Homo sapiens complex locus TUBD1, encoding tubulin, delta 1.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), 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 17 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 well expressed, 1.3 times the average gene in this release. The sequence of this gene is defined by 161 GenBank accessions from 138 cDNA clones, some from pancreas (seen 15 times), insulinoma (13), testis (9), uterus (8), brain (7), eye (6), stomach (6) and 60 other tissues. We annotate structural defects or features in 14 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 22 distinct gt-ag introns. Transcription produces 18 different mRNAs, 17 alternatively spliced variants and 1 unspliced form. There are 3 probable alternative promotors, 3 non overlapping alternative last exons and 2 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 14 cassette exons, overlapping exons with different boundaries.
Note that mRNA .nAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant cAug10).
Function: There are 5 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in processes (cell differentiation, microtubule-based movement, multicellular organismal development, protein polymerization, spermatogenesis). Proteins are expected to have molecular functions (GTP binding, GTPase activity, nucleotide binding, structural molecule activity) and to localize in various compartments (cytoplasm, nucleus, centriole, cytoskeleton, microtubule).
Protein coding potential: 16 spliced mRNAs putatively encode good proteins, altogether 16 different isoforms (11 complete, 5 partial), some containing Tubulin/FtsZ family, GTPase domain [Pfam]. The remaining 2 mRNA variants (1 spliced, 1 unspliced; 1 partial) appear not to encode good proteins.

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 TUBD1 maps on chromosome 17, at 17q23.1 according to Entrez Gene. In AceView, it covers 33.46 kb, from 57970284 to 57936828 (NCBI 37, August 2010), on the reverse strand.
Links to: the SNP view, gene overviews from Entrez Gene 51174, 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 TUBD1, TUBD or FLJ12709, LOC51174. It has been described as tubulin delta chain, delta-tubulin.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Tubd1 (e=0.0).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes rot-2 (e=3 10-30), tbb-1 (e=10-29), ben-1 (e=2 10-29), tbb-4 (e=8 10-29), tbb-6 (e=2 10-26), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes ATGCP2\/TUBG2 (e=6 10-37), TUBG1 (e=2 10-36), 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
TUBD1 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 10.1 4.10 1.45 4.39 3.10 5.04 3.82 6.65 6.21 5.79 2.35 6.21 3.10 4.71 2.35 4.71 7.64 3.57 5.79 8.78 3.57 7.64 5.04 1.45 0.89 0.83 1.26 3.57 7.64 5.04 8.19 9.41 9.41 4.10 2.90 2.35 3.10 4.71 9.41 8.19 7.64 7.64 9.41 5.40 10.8 9.41 9.41 12.4 10.8 3.82 7.64 9.41 7.13 4.39 6.65 8.19 5.79 5.79 3.10 4.71 7.13 8.78 5.79 6.21 6.65 8.78 7.13 8.78 5.40 8.78 6.65 6.21 6.65 8.19 4.39 5.40 6.21 8.19 5.40 6.21 7.64 8.78 6.65 9.41 6.65 8.78 9.41 5.79 8.19 6.65 4.39 7.64 3.57 9.41 6.65 4.10 7.64 6.21 3.82 12.4 8.78 8.78 8.78 10.8 17.6 9.41 7.13 9.41 15.3 7.13 7.64 10.1 8.19 3.10 6.65 5.40 9.41 6.65 5.40 8.78 7.13 7.64 3.57 5.79 2.70 4.71 4.71 3.10 8.19 13.3 10.1 6.65 4.71 3.10 6.21 0.55 1.10 1.02 10.1 10.1 8.19 4.10 10.8 6.21 9.41 6.65 13.3 8.19 1.91 3.57 6.65 3.33 8.78 8.78 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 TUBD1 5' 3' encoded on minus strand of chromosome 17 from 57,970,284 to 57,936,828 7777 11615 11446 10315 11958 9382 14722 19798 a [NM] 7777 11615 11446 10315 3207 14722 19798 b 7777 11615 11446 10315 