Homo sapiens complex locus MTMR3, encoding myotubularin related protein 3.
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SUMMARY back to top
RefSeq summary
[MTMR3] This gene encodes a member of the myotubularin dual specificity protein phosphatase gene family. The encoded protein is structurally similar to myotubularin but in addition contains a FYVE domain and an N-terminal PH-GRAM domain. The protein can self-associate and also form heteromers with another myotubularin related protein. The protein binds to phosphoinositide lipids through the PH-GRAM domain, and can hydrolyze phosphatidylinositol(3)-phosphate and phosphatidylinositol(3,5)-biphosphate in vitro. The encoded protein has been observed to have a perinuclear, possibly membrane-bound, distribution in cells, but it has also been found free in the cytoplasm. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq].

RefSeq annotates 3 representative transcripts (NM included in AceView variants .a, .b and .c), 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 very high level, 4.1 times the average gene in this release. The sequence of this gene is defined by 484 GenBank accessions from 430 cDNA clones, some from lung (seen 42 times), brain (31), carcinoid (29), prostate (22), eye (18), breast (15), neuroblastoma cot 25-normalized (15) and 131 other tissues. We annotate structural defects or features in 13 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 28 distinct gt-ag introns. Transcription produces 16 different mRNAs, 10 alternatively spliced variants and 6 unspliced forms. There are 4 probable alternative promotors, 3 non overlapping alternative last exons and 12 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 7 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron. 225 bp of this gene are antisense to spliced gene hisa, raising the possibility of regulated alternate expression.
Function: There are 17 articles specifically referring to this gene in PubMed. Functionally, the gene has been proposed to participate in a process (protein amino acid dephosphorylation). Proteins are expected to have molecular functions (protein serine/threonine phosphatase activity, protein tyrosine phosphatase activity, hydrolase activity, metal ion binding, zinc ion binding) and to localize in various compartments (cytoplasm, membrane fraction).
Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (6 complete, 3 partial), some containing domains FYVE zinc finger, Myotubularin-related [Pfam], a coiled coil stretch [Psort2]. The remaining 7 mRNA variants (1 spliced, 6 unspliced; 2 partial) appear not to encode good proteins.
Isoform MTMR3.eAug10 is annotated using as Met a Kozak-compatible g..CTGg start, thereby gaining 178 amino acids N-terminal to the first AUG. 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 22, links to other databases and other names
Map: This gene MTMR3 maps on chromosome 22, at 22q12.2 according to Entrez Gene. In AceView, it covers 148.37 kb, from 30279144 to 30427511 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 8897, 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 MTMR3, hCG_2011013, ZFYVE10, FLJ32333, KIAA0371 or FYVE-DSP1, LOC8897. It has been described as myotubularin-related protein 3, OTTHUMP00000199667, OTTHUMP00000199668, OTTHUMP00000199669, zinc finger, FYVE domain containing 10, zinc finger FYVE domain-containing protein 10, FYVE domain-containing dual specificity protein phosphatase 1, FYVE (Fab1 YGLO23 Vsp27 EEA1 domain) dual-specificity protein phosphatase.
EC number: This gene encodes protein number: 3.1.3.48.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Mtmr3 (e=8 10-76).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes mtm-3 (e=7 10-67), mtm-6 (e=4 10-62), mtm-1 (e=10-60), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes AT5G04540 (e=10-59), AT3G10550 (e=10-52), 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
