accessions morswy, 1 accession sposorbo, 1 accession mimoru, 1 accession morsky, 73 accessions narswy, 1 accession nawswy, 1 accession neeswy, 1 accession neyswy, 1 accession noyswy, 2 accessions pluchabu, 3 accessions puswy, 1 accession farkarby, 1 accession parswy, 1 accession pawswy, 2 accessions peeswy, 1 accession perswy, 3 accessions porswy, 2 accessions poyswy, 1 accession ryswy, 1 accession geeder, 4 accessions rarswy, 1 accession nusky, 5 accessions gukarby, 1 accession rawswy, 1 accession gokarby, 1 accession jarkarby, 1 accession joykarby, 1 accession rerswy, 1 accession reyswy, 1 accession rorswy, 1 accession royswy, 3 accessions saswy, 1 accession soswy, 1 accession skarzaw, 3 accessions jerswy, 1 accession floychabu, 1 accession kuswy, 1 accession pluzaw, 6 accessions glychabu, 1 accession dasky, 17 accessions spysorbo, 3 accessions deysky, 4 accessions kawswy, 2 accessions keeswy, 1 accession feysky, 2 accessions glochabu, 1 accession glawchabu, 1 accession gleechabu, 1 accession glerchabu, 1 accession flytar, 1 accession gleychabu, 1 accession spusorbo, 1 accession speekoby, 1 accession larswy, 1 accession lawswy, 1 accession kluchabu, 1 accession klochabu, 1 accession klarchabu, 2 accessions lerswy, 1 accession kleechabu, 1 accession reroru, 1 accession leyswy, 1 accession maswy, 2 accessions stokoby, 1 accession flertar, 1 accession moswy, 1 accession swykoby, 1 accession klorchabu, 1 accession fleytar, 1 accession glutar, 1 accession plachabu, 1 accession merswy, 1 accession sweekoby, 1 accession deykarby, 1 accession doykarby, 1 accession skazaw, 3 accessions nerswy, 1 accession norswy, 1 accession paswy, 1 accession poswy, 1 accession peyswy, 1 accession raswy, 2 accessions ruswy, 1 accession roswy, 1 accession glotar, 1 accession glortar, 1 accession gorkarby, 1 accession reeswy, 1 accession plawchabu, 1 accession plartar, 1 accession pleytar, 1 accession syswy, 1 accession pleechabu, 1 accession sarswy, 1 accession plortar, 2 accessions DET1andMRPL46, 355 accessions 22 variants nikama, 4 accessions, 3 variants slerkoby, 7 accessions HAPLN3, 135 accessions 9 variants MFGE8, 457 accessions 12 variants LOC100129942, 3 accessions plorzaw, 4 accessions 2 variants RLBP1, 102 accessions 6 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               69 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i-u, .j, .k, .l-u, .m-u, .n-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'.

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