11958 9382 8 c 7 14 11615 11446 10315 919 19798 d 2153 2653 11958 9382 14722 19798 e 7777 11615 515 376 10315 3207 14722 19798 f r-u 10315 3207 14722 g 2153 11446 10315 11958 h 954 11958 9382 14722 19798 i 7777 18 14722 19798 j 954 3207 14722 19798 k 2 11958 9382 l 7777 11615 81 m 7777 11615 2653 11958 n 11958 o 2153 302 14722 p 2153 515 376 10315 q 1 2kb 0 227 bp exon 1655 bp [gt-ag] intron 50 GenBank accessions 7727 RNA-seq supporting reads 1733 UHR pooled cells 593 Brain 1479 Blood 3904 Neuroblastoma 18 Other (also 535 Primates bodymap) 211 bp exon 211 bp exon 4600 bp [gt-ag] intron 61 GenBank accessions 11554 RNA-seq supporting reads 2964 UHR pooled cells 702 Brain 1929 Blood 5905 Neuroblastoma 54 Other (also 4080 Primates bodymap) 148 bp exon 4972 bp [gt-ag] intron 43 GenBank accessions 11403 RNA-seq supporting reads 3691 UHR pooled cells 604 Brain 986 Blood 6089 Neuroblastoma 33 Other (also 3336 Primates bodymap) 217 bp exon 2559 bp [gt-ag] intron 32 GenBank accessions 10283 RNA-seq supporting reads 3144 UHR pooled cells 643 Brain 896 Blood 5555 Neuroblastoma 45 Other (also 2903 Primates bodymap) 232 bp exon 3399 bp [gt-ag] intron 20 GenBank accessions 11938 RNA-seq supporting reads 2406 UHR pooled cells 985 Brain 1397 Blood 7084 Neuroblastoma 66 Other (also 2588 Primates bodymap) 165 bp exon 7789 bp [gt-ag] intron 16 GenBank accessions 9366 RNA-seq supporting reads 2039 UHR pooled cells 808 Brain 666 Blood 5799 Neuroblastoma 54 Other (also 1988 Primates bodymap) 141 bp exon 2761 bp [gt-ag] intron 35 GenBank accessions 14687 RNA-seq supporting reads 3632 UHR pooled cells 1394 Brain 1245 Blood 8348 Neuroblastoma 68 Other (also 2655 Primates bodymap) 184 bp exon 3239 bp [gt-ag] intron 47 GenBank accessions 19751 RNA-seq supporting reads 5277 UHR pooled cells 1974 Brain 1502 Blood 10895 Neuroblastoma 103 Other (also 2347 Primates bodymap) 943 bp exon 69 accessions, NM_016261.2 some from brain (seen 6 times) testis (5), eye (4), uterus (4) pancreas (3) capped 5' end, 19 accessions 943 bp exon 224 bp exon 1655 bp [gt-ag] intron 50 GenBank accessions 7727 RNA-seq supporting reads 1733 UHR pooled cells 593 Brain 1479 Blood 3904 Neuroblastoma 18 Other (also 535 Primates bodymap) 211 bp exon 211 bp exon 4600 bp [gt-ag] intron 61 GenBank accessions 11554 RNA-seq supporting reads 2964 UHR pooled cells 702 Brain 1929 Blood 5905 Neuroblastoma 54 Other (also 4080 Primates bodymap) 148 bp exon 4972 bp [gt-ag] intron 43 GenBank accessions 11403 RNA-seq supporting reads 3691 UHR pooled cells 604 Brain 986 Blood 6089 Neuroblastoma 33 Other (also 3336 Primates bodymap) 217 bp exon 2559 bp [gt-ag] intron 32 GenBank accessions 10283 RNA-seq supporting reads 3144 UHR pooled cells 643 Brain 896 Blood 5555 Neuroblastoma 45 Other (also 2903 Primates bodymap) 232 bp exon 11353 bp [gt-ag] intron 10 GenBank accessions 3197 RNA-seq supporting reads 1068 UHR pooled cells 301 Brain 226 Blood 1586 Neuroblastoma 16 Other (also 132 Primates bodymap) 141 bp exon 2761 bp [gt-ag] intron 35 GenBank accessions 14687 RNA-seq supporting reads 3632 UHR pooled cells 1394 Brain 1245 Blood 8348 Neuroblastoma 68 Other (also 2655 Primates bodymap) 184 bp exon 3239 bp [gt-ag] intron 47 GenBank accessions 19751 RNA-seq supporting reads 5277 UHR pooled cells 1974 Brain 1502 Blood 10895 Neuroblastoma 103 Other (also 2347 Primates bodymap) 391 bp exon 7 accessions, some from eye retinoblastoma (seen once) 391 bp exon 162 bp exon 162 bp exon 42 bp uORF 162 bp exon 1655 bp [gt-ag] intron 50 GenBank accessions 7727 RNA-seq supporting reads 1733 UHR pooled cells 593 Brain 1479 Blood 3904 Neuroblastoma 18 Other (also 535 Primates bodymap) 211 bp