MTMR3 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 13.3 16.4 20.2 5.40 18.8 18.8 20.2 53.2 32.8 20.2 35.1 24.8 18.8 26.6 24.8 12.4 24.8 32.8 35.1 35.1 53.2 61.1 21.6 15.3 17.6 16.4 17.6 14.3 21.6 35.1 20.2 40.3 20.2 18.8 17.6 43.2 11.6 10.1 12.4 43.2 18.8 12.4 18.8 13.3 15.3 7.13 15.3 16.4 20.2 18.8 12.4 6.21 24.8 20.2 15.3 17.6 15.3 16.4 30.6 16.4 12.4 13.3 17.6 20.2 16.4 57.1 10.1 14.3 14.3 18.8 16.4 12.4 14.3 14.3 14.3 11.6 10.8 24.8 11.6 18.8 14.3 10.8 10.8 13.3 17.6 12.4 10.1 14.3 12.4 10.1 14.3 14.3 14.3 12.4 4.10 15.3 10.1 13.3 13.3 12.4 8.78 20.2 21.6 14.3 12.4 18.8 32.8 15.3 15.3 21.6 14.3 18.8 14.3 14.3 16.4 4.39 12.4 32.8 15.3 15.3 16.4 13.3 13.3 9.41 14.3 14.3 7.64 24.8 20.2 13.3 15.3 18.8 18.8 21.6 16.4 17.6 20.2 6.65 26.6 15.3 12.4 16.4 17.6 6.21 23.2 13.3 17.6 14.3 23.2 16.4 49.7 24.8 16.4 13.3 17.6 20.2 40.3 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 MTMR3 5' 3' encoded on plus strand of chromosome 22 from 30,279,144 to 30,427,511 29545 35424 36084 45392 49912 38092 37564 43392 38579 47424 51857 53726 42019 58006 61761 26897 56403 a [NM] 29545 35424 36084 45392 49912 38092 37564 43392 38579 47424 51857 53726 42019 58006 61761 13415 13964 13139 b [NM] 29545 35424 36084 45392 49912 38092 37564 43392 38579 47424 51857 53726 42019 58006 61761 13415 56403 c [NM] 29545 4856 45392 49912 38092 37564 e 61761 d n-u 29545 35424 349 45392 49912 f 592 1052 47424 p k-u 56403 h 116 36084 45392 49912 38092 g l-u j-u 29545 35424 36084 45392 686 i m-u o-u 5kb 0 205 bp exon 73676 bp [gt-ag] intron 24 GenBank accessions 29521 RNA-seq supporting reads 814 UHR pooled cells 1719 Brain 14699 Blood 12231 Neuroblastoma 58 Other (also 4079 Primates bodymap) 53 bp exon 13887 bp [gt-ag] intron 23 GenBank accessions 35401 RNA-seq supporting reads 1111 UHR pooled cells 2399 Brain 15913 Blood 15866 Neuroblastoma 112 Other (also 6889 Primates bodymap) 87 bp exon 87 bp exon 7379 bp [gt-ag] intron 27 GenBank accessions 36057 RNA-seq supporting reads 1220 UHR pooled cells 2693 Brain 14654 Blood 17369 Neuroblastoma 121 Other (also 6730 Primates bodymap) 90 bp exon 404 bp [gt-ag] intron 36 GenBank accessions 45356 RNA-seq supporting reads 1486 UHR pooled cells 3019 Brain 20538 Blood 20163 Neuroblastoma 150 Other (also 13404 Primates bodymap) 117 bp exon 9427 bp [gt-ag] intron 33 GenBank accessions 49879 RNA-seq supporting reads 1468 UHR pooled cells 2976 Brain 25635 Blood 19588 Neuroblastoma 212 Other (also 10679 Primates bodymap) 83 bp exon 2941 bp [gt-ag] intron 28 GenBank accessions 38064 RNA-seq supporting reads 1433 UHR pooled cells 2910 Brain 13681 Blood 19804 Neuroblastoma 236 Other (also 9642 Primates bodymap) 167 bp exon 7090 bp [gt-ag] intron 26 GenBank accessions 37538 RNA-seq supporting reads 1359 UHR pooled cells 2755 Brain 15493 Blood 17768 Neuroblastoma 163 Other (also 8400 Primates bodymap) 97 bp exon 4022 bp [gt-ag] intron 24 GenBank accessions 43368 RNA-seq supporting reads 1448 UHR pooled cells 2973 Brain 18503 Blood 20197 Neuroblastoma 247 Other (also 9183 Primates bodymap) 114 bp exon 4120 bp [gt-ag] intron 26 GenBank accessions 38553 RNA-seq supporting reads 1413 UHR pooled cells 2994 Brain 15088 Blood 18874 Neuroblastoma 184 Other (also 5585 Primates bodymap) 206 bp exon 581 bp [gt-ag] intron 30 GenBank accessions 47394 RNA-seq supporting reads 2030 UHR pooled cells 4126 Brain 15359 Blood 25630 Neuroblastoma 249 Other (also 8070 Primates bodymap) 132 bp exon 985 bp [gt-ag] intron 30 GenBank accessions 51827 RNA-seq supporting reads 1789 UHR pooled cells 3576 Brain 22624 Blood 23610 Neuroblastoma 228 Other (also 8819 Primates bodymap) 112 bp exon 3238 bp [gt-ag] intron 27 GenBank accessions 53699 RNA-seq supporting reads 2252 UHR pooled cells 4216 Brain 19328 Blood 27709 Neuroblastoma 194 Other (also 8495 Primates bodymap) 196 bp exon 792 bp [gt-ag] intron 26 GenBank accessions 41993 RNA-seq supporting reads 2139 UHR pooled cells 3658 Brain 11828 Blood 24136 Neuroblastoma 232 Other (also 5402 Primates bodymap) 186 bp exon 2986 bp [gt-ag] intron 19 GenBank accessions 57987 RNA-seq supporting reads 2519 UHR pooled cells 4700 Brain 20833 Blood 29635 Neuroblastoma 300 Other (also 9683 Primates bodymap) 171 bp exon 1228 bp [gt-ag] intron 20 GenBank accessions 38684 RNA-seq supporting reads 1607 UHR pooled cells 3009 Brain 12641 Blood 21121 Neuroblastoma 306 Other (also 5182 Primates bodymap) 146 bp exon 1407 bp [gt-ag] intron 28 GenBank accessions 61733 RNA-seq supporting reads 2349 UHR pooled cells 4113 Brain 24355 Blood 30659 Neuroblastoma 257 Other (also 8618 Primates bodymap) 1405 bp exon 1144 bp [gt-ag] intron 27 GenBank accessions 26870 RNA-seq supporting reads 1660 UHR pooled cells 1949 Brain 8100 Blood 14993 Neuroblastoma 168 Other (also 2855 Primates bodymap) 111 bp exon 469 bp [gt-ag] intron 31 GenBank accessions 33820 RNA-seq supporting reads 1944 UHR pooled cells 2319 Brain 11884 Blood 17504 Neuroblastoma 169 Other (also 2551 Primates bodymap) 89 bp exon 2932 bp [gt-ag] intron 41 GenBank accessions 56362 RNA-seq supporting reads 3071 UHR pooled cells 4695 Brain 11706 Blood 36628 Neuroblastoma 262 Other (also 5495 Primates bodymap) 5237 bp exon 29 accessions, NM_021090.3 some from brain (seen 3 times) eye (3), neuroblastoma cot 25-normalized (3) islets of langerhans (2) lung tumor (2) Validated 3' end, 3 accessions Validated 3' end, 1 accession Validated 3' end, 1 accession 5237 bp exon 190 bp exon 73676 bp [gt-ag] intron 24 GenBank accessions 29521 RNA-seq supporting reads 814 UHR pooled cells 1719 Brain 14699 Blood 12231 Neuroblastoma 58 Other (also 4079 Primates bodymap) 53 bp exon 13887 bp [gt-ag] intron 23 GenBank accessions 35401 RNA-seq supporting reads 1111 UHR pooled cells 2399 Brain 15913 Blood 15866 Neuroblastoma 112 Other (also 6889 Primates bodymap) 87 bp exon 87 bp exon 7379 bp [gt-ag] intron 27 GenBank accessions 36057 RNA-seq supporting reads 1220 UHR pooled cells 2693 Brain 14654 Blood 17369 Neuroblastoma 121 Other (also 6730 Primates bodymap) 90 bp exon 404 bp [gt-ag] intron 36 GenBank accessions 45356 RNA-seq supporting reads 1486 UHR pooled cells 3019 Brain 20538 Blood 20163 Neuroblastoma 150 Other (also 13404 Primates bodymap) 117 bp exon 9427 bp [gt-ag] intron 33 GenBank accessions 49879 RNA-seq supporting reads 1468 UHR pooled cells 2976 Brain 25635 Blood 19588 Neuroblastoma 212 Other (also 10679 Primates bodymap) 83 bp exon 2941 bp [gt-ag] intron 28 GenBank accessions 38064 RNA-seq supporting reads 1433 UHR pooled cells 2910 Brain 13681 Blood 19804 Neuroblastoma 236 Other (also 9642 Primates bodymap) 167 bp exon 7090 bp [gt-ag] intron 26 GenBank accessions 37538 RNA-seq supporting reads 1359 UHR pooled cells 2755 Brain 15493 Blood 17768 Neuroblastoma 163 Other (also 8400 Primates bodymap) 97 bp exon 4022 bp [gt-ag] intron 24 GenBank accessions 43368 RNA-seq supporting reads 1448 UHR pooled cells 2973 Brain 18503 Blood 20197 Neuroblastoma 247 Other (also 9183 Primates bodymap) 114 bp exon 4120 bp [gt-ag] intron 26 GenBank accessions 38553 RNA-seq supporting reads 1413 UHR pooled cells 2994 Brain 15088 Blood 18874 Neuroblastoma 184 Other (also 5585 Primates bodymap) 206 bp exon 581 bp [gt-ag] intron 30 GenBank accessions 47394 RNA-seq supporting reads 2030 UHR pooled cells 4126 Brain 15359 Blood 25630 Neuroblastoma 249 Other (also 8070 Primates bodymap) 132 bp exon 985 bp [gt-ag] intron 30 GenBank accessions 51827 RNA-seq supporting reads 1789 UHR pooled cells 3576 Brain 22624 Blood 23610 Neuroblastoma 228 Other (also 8819 Primates bodymap) 112 bp exon 3238 bp [gt-ag] intron 27 GenBank accessions 53699 RNA-seq supporting