exon 211 bp exon 211 bp exon 4600 bp [gt-ag] intron 61 GenBank accessions 11554 RNA-seq supporting reads 2964 UHR pooled cells 702 Brain 1929 Blood 5905 Neuroblastoma 54 Other (also 4080 Primates bodymap) 148 bp exon 148 bp exon 4972 bp [gt-ag] intron 43 GenBank accessions 11403 RNA-seq supporting reads 3691 UHR pooled cells 604 Brain 986 Blood 6089 Neuroblastoma 33 Other (also 3336 Primates bodymap) 217 bp exon 217 bp exon 2559 bp [gt-ag] intron 32 GenBank accessions 10283 RNA-seq supporting reads 3144 UHR pooled cells 643 Brain 896 Blood 5555 Neuroblastoma 45 Other (also 2903 Primates bodymap) 232 bp exon 232 bp exon 3399 bp [gt-ag] intron 20 GenBank accessions 11938 RNA-seq supporting reads 2406 UHR pooled cells 985 Brain 1397 Blood 7084 Neuroblastoma 66 Other (also 2588 Primates bodymap) 165 bp exon 165 bp exon 7789 bp [gt-ag] intron 16 GenBank accessions 9366 RNA-seq supporting reads 2039 UHR pooled cells 808 Brain 666 Blood 5799 Neuroblastoma 54 Other (also 1988 Primates bodymap) 154 bp exon 154 bp exon 6171 bp [gt-ag] intron 2 GenBank accessions 6 RNA-seq supporting reads 2 UHR pooled cells 1 Brain 3 Neuroblastoma (also 6 Primates bodymap) 391 bp exon 391 bp exon 2 accessions, some from mammary gland (seen 2 times) capped 5' end, 1 accession 391 bp exon 227 bp exon 736 bp [gt-ag] fuzzy intron 1 GenBank accession 6 RNA-seq supporting reads 4 UHR pooled cells 2 Blood 147 bp exon 147 bp exon 772 bp [gt-ag] intron 1 GenBank accession 13 RNA-seq supporting reads 5 UHR pooled cells 2 Blood 6 Neuroblastoma 211 bp exon 4600 bp [gt-ag] intron 61 GenBank accessions 11554 RNA-seq supporting reads 2964 UHR pooled cells 702 Brain 1929 Blood 5905 Neuroblastoma 54 Other (also 4080 Primates bodymap) 148 bp exon 4972 bp [gt-ag] intron 43 GenBank accessions 11403 RNA-seq supporting reads 3691 UHR pooled cells 604 Brain 986 Blood 6089 Neuroblastoma 33 Other (also 3336 Primates bodymap) 217 bp exon 2559 bp [gt-ag] intron 32 GenBank accessions 10283 RNA-seq supporting reads 3144 UHR pooled cells 643 Brain 896 Blood 5555 Neuroblastoma 45 Other (also 2903 Primates bodymap) 232 bp exon 14255 bp [gt-ag] intron 1 GenBank accession 918 RNA-seq supporting reads 200 UHR pooled cells 167 Brain 93 Blood 450 Neuroblastoma 8 Other (also 8 Primates bodymap) 184 bp exon 3239 bp [gt-ag] intron 47 GenBank accessions 19751 RNA-seq supporting reads 5277 UHR pooled cells 1974 Brain 1502 Blood 10895 Neuroblastoma 103 Other (also 2347 Primates bodymap) 954 bp exon 20 accessions, some from germinal center B cell (seen 2 times) parathyroid gland (2) parathyroid tumor (2) pooled germ cell tumors (2) prostate (2) capped 5' end, 1 accession Validated 3' end, 3 accessions 954 bp exon 187 bp exon 6466 bp [gt-ag] intron 19 GenBank accessions 2134 RNA-seq supporting reads 657 UHR pooled cells 204 Brain 425 Blood 836 Neuroblastoma 12 Other (also 55 Primates bodymap) 148 bp exon 148 bp exon 7748 bp [gt-ag] intron 13 GenBank accessions 2640 RNA-seq supporting reads 441 UHR pooled cells 586 Brain 210 Blood 1364 Neuroblastoma 39 Other (also 38 Primates bodymap) 232 bp exon 3399 bp [gt-ag] intron 20 GenBank accessions 11938 RNA-seq supporting reads 2406 UHR pooled cells 985 Brain 1397 Blood 7084 Neuroblastoma 66 Other (also 2588 Primates bodymap) 165 bp exon 7789 bp [gt-ag] intron 16 GenBank accessions 9366 RNA-seq supporting reads 2039 UHR pooled cells 808 Brain 666 Blood 5799 Neuroblastoma 54 Other (also 1988 Primates bodymap) 141 bp exon 2761 bp [gt-ag] intron 35 GenBank accessions 14687 RNA-seq supporting reads 3632 UHR pooled cells 1394 Brain 1245 Blood 8348 Neuroblastoma 68 Other (also 2655 Primates bodymap) 184 bp exon 3239 bp [gt-ag] intron 47 GenBank accessions 19751 RNA-seq supporting reads 5277 UHR pooled cells 1974 Brain 1502 Blood 10895 Neuroblastoma 103 Other (also 2347 Primates bodymap) 410 bp exon 11 accessions, some from insulinoma (seen 11 times) pancreas (11) 410 bp exon 227 bp exon 1655 bp [gt-ag] intron 50 GenBank accessions 7727 RNA-seq supporting reads 1733 UHR pooled cells 593 Brain 1479 Blood 3904 Neuroblastoma 18 Other (also 535 Primates bodymap) 211 bp exon 4600 bp [gt-ag] intron 61 GenBank accessions 11554 RNA-seq supporting reads 2964 UHR pooled cells 702 Brain 1929 Blood 5905 Neuroblastoma 54 Other (also 4080 Primates bodymap) 148 bp exon 1326 bp [gt-ag] intron 2 GenBank accessions 513 RNA-seq supporting reads 117 UHR pooled cells 42 Brain 91 Blood 262 Neuroblastoma 1 Other (also 2 Primates bodymap) 96 bp exon 3550 bp [gt-ag] intron 3 GenBank accessions 373 RNA-seq supporting reads 87 UHR pooled cells 30 Brain 53 Blood 202 Neuroblastoma 1 Other 217 bp exon 217 bp exon 2559 bp [gt-ag] intron 32 GenBank accessions 10283 RNA-seq supporting reads 3144 UHR pooled cells 643 Brain 896 Blood 5555 Neuroblastoma 45 Other (also 2903 Primates bodymap) 232 bp exon 11353 bp [gt-ag] intron 10 GenBank accessions 3197 RNA-seq supporting reads 1068 UHR pooled cells 301 Brain 226 Blood 1586 Neuroblastoma 16 Other (also 132 Primates bodymap) 141 bp exon 2761 bp [gt-ag] intron 35 GenBank accessions 14687 RNA-seq supporting reads 3632 UHR pooled cells 1394 Brain 1245 Blood 8348 Neuroblastoma 68 Other (also 2655 Primates bodymap) 184 bp exon 3239 bp [gt-ag] intron 47 GenBank accessions 19751 RNA-seq supporting reads 5277 UHR pooled cells 1974 Brain 1502 Blood 10895 Neuroblastoma 103 Other (also 2347 Primates bodymap) 2 accessions, some from prostate (seen once) testis (once) 103 bp exon 431 bp exon 431 bp exon 1 accession from testis 431 bp exon 255 bp exon 2559 bp [gt-ag] intron 32 GenBank accessions 10283 RNA-seq supporting reads 3144 UHR pooled cells 643 Brain 896 Blood 5555 Neuroblastoma 45 Other (also 2903 Primates bodymap) 232 bp exon 11353 bp [gt-ag] intron 10 GenBank accessions 3197 RNA-seq supporting reads 1068 UHR pooled cells 301 Brain 226 Blood 1586 Neuroblastoma 16 Other (also 132 Primates bodymap) 141 bp exon 2761 bp [gt-ag] intron 35 GenBank accessions 14687 RNA-seq supporting reads 3632 UHR pooled cells 1394 Brain 1245 Blood 8348 Neuroblastoma 68 Other (also 2655 Primates bodymap) 184 bp exon 1 accession from testis 184 bp exon 227 bp exon 6466 bp [gt-ag] intron 19 GenBank accessions 2134 RNA-seq supporting reads 657 UHR pooled cells 204 Brain 425 Blood 836 Neuroblastoma 12 Other (also 55 Primates bodymap) 148 bp exon 148 bp exon 4972 bp [gt-ag] intron 43 GenBank accessions 11403 RNA-seq supporting reads 3691 UHR pooled cells 604 Brain 986 Blood 6089 Neuroblastoma 33 Other (also 3336 Primates bodymap) 217 bp exon 2559 bp [gt-ag] intron 32 GenBank accessions 10283 RNA-seq supporting reads 3144 UHR pooled cells 643 Brain 896 Blood 5555 Neuroblastoma 45 Other (also 2903 Primates bodymap) 232 bp exon 3399 bp [gt-ag] intron 20 GenBank accessions 11938 RNA-seq supporting reads 2406 UHR pooled cells 985 Brain 1397 Blood 7084 Neuroblastoma 66 Other (also 2588 Primates bodymap) 165 bp exon 6 accessions, some from kidney (seen 2 times) brain (once), fetal brain (once) human embryonic stem cells (once) prostate (once) capped 5' end, 2 accessions 165 bp exon 197 bp exon 14362 bp [gt-ag] intron 3 GenBank accessions 951 RNA-seq supporting reads 114 UHR pooled cells 313 Brain 19 Blood 502 Neuroblastoma 3 Other (also 5 Primates bodymap) 232 bp exon 232 bp exon 3399 bp [gt-ag] intron 20 GenBank accessions 11938 RNA-seq supporting reads 