reads 2252 UHR pooled cells 4216 Brain 19328 Blood 27709 Neuroblastoma 194 Other (also 8495 Primates bodymap) 196 bp exon 792 bp [gt-ag] intron 26 GenBank accessions 41993 RNA-seq supporting reads 2139 UHR pooled cells 3658 Brain 11828 Blood 24136 Neuroblastoma 232 Other (also 5402 Primates bodymap) 186 bp exon 2986 bp [gt-ag] intron 19 GenBank accessions 57987 RNA-seq supporting reads 2519 UHR pooled cells 4700 Brain 20833 Blood 29635 Neuroblastoma 300 Other (also 9683 Primates bodymap) 171 bp exon 1228 bp [gt-ag] intron 20 GenBank accessions 38684 RNA-seq supporting reads 1607 UHR pooled cells 3009 Brain 12641 Blood 21121 Neuroblastoma 306 Other (also 5182 Primates bodymap) 146 bp exon 1407 bp [gt-ag] intron 28 GenBank accessions 61733 RNA-seq supporting reads 2349 UHR pooled cells 4113 Brain 24355 Blood 30659 Neuroblastoma 257 Other (also 8618 Primates bodymap) 1405 bp exon 1724 bp [gt-ag] intron 10 GenBank accessions 13405 RNA-seq supporting reads 663 UHR pooled cells 1783 Brain 1191 Blood 9652 Neuroblastoma 116 Other (also 1857 Primates bodymap) 89 bp exon 759 bp [gt-ag] intron 5 GenBank accessions 13959 RNA-seq supporting reads 420 UHR pooled cells 1105 Brain 6372 Blood 5970 Neuroblastoma 92 Other (also 2251 Primates bodymap) 27 bp exon 2146 bp [gt-ag] intron 6 GenBank accessions 13133 RNA-seq supporting reads 454 UHR pooled cells 1164 Brain 5227 Blood 6193 Neuroblastoma 95 Other (also 2507 Primates bodymap) 5237 bp exon 6 accessions, NM_153050.2 some from colon normal (seen 2 times) heart (once), lung (once) Validated 3' end, 1 accession 5237 bp exon 190 bp exon 73676 bp [gt-ag] intron 24 GenBank accessions 29521 RNA-seq supporting reads 814 UHR pooled cells 1719 Brain 14699 Blood 12231 Neuroblastoma 58 Other (also 4079 Primates bodymap) 53 bp exon 13887 bp [gt-ag] intron 23 GenBank accessions 35401 RNA-seq supporting reads 1111 UHR pooled cells 2399 Brain 15913 Blood 15866 Neuroblastoma 112 Other (also 6889 Primates bodymap) 87 bp exon 87 bp exon 7379 bp [gt-ag] intron 27 GenBank accessions 36057 RNA-seq supporting reads 1220 UHR pooled cells 2693 Brain 14654 Blood 17369 Neuroblastoma 121 Other (also 6730 Primates bodymap) 90 bp exon 404 bp [gt-ag] intron 36 GenBank accessions 45356 RNA-seq supporting reads 1486 UHR pooled cells 3019 Brain 20538 Blood 20163 Neuroblastoma 150 Other (also 13404 Primates bodymap) 117 bp exon 9427 bp [gt-ag] intron 33 GenBank accessions 49879 RNA-seq supporting reads 1468 UHR pooled cells 2976 Brain 25635 Blood 19588 Neuroblastoma 212 Other (also 10679 Primates bodymap) 83 bp exon 2941 bp [gt-ag] intron 28 GenBank accessions 38064 RNA-seq supporting reads 1433 UHR pooled cells 2910 Brain 13681 Blood 19804 Neuroblastoma 236 Other (also 9642 Primates bodymap) 167 bp exon 7090 bp [gt-ag] intron 26 GenBank accessions 37538 RNA-seq supporting reads 1359 UHR pooled cells 2755 Brain 15493 Blood 17768 Neuroblastoma 163 Other (also 8400 Primates bodymap) 97 bp exon 4022 bp [gt-ag] intron 24 GenBank accessions 43368 RNA-seq supporting reads 1448 UHR pooled cells 2973 Brain 18503 Blood 20197 Neuroblastoma 247 Other (also 9183 Primates bodymap) 114 bp exon 4120 bp [gt-ag] intron 26 GenBank accessions 38553 RNA-seq supporting reads 1413 UHR pooled cells 2994 Brain 15088 Blood 18874 Neuroblastoma 184 Other (also 5585 Primates bodymap) 206 bp exon 581 bp [gt-ag] intron 30 GenBank accessions 47394 RNA-seq supporting reads 2030 UHR pooled cells 4126 Brain 15359 Blood 25630 Neuroblastoma 249 Other (also 8070 Primates bodymap) 132 bp exon 985 bp [gt-ag] intron 30 GenBank accessions 51827 RNA-seq supporting reads 1789 UHR pooled cells 3576 Brain 22624 Blood 23610 Neuroblastoma 228 Other (also 8819 Primates bodymap) 112 bp exon 3238 bp [gt-ag] intron 27 GenBank accessions 53699 RNA-seq supporting reads 2252 UHR pooled cells 4216 Brain 19328 Blood 27709 Neuroblastoma 