2406 UHR pooled cells 985 Brain 1397 Blood 7084 Neuroblastoma 66 Other (also 2588 Primates bodymap) 165 bp exon 7789 bp [gt-ag] intron 16 GenBank accessions 9366 RNA-seq supporting reads 2039 UHR pooled cells 808 Brain 666 Blood 5799 Neuroblastoma 54 Other (also 1988 Primates bodymap) 141 bp exon 2761 bp [gt-ag] intron 35 GenBank accessions 14687 RNA-seq supporting reads 3632 UHR pooled cells 1394 Brain 1245 Blood 8348 Neuroblastoma 68 Other (also 2655 Primates bodymap) 184 bp exon 3239 bp [gt-ag] intron 47 GenBank accessions 19751 RNA-seq supporting reads 5277 UHR pooled cells 1974 Brain 1502 Blood 10895 Neuroblastoma 103 Other (also 2347 Primates bodymap) 108 bp exon 2 accessions, some from stomach (seen 2 times) 108 bp exon 20 bp exon 1655 bp [gt-ag] intron 50 GenBank accessions 7727 RNA-seq supporting reads 1733 UHR pooled cells 593 Brain 1479 Blood 3904 Neuroblastoma 18 Other (also 535 Primates bodymap) 211 bp exon 211 bp exon 24081 bp [gt-ag] intron 2 GenBank accessions 16 RNA-seq supporting reads 9 UHR pooled cells 2 Brain 5 Neuroblastoma 141 bp exon 2761 bp [gt-ag] intron 35 GenBank accessions 14687 RNA-seq supporting reads 3632 UHR pooled cells 1394 Brain 1245 Blood 8348 Neuroblastoma 68 Other (also 2655 Primates bodymap) 184 bp exon 3239 bp [gt-ag] intron 47 GenBank accessions 19751 RNA-seq supporting reads 5277 UHR pooled cells 1974 Brain 1502 Blood 10895 Neuroblastoma 103 Other (also 2347 Primates bodymap) 935 bp exon 2 accessions, some from whole embryo mainly head (seen 2 times) capped 5' end, 1 accession Validated 3' end, 1 accession 935 bp exon 139 bp exon 14362 bp [gt-ag] intron 3 GenBank accessions 951 RNA-seq supporting reads 114 UHR pooled cells 313 Brain 19 Blood 502 Neuroblastoma 3 Other (also 5 Primates bodymap) 232 bp exon 232 bp exon 11353 bp [gt-ag] intron 10 GenBank accessions 3197 RNA-seq supporting reads 1068 UHR pooled cells 301 Brain 226 Blood 1586 Neuroblastoma 16 Other (also 132 Primates bodymap) 141 bp exon 2761 bp [gt-ag] intron 35 GenBank accessions 14687 RNA-seq supporting reads 3632 UHR pooled cells 1394 Brain 1245 Blood 8348 Neuroblastoma 68 Other (also 2655 Primates bodymap) 184 bp exon 3239 bp [gt-ag] intron 47 GenBank accessions 19751 RNA-seq supporting reads 5277 UHR pooled cells 1974 Brain 1502 Blood 10895 Neuroblastoma 103 Other (also 2347 Primates bodymap) 147 bp exon 1 accession from human embryonic stem cells 147 bp exon 200 bp exon 14420 bp [gt-ag] intron 1 GenBank accession 1 RNA-seq supporting reads 1 Neuroblastoma 174 bp exon 174 bp exon 3399 bp [gt-ag] intron 20 GenBank accessions 11938 RNA-seq supporting reads 2406 UHR pooled cells 985 Brain 1397 Blood 7084 Neuroblastoma 66 Other (also 2588 Primates bodymap) 165 bp exon 7789 bp [gt-ag] intron 16 GenBank accessions 9366 RNA-seq supporting reads 2039 UHR pooled cells 808 Brain 666 Blood 5799 Neuroblastoma 54 Other (also 1988 Primates bodymap) 314 bp exon 2 accessions, some from colon (seen once) skeletal muscle (once) capped 5' end, 1 accession 314 bp exon 211 bp exon 1655 bp [gt-ag] intron 50 GenBank accessions 7727 RNA-seq supporting reads 1733 UHR pooled cells 593 Brain 1479 Blood 3904 Neuroblastoma 18 Other (also 535 Primates bodymap) 211 bp exon 211 bp exon 4600 bp [gt-ag] intron 61 GenBank accessions 11554 RNA-seq supporting reads 2964 UHR pooled cells 702 Brain 1929 Blood 5905 Neuroblastoma 54 Other (also 4080 Primates bodymap) 148 bp exon 22235 bp [gt-ag] intron 1 GenBank accession 80 RNA-seq supporting reads 42 UHR pooled cells 9 Brain 29 Neuroblastoma 184 bp exon 2 accessions, some from leiomyosarcoma cell line (seen once) thymus (once), uterus (once) capped 5' end, 1 accession 184 bp