194 Other (also 8495 Primates bodymap) 196 bp exon 792 bp [gt-ag] intron 26 GenBank accessions 41993 RNA-seq supporting reads 2139 UHR pooled cells 3658 Brain 11828 Blood 24136 Neuroblastoma 232 Other (also 5402 Primates bodymap) 186 bp exon 2986 bp [gt-ag] intron 19 GenBank accessions 57987 RNA-seq supporting reads 2519 UHR pooled cells 4700 Brain 20833 Blood 29635 Neuroblastoma 300 Other (also 9683 Primates bodymap) 171 bp exon 1228 bp [gt-ag] intron 20 GenBank accessions 38684 RNA-seq supporting reads 1607 UHR pooled cells 3009 Brain 12641 Blood 21121 Neuroblastoma 306 Other (also 5182 Primates bodymap) 146 bp exon 1407 bp [gt-ag] intron 28 GenBank accessions 61733 RNA-seq supporting reads 2349 UHR pooled cells 4113 Brain 24355 Blood 30659 Neuroblastoma 257 Other (also 8618 Primates bodymap) 1405 bp exon 1724 bp [gt-ag] intron 10 GenBank accessions 13405 RNA-seq supporting reads 663 UHR pooled cells 1783 Brain 1191 Blood 9652 Neuroblastoma 116 Other (also 1857 Primates bodymap) 89 bp exon 2932 bp [gt-ag] intron 41 GenBank accessions 56362 RNA-seq supporting reads 3071 UHR pooled cells 4695 Brain 11706 Blood 36628 Neuroblastoma 262 Other (also 5495 Primates bodymap) 5237 bp exon 309 accessions, NM_153051.2 some from lung (seen 31 times) carcinoid (23), brain (20) prostate (20), breast (14) capped 5' end, 38 accessions Validated 3' end, 2 accessions Validated 3' end, 1 accession Validated 3' end, 31 accessions Validated 3' end, 1 accession 5237 bp exon 179 bp exon 179 bp exon 73676 bp [gt-ag] intron 24 GenBank accessions 29521 RNA-seq supporting reads 814 UHR pooled cells 1719 Brain 14699 Blood 12231 Neuroblastoma 58 Other (also 4079 Primates bodymap) 53 bp exon 21353 bp [gt-ag] intron 3 GenBank accessions 4853 RNA-seq supporting reads 210 UHR pooled cells 231 Brain 2360 Blood 2036 Neuroblastoma 16 Other (also 501 Primates bodymap) 90 bp exon 404 bp [gt-ag] intron 36 GenBank accessions 45356 RNA-seq supporting reads 1486 UHR pooled cells 3019 Brain 20538 Blood 20163 Neuroblastoma 150 Other (also 13404 Primates bodymap) 117 bp exon 9427 bp [gt-ag] intron 33 GenBank accessions 49879 RNA-seq supporting reads 1468 UHR pooled cells 2976 Brain 25635 Blood 19588 Neuroblastoma 212 Other (also 10679 Primates bodymap) 83 bp exon 2941 bp [gt-ag] intron 28 GenBank accessions 38064 RNA-seq supporting reads 1433 UHR pooled cells 2910 Brain 13681 Blood 19804 Neuroblastoma 236 Other (also 9642 Primates bodymap) 167 bp exon 7090 bp [gt-ag] intron 26 GenBank accessions 37538 RNA-seq supporting reads 1359 UHR pooled cells 2755 Brain 15493 Blood 17768 Neuroblastoma 163 Other (also 8400 Primates bodymap) 229 bp exon 4 accessions, some from testis (seen 2 times) bone marrow (once), kidney (once) Validated 3' end, 1 accession 229 bp exon 391 bp exon 391 bp exon 21 bp uORF 391 bp exon 391 bp exon 1407 bp [gt-ag] intron 28 GenBank accessions 61733 RNA-seq supporting reads 2349 UHR pooled cells 4113 Brain 24355 Blood 30659 Neuroblastoma 257 Other (also 8618 Primates bodymap) 587 bp exon 587 bp exon 5 accessions, some from brain (seen 2 times) cerebellum (once), testis (once) capped 5' end, 3 accessions 587 bp exon 585 bp exon 585 bp exon 1 accession from brain 585 bp exon 180 bp exon 73676 bp [gt-ag] intron 24 GenBank accessions 29521 RNA-seq supporting reads 814 UHR pooled cells 1719 Brain 14699 Blood 12231 Neuroblastoma 58 Other (also 4079 Primates bodymap) 53 bp exon 53 bp exon 13887 bp [gt-ag] intron 23 GenBank accessions 35401 RNA-seq supporting reads 1111 UHR pooled cells 2399 Brain 15913 Blood 15866 Neuroblastoma 112 Other (also 6889 Primates bodymap) 87 bp exon 7362 bp [gt-ag] intron 1 GenBank accession 348 RNA-seq supporting reads 6 UHR pooled cells 18 Brain 156 Blood 165 Neuroblastoma 3 Other (also 83 Primates bodymap) 107 bp exon 404 bp [gt-ag] intron 36 GenBank accessions 45356 RNA-seq