exon 200 bp exon 1655 bp [gt-ag] intron 50 GenBank accessions 7727 RNA-seq supporting reads 1733 UHR pooled cells 593 Brain 1479 Blood 3904 Neuroblastoma 18 Other (also 535 Primates bodymap) 211 bp exon 211 bp exon 4600 bp [gt-ag] intron 61 GenBank accessions 11554 RNA-seq supporting reads 2964 UHR pooled cells 702 Brain 1929 Blood 5905 Neuroblastoma 54 Other (also 4080 Primates bodymap) 148 bp exon 7748 bp [gt-ag] intron 13 GenBank accessions 2640 RNA-seq supporting reads 441 UHR pooled cells 586 Brain 210 Blood 1364 Neuroblastoma 39 Other (also 38 Primates bodymap) 232 bp exon 232 bp exon 3399 bp [gt-ag] intron 20 GenBank accessions 11938 RNA-seq supporting reads 2406 UHR pooled cells 985 Brain 1397 Blood 7084 Neuroblastoma 66 Other (also 2588 Primates bodymap) 2 accessions, some from ascites (seen once) eye (once), pterygium (once) stomach (once) 28 bp exon 660 bp exon 660 bp exon 24 bp uORF 660 bp exon 660 bp exon 3399 bp [gt-ag] intron 20 GenBank accessions 11938 RNA-seq supporting reads 2406 UHR pooled cells 985 Brain 1397 Blood 7084 Neuroblastoma 66 Other (also 2588 Primates bodymap) 164 bp exon 1 accession from white matter 164 bp exon 197 bp exon 6466 bp [gt-ag] intron 19 GenBank accessions 2134 RNA-seq supporting reads 657 UHR pooled cells 204 Brain 425 Blood 836 Neuroblastoma 12 Other (also 55 Primates bodymap) 148 bp exon 148 bp exon 19333 bp [gt-ag] intron 2 GenBank accessions 300 RNA-seq supporting reads 173 UHR pooled cells 17 Brain 17 Blood 93 Neuroblastoma (also 8 Primates bodymap) 141 bp exon 2761 bp [gt-ag] intron 35 GenBank accessions 14687 RNA-seq supporting reads 3632 UHR pooled cells 1394 Brain 1245 Blood 8348 Neuroblastoma 68 Other (also 2655 Primates bodymap) 1 accession from uterus 65 bp exon 168 bp exon 6466 bp [gt-ag] intron 19 GenBank accessions 2134 RNA-seq supporting reads 657 UHR pooled cells 204 Brain 425 Blood 836 Neuroblastoma 12 Other (also 55 Primates bodymap) 148 bp exon 148 bp exon 1326 bp [gt-ag] intron 2 GenBank accessions 513 RNA-seq supporting reads 117 UHR pooled cells 42 Brain 91 Blood 262 Neuroblastoma 1 Other (also 2 Primates bodymap) 96 bp exon 3550 bp [gt-ag] intron 3 GenBank accessions 373 RNA-seq supporting reads 87 UHR pooled cells 30 Brain 53 Blood 202 Neuroblastoma 1 Other 217 bp exon 217 bp exon 2559 bp [gt-ag] intron 32 GenBank accessions 10283 RNA-seq supporting reads 3144 UHR pooled cells 643 Brain 896 Blood 5555 Neuroblastoma 45 Other (also 2903 Primates bodymap) 1 accession from embryonal carcinoma cell line from testis 117 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 2468 bp 453 aa 266 bp 840 bp 2kb including Promoter 33442 bp 1kb
bAug10 1748 bp 398 aa 263 bp 288 bp 2kb probably including promoter 32887 bp 1kb
cAug10 1680 bp 396 aa 201 bp 288 bp 39 bp 2kb including Promoter 32825 bp 1kb
dAug10 2320 bp 365 aa 371 bp 851 bp 2kb including Promoter 33453 bp 1kb
eAug10 1467 bp 296 aa 269 bp 307 bp 2kb probably including promoter 32869 bp 1kb
fAug10 1559 bp 279 aa 719 bp 2kb probably including promoter 32602 bp 1kb
gAug10 812 bp 270 aa 2kb 17485 bp 1kb
hAug10 989 bp 244 aa 256 bp 2kb including Promoter 18385 bp 1kb
iAug10 1027 bp 237 aa 308 bp 5 bp 2kb probably including promoter 32577 bp 1kb
jAug10 1491 bp 199 aa 59 bp 832 bp 2kb including Promoter 33227 bp 1kb
kAug10 843 bp 182 aa 250 bp 44 bp 2kb possibly including promoter 32558 bp 1kb
lAug10 853 bp 147 aa 253 bp 156 bp 2kb including Promoter 26461 bp 1kb
mAug10 754 bp 129 aa 365 bp 2kb including Promoter 29244 bp 1kb
nAug10 819 bp 116 aa 239 bp 229 bp 2kb probably including promoter 18221 bp 1kb
oAug10 824 bp 95 aa 539 bp 21 bp 2kb possibly including promoter 4223 bp 1kb