supporting reads 1486 UHR pooled cells 3019 Brain 20538 Blood 20163 Neuroblastoma 150 Other (also 13404 Primates bodymap) 117 bp exon 9427 bp [gt-ag] intron 33 GenBank accessions 49879 RNA-seq supporting reads 1468 UHR pooled cells 2976 Brain 25635 Blood 19588 Neuroblastoma 212 Other (also 10679 Primates bodymap) 95 bp exon 2 accessions, some from lung normal (seen once) uterus (once) capped 5' end, 1 accession 95 bp exon 16 bp exon 904 bp [gt-ag] intron 2 GenBank accessions 590 RNA-seq supporting reads 13 UHR pooled cells 2 Brain 249 Blood 326 Neuroblastoma (also 24 Primates bodymap) 124 bp exon 3092 bp [gt-ag] intron 2 GenBank accessions 1050 RNA-seq supporting reads 32 UHR pooled cells 22 Brain 326 Blood 668 Neuroblastoma 2 Other (also 85 Primates bodymap) 206 bp exon 206 bp exon 206 bp exon 581 bp [gt-ag] intron 30 GenBank accessions 47394 RNA-seq supporting reads 2030 UHR pooled cells 4126 Brain 15359 Blood 25630 Neuroblastoma 249 Other (also 8070 Primates bodymap) 2 accessions, some from marrow (seen 2 times) 80 bp exon 2136 bp exon 11 accessions, some from liver and spleen (seen 2 times) colon (once), colon normal (once) eye (once), hippocampus (once) 2136 bp exon 748 bp exon 748 bp exon 2932 bp [gt-ag] intron 41 GenBank accessions 56362 RNA-seq supporting reads 3071 UHR pooled cells 4695 Brain 11706 Blood 36628 Neuroblastoma 262 Other (also 5495 Primates bodymap) 334 bp exon 4 accessions, some from colon (seen once) testis (once), thalamus (once) thymus (once) capped 5' end, 3 accessions 334 bp exon 163 bp exon 87616 bp [gt-ag] intron 1 GenBank accession 115 RNA-seq supporting reads 1 UHR pooled cells 8 Brain 24 Blood 82 Neuroblastoma (also 80 Primates bodymap) 87 bp exon 87 bp exon 7379 bp [gt-ag] intron 27 GenBank accessions 36057 RNA-seq supporting reads 1220 UHR pooled cells 2693 Brain 14654 Blood 17369 Neuroblastoma 121 Other (also 6730 Primates bodymap) 90 bp exon 404 bp [gt-ag] intron 36 GenBank accessions 45356 RNA-seq supporting reads 1486 UHR pooled cells 3019 Brain 20538 Blood 20163 Neuroblastoma 150 Other (also 13404 Primates bodymap) 117 bp exon 9427 bp [gt-ag] intron 33 GenBank accessions 49879 RNA-seq supporting reads 1468 UHR pooled cells 2976 Brain 25635 Blood 19588 Neuroblastoma 212 Other (also 10679 Primates bodymap) 83 bp exon 2941 bp [gt-ag] intron 28 GenBank accessions 38064 RNA-seq supporting reads 1433 UHR pooled cells 2910 Brain 13681 Blood 19804 Neuroblastoma 236 Other (also 9642 Primates bodymap) 125 bp exon 1 accession from embryonic stem cells cell lines H1, H7, andh9 125 bp exon 848 bp exon 848 bp exon 2 accessions, some from thymus (seen 2 times) capped 5' end, 2 accessions 848 bp exon 2883 bp exon 2883 bp exon 56 accessions, some from brain (seen 5 times) glioblastoma (pooled) (4) lung (4), eye (3), placenta (3) capped 5' end, 1 accession Validated 3' end, 1 accession Validated 3' end, 9 accessions Validated 3' end, 5 accessions 2883 bp exon 91 bp exon 73676 bp [gt-ag] intron 24 GenBank accessions 29521 RNA-seq supporting reads 814 UHR pooled cells 1719 Brain 14699 Blood 12231 Neuroblastoma 58 Other (also 4079 Primates bodymap) 53 bp exon 13887 bp [gt-ag] intron 23 GenBank accessions 35401 RNA-seq supporting reads 1111 UHR pooled cells 2399 Brain 15913 Blood 15866 Neuroblastoma 112 Other (also 6889 Primates bodymap) 87 bp exon 87 bp exon 7379 bp [gt-ag] intron 27 GenBank accessions 36057 RNA-seq supporting reads 1220 UHR pooled cells 2693 Brain 14654 Blood 17369 Neuroblastoma 121 Other (also 6730 Primates bodymap) 90 bp exon 404 bp [gt-ag] intron 36 GenBank accessions 45356 RNA-seq supporting reads 1486 UHR pooled cells 3019 Brain 20538 Blood 20163 Neuroblastoma 150 Other (also 13404 Primates bodymap) 117 bp exon 12451 bp [gt-ag] intron 1 GenBank accession 685 RNA-seq supporting reads 34 UHR pooled cells 58 Brain 81 Blood 503 Neuroblastoma 9 Other (also 21 Primates bodymap) 166 bp exon 1 accession from embryonic stem cells cell lines H1, H7, andh9 166 bp exon 614 bp exon 3 accessions, some from breast (seen once) cornea (once), eye (once) prostate (once) 614 bp exon 499 bp exon 499 bp exon 1 accession from placenta normal 499 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 9004 bp 1198 aa 342 bp 5065 bp 2kb possibly including promoter 147712 bp 1kb
bAug10 8905 bp 1170 aa 327 bp 5065 bp 2kb possibly including promoter 147697 bp 1kb
cAug10 8878 bp 1161 aa 327 bp 5065 bp 2kb including Promoter 147697 bp 1kb
dAug10 978 bp 233 aa 278 bp 18 bp 2kb including Promoter 2385 bp 1kb
eAug10 918 bp 227 aa 106 bp 128 bp 2kb possibly including promoter 115809 bp 1kb
fAug10 639 bp 143 aa 208 bp 2kb including Promoter 105395 bp 1kb
gAug10 665 bp 139 aa 247 bp 2kb possibly including promoter 108432 bp 1kb
hAug10 1082 bp 86 aa 659 bp 162 bp 2kb including Promoter 4014 bp 1kb
iAug10 604 bp 76 aa 228 bp 145 bp 2kb possibly including promoter 108401 bp 1kb
jAug10-unspliced 2883 bp 43 aa 285 bp 2466 bp 2kb including Promoter 2883 bp 1kb
kAug10-unspliced 2136 bp 78 aa 1899 bp 2kb 2136 bp 1kb
lAug10-unspliced 848 bp 44 aa 646 bp 67 bp 2kb including Promoter 848 bp 1kb
mAug10-unspliced 614 bp 38 aa 500 bp 2kb 614 bp 1kb
nAug10-unspliced 585 bp 85 aa 70 bp 257 bp 2kb 585 bp 1kb
oAug10-unspliced 499 bp 82 aa 177 bp 73 bp 2kb 499 bp 1kb
pAug10 426 bp 29 aa 151 bp 185 bp 2kb 5003 bp 1kb

Gene neighbors and Navigator on chromosome 22q12.2 back to top
NEFH R C NF2 D C I R P CABP7 C R P UQCR10 R P MTMR3 D C R P HORMAD2 D C R P R CCDC157 C R SEC14L2andMTP18 D C I R P MGC20647 D C I R P THOC5 D C I R P NIPSNAP1 R C I R P ZMAT5 C I R P ASCC2 R D C I R P LIF D C I R P OSM C I R P TBC1D10AandGATSL3 C I R P SF3A1 C R P RNF215 R 100kb 0 NEFH, 207 accessions, 2 variants plobo, 2 accessions shawsubo, 1 accession NF2, 333 accessions, 18 variants CABP7, 29 accessions UQCR10, 442 accessions 4 variants MTMR3, 451 accessions 16 variants HORMAD2, 50 accessions 4 variants chorvaw, 11 accessions CCDC157, 32 accessions 6 variants SEC14L2andMTP18, 565 accessions 27 variants kleypor, 1 accession flerter, 3 accessions shorwaw, 3 accessions plarpor, 1 accession pleepor, 1 accession sherkee, 1 accession terfo, 1 accession blarkee, 1 accession bleekee, 1 accession blerkee, 1 accession skopor, 2 accessions bleykee, 1 accession sneewaw, 1 accession skarpor, 2 accessions skawpor, 1 accession skerpor, 2 accessions skeypor, 1 accession skorpor, 1 accession skabo, 5 accessions berwee, 1 accession florkee, 1 accession slawpor, 1 accession leefey, 8 accessions vorfo, 1 accession smypor, 1 accession smupor, 2 accessions lerfey, 1 accession beywee, 1 accession smopor, 1 accession smawpor, 1 accession smerpor, 2 accessions gluter, 1 accession snopor, 1 accession glawkee, 1 accession vowee, 1 accession klukee, 1 accession spypor, 1 accession spupor, 2 accessions speepor, 1 accession spoypor, 1 accession morfey, 12 accessions starpor, 3 accessions 2 variants steepor, 2 accessions moyfey, 8 accessions sterpor, 2 accessions zawee, 1 accession swypor, 3 accessions glarter, 4 accessions swopor, 1 accession glerwee, 1 accession plerwee, 1 accession chawfo, 1 accession sweepor, 1 accession stoywee, 1 accession plukee, 1 accession bapoy, 1 accession bawpoy, 2 accessions beepoy, 1 accession borpoy, 5 accessions doywer, 1 accession kawpa, 10 accessions shyfo, 1 accession norfey, 1 accession skykee, 1 accession gleeter, 2 accessions fupoy, 2 accessions farpoy, 1 accession ferpoy, 1 accession gower, 2 accessions feypoy, 3 accessions forpoy, 1 accession foypoy, 3 accessions nohera, 1 accession gopoy, 3 accessions garpoy, 1 accession kiheru, 2 accessions rerfey, 1 accession gerpoy, 1 accession sherfo, 1 accession jypoy, 1 accession kawer, 1 accession jarpoy, 1 accession rorfey, 4 