pAug10 551 bp 88 aa 287 bp 2kb probably including promoter 29111 bp 1kb
qAug10 746 bp 63 aa 258 bp 296 bp 2kb 14647 bp 1kb
rAug10-unspliced 431 bp 26 aa 352 bp 2kb probably including promoter 431 bp 1kb

Gene neighbors and Navigator on chromosome 17q23.1 back to top
DHX40 C I R P CLTC D C I R P TMEM49 C I R P RPS6KB1 D C I R P R CA4 D C I R P NDUFB8P2 R R C I R P PTRH2 C R P TUBD1 C R DHX40P1andTBC1D3P1andRNFT1 D C R P HEATR6 G C R G C C I R P USP32 P SCARNA20 100kb 0 YPEL2, 149 accessions 5 variants DHX40, 466 accessions 11 variants CLTC, 501 accessions, 18 variants TMEM49, 590 accessions 17 variants RPS6KB1, 368 accessions 17 variants poyzer, 3 accessions CA4, 80 accessions, 7 variants slasley, 3 accessions slysley, 1 accession karserbo, 1 accession slarsley, 2 accessions vasko, 7 accessions blersko, 1 accession flermey, 1 accession cheyzee, 2 accessions glersko, 1 accession berdy, 2 accessions juslor, 1 accession charvoybu, 1 accession fluwubo, 1 accession glamey, 1 accession smusley, 1 accession blyty, 3 accessions smawsley, 2 accessions skoysko, 1 accession chawvoybu, 1 accession smeesley, 1 accession smersley, 1 accession cheevoybu, 2 accessions smoysley, 3 accessions cheyvoybu, 3 accessions snasley, 2 accessions snusley, 1 accession glumey, 1 accession sneysley, 1 accession smusko, 1 accession snorsley, 1 accession gleymey, 2 accessions chorvoybu, 2 accessions plamey, 2 accessions matama, 2 accessions, 2 variants sporsley, 1 accession seturi, 1 accession shovoybu, 1 accession stersko, 2 accessions stysley, 1 accession stosley, 1 accession swusko, 0 accession stawsley, 1 accession steesley, 1 accession stersley, 2 accessions swysko, 1 accession steysley, 1 accession storsley, 1 accession plumey, 1 accession swysley, 1 accession swusley, 1 accession shervoybu, 1 accession sheyvoybu, 1 accession soturi, 2 accessions sweesley, 1 accession swersley, 2 accessions sweysley, 1 accession baslor, 1 accession byslor, 1 accession barslor, 1 accession keyserbo, 1 accession beeslor, 3 accessions beyslor, 1 accession skawmey, 1 accession slumey, 1 accession slawmey, 2 accessions duslor, 1 accession darslor, 1 accession keeskar, 1 accession kloyzee, 1 accession bluvoybu, 1 accession faslor, 3 accessions doyslor, 1 accession narskar, 2 accessions teeskar, 1 accession NDUFB8P2, 1 accession wyskar, 1 accession ferslor, 3 accessions shawskar, 2 accessions bloyvoybu, 1 accession gloyskar, 1 accession gyslor, 1 accession flyvoybu, 1 accession flovoybu, 2 accessions plarskar, 1 accession laserbo, 1 accession gawslor, 3 accessions geeslor, 2 accessions karwey, 1 accession fleevoybu, 1 accession gerslor, 1 accession geyslor, 2 accessions skoskar, 1 accession smeeskar, 1 accession snyskar, 1 accession starmey, 1 accession flasa, 2 accessions swomey, 1 accession jarslor, 3 accessions keewey, 1 accession glarvoybu, 1 accession neezer, 1 accession beemor, 1 accession stuskar, 1 accession joyslor, 1 accession kyslor, 2 accessions starskar, 1 accession lyserbo, 1 accession kuslor, 1 accession steeskar, 1 accession bormor, 1 accession korwey, 10 accessions keeslor, 2 accessions kerslor, 1 accession korslor, 2 accessions gleyvoybu, 1 accession gloyvoybu, 1 accession kituri, 1 accession voyzer, 7 accessions luslor, 1 accession germor, 1 accession goymor, 1 accession swoyslor, 1 accession lorslor, 1 accession luserbo, 4 accessions sluzer, 1 accession deedy, 4 accessions maslor, 2 accessions myslor, 1 accession deyskaw, 1 accession marslor, 1 accession mawslor, 1 accession fawskaw, 1 accession jarskaw, 1 accession mitama, 2 accessions, 2 variants buslu, 1 accession naslor, 1 accession noslor, 1 accession myskaw, 1 accession lamor, 0 