accessions MGC20647, 4 accessions joypoy, 1 accession luwer, 1 accession sloykee, 1 accession smoykee, 1 accession keypoy, 1 accession lupoy, 1 accession lawpoy, 1 accession lerpoy, 1 accession leesey, 2 accessions bleyfo, 1 accession meypoy, 1 accession sneekee, 2 accessions shavaw, 7 accessions moypoy, 1 accession seefey, 1 accession nupoy, 1 accession nopoy, 2 accessions narpoy, 1 accession neypoy, 1 accession stawkee, 1 accession flufo, 1 accession pypoy, 4 accessions pupoy, 1 accession popoy, 2 accessions perpoy, 1 accession beeker, 1 accession fleefo, 1 accession peypoy, 1 accession tarfey, 2 accessions klorpor, 1 accession woywaw, 1 accession plypor, 1 accession tofo, 1 accession plupor, 1 accession glowaw, 6 accessions huwara, 1 accession plopor, 1 accession chykee, 1 accession kawfey, 1 accession ploypor, 1 accession charkee, 2 accessions nawara, 2 accessions skypor, 1 accession pleywaw, 2 accessions plarbo, 1 accession sharsubo, 3 accessions veefo, 1 accession snuwaw, 1 accession zoyvaw, 1 accession snerwaw, 1 accession fleykee, 1 accession sparwaw, 1 accession slapor, 1 accession chavaw, 3 accessions lawfey, 4 accessions slarpor, 1 accession floykee, 1 accession slerpor, 1 accession slorpor, 1 accession smarpor, 1 accession smeepor, 1 accession smeypor, 1 accession farwee, 1 accession smorpor, 1 accession glarkee, 1 accession sheesubo, 1 accession mawee, 1 accession smoypor, 6 accessions voyfo, 1 accession snypor, 2 accessions sorwee, 1 accession sneepor, 3 accessions snoypor, 1 accession spapor, 1 accession chovaw, 3 accessions tawara, 1 accession speypor, 2 accessions stopor, 1 accession stawpor, 1 accession wufo, 1 accession steypor, 1 accession woywee, 1 accession storpor, 3 accessions plykee, 1 accession sheysubo, 1 accession klywee, 1 accession sweypor, 3 accessions sworpor, 1 accession shorsubo, 1 accession charvaw, 1 accession bypoy, 1 accession plawkee, 1 accession bopoy, 1 accession chawvaw, 2 accessions cheefo, 1 accession shoysubo, 8 accessions plerkee, 1 accession dawpoy, 1 accession skorkee, 1 accession shawfo, 1 accession fopoy, 1 accession slerkee, 1 accession fawpoy, 1 accession ferwer, 1 accession gapoy, 2 accessions tehera, 1 accession slorkee, 1 accession geepoy, 1 accession jower, 2 accessions geypoy, 1 accession japoy, 1 accession slardoy, 1 accession kuwer, 1 accession jawpoy, 1 accession jerpoy, 1 accession koywer, 2 accessions kapoy, 1 accession blasubo, 2 accessions siwara, 1 accession rawror, 2 accessions kerpoy, 1 accession shoyfo, 1 accession temaru, 2 accessions koypoy, 1 accession blerfo, 1 accession leepoy, 1 accession marpoy, 1 accession nower, 1 accession keepa, 6 accessions kloter, 1 accession morpoy, 1 accession spokee, 1 accession klarter, 3 accessions klawter, 1 accession nypoy, 1 accession spawkee, 1 accession sperkee, 1 accession seywer, 1 accession sporkee, 1 accession blusubo, 1 accession norpoy, 1 accession spoykee, 1 accession starkee, 1 accession shyvaw, 2 accessions blosubo, 3 accessions swerkee, 1 accession blawer, 1 accession tufey, 7 accessions tofey, 1 accession doker, 1 accession RFPL1S, 62 accessions 3 variants THOC5, 395 accessions 19 variants NIPSNAP1, 316 accessions 9 variants fleyter, 9 accessions 2 variants ZMAT5, 200 accessions 9 variants ASCC2, 529 accessions 40 variants hisa, 9 accessions, 3 variants LIF, 93 accessions, 2 variants OSM, 52 accessions, 5 variants TBC1D10AandGATSL3, 540 accessions 35 variants SF3A1, 361 accessions 9 variants RNF215, 53 accessions 10 variants swarkee, 3 accessions ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               17 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j-u, .k-u, .l-u, .m-u, .n-u, .o-u, .p Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

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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