accession nawslor, 1 accession meeskaw, 1 accession pluvoybu, 1 accession plovoybu, 1 accession plarvoybu, 1 accession pleevoybu, 1 accession plervoybu, 1 accession plorvoybu, 1 accession blersa, 2 accessions slosley, 1 accession slawsley, 1 accession sleesley, 1 accession glarsko, 1 accession gleysko, 2 accessions sleysley, 1 accession kawserbo, 1 accession glorsko, 1 accession jyslor, 1 accession smysley, 1 accession floymey, 1 accession kleysko, 1 accession jorwey, 16 accessions smosley, 2 accessions smarsley, 1 accession skysko, 1 accession smeysley, 2 accessions slysko, 1 accession smorsley, 3 accessions chervoybu, 1 accession slorsko, 1 accession snysley, 1 accession snosley, 1 accession snawsley, 5 accessions sneesley, 1 accession snersley, 2 accessions smorsko, 1 accession snoysley, 1 accession spasley, 6 accessions spysley, 1 accession fleyzee, 1 accession speesley, 11 accessions choyvoybu, 1 accession snysko, 1 accession steesko, 2 accessions keeserbo, 1 accession shyvoybu, 1 accession joywey, 3 accessions stasley, 1 accession kawey, 1 accession stusley, 2 accessions sharvoybu, 1 accession starsley, 1 accession swoysley, 1 accession doskar, 1 accession sheevoybu, 1 accession swosley, 2 accessions swawsley, 1 accession foyskar, 1 accession sworsley, 1 accession shorvoybu, 3 accessions kerserbo, 1 accession beydy, 2 accessions berslor, 1 accession koskar, 1 accession boyslor, 1 accession kywey, 1 accession doslor, 1 accession klozee, 1 accession smumey, 1 accession larskar, 1 accession smormey, 1 accession snamey, 1 accession deeslor, 1 accession derslor, 6 accessions dorslor, 1 accession fyslor, 1 accession slozee, 1 accession pyskar, 1 accession spamey, 1 accession farslor, 1 accession spymey, 1 accession fawslor, 1 accession sparmey, 1 accession feyslor, 1 accession flavoybu, 1 accession guslor, 1 accession fleyvoybu, 2 accessions smawskar, 1 accession swymey, 1 accession gleesa, 2 accessions joslor, 1 accession jawslor, 1 accession jeeslor, 1 accession kerwey, 1 accession jorslor, 1 accession kaslor, 1 accession gluvoybu, 2 accessions katuri, 3 accessions karslor, 1 accession swarskar, 1 accession damor, 1 accession glyvoybu, 1 accession darmor, 1 accession fomor, 3 accessions fleesa, 30 accessions 3 variants glorvoybu, 2 accessions laslor, 1 accession lyslor, 2 accessions fermor, 1 accession leeslor, 1 accession lerslor, 1 accession leyslor, 2 accessions muslor, 2 accessions moslor, 1 accession klarvoybu, 1 accession klawvoybu, 2 accessions kleevoybu, 1 accession loserbo, 1 accession kaskaw, 1 accession snarzer, 3 accessions meeslor, 1 accession merslor, 1 accession jymor, 1 accession meyslor, 1 accession swawvybu, 1 accession komor, 1 accession luwey, 2 accessions keemor, 1 accession plavoybu, 1 accession keyskaw, 1 accession leeserbo, 4 accessions 2 variants neeslor, 3 accessions narslor, 2 accessions nerslor, 2 accessions kuturi, 1 accession sweyzer, 1 accession klarsa, 3 accessions noyslor, 1 accession mumor, 1 accession lowey, 2 accessions bleysa, 25 accessions 2 variants hehori, 3 accessions, 2 variants PTRH2, 202 accessions 6 variants TUBD1, 141 accessions 18 variants DHX40P1andTBC1D3P1andRNFT1 312 accessions, 20 variants HEATR6, 202 accessions 12 variants LOC645638, 161 accessions 12 variants LOC653653, 3 accessions USP32, 322 accessions 19 variants SCARNA20, 1 accession ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               5 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j, .k, .l, .m, .n, .o, .p, .q, .r-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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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