Homo sapiens complex locus ARMC2, encoding armadillo repeat containing 2.
TABLE OF CONTENTS / OPEN CLOSE ALL PARAGRAPHS
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 23 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, 1.0 times the average gene in this release. The sequence of this gene is defined by 116 GenBank accessions from 104 cDNA clones, some from testis (seen 26 times), lung (8), brain (6), eye (5), multiple sclerosis lesions (5), carcinoid (4), cerebellum (3) and 39 other tissues. We annotate structural defects or features in 3 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 43 distinct gt-ag introns. Transcription produces 24 different mRNAs, 23 alternatively spliced variants and 1 unspliced form. There are 7 probable alternative promotors, 10 non overlapping alternative last exons and 6 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 9 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron.
Function: There are 2 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Cleft Lip; Cleft Palate; Tooth Abnormalities). Proteins are expected to have molecular function (binding).
Protein coding potential: 13 spliced and the unspliced mRNAs putatively encode good proteins, altogether 14 different isoforms (5 complete, 6 COOH complete, 3 partial). The remaining 10 mRNA variants (10 spliced; 4 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 6, links to other databases and other names
Map: This gene ARMC2 maps on chromosome 6, at 6q21 according to Entrez Gene. In AceView, it covers 235.19 kb, from 109060487 to 109295675 (NCBI 37, August 2010), on the direct strand.
Links to: , manual annotations from GAD, PhosphoSite, the SNP view, gene overviews from Entrez Gene 84071, 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 ARMC2, bA787I22.1, DKFZp434P0714, RP11-787I22.1 or LOC84071, fuglorby. It has been described as armadillo repeat-containing protein 2.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Armc2 (e=6 10-47).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene gcy-7 (e=0.49), which may contain interesting functional annotation.
The closest A.thaliana genes, according to BlastP, are the AceView genes AT2G44900 (e=0.030), AT3G11840 (e=0.038), 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
ARMC2 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 2.52 5.79 4.71 0.48 3.57 0.55 3.57 2.35 14.3 18.8 10.8 1.26 0.72 1.78 1.10 0.39 2.52 0.59 0.96 2.70 13.3 0.51 6.21 2.35 1.26 0.89 1.35 0.18 2.05 8.78 6.21 3.57 10.1 15.3 7.13 6.65 1.10 1.18 2.19 8.78 6.21 3.33 4.10 5.40 2.52 5.40 5.79 3.82 2.70 2.70 12.4 6.21 2.90 1.91 1.55 1.55 1.91 0.72 5.79 9.41 3.10 2.19 10.1 3.57 2.05 5.79 10.8 8.78 8.19 5.04 5.04 2.35 4.71 8.78 9.41 3.57 3.10 10.8 12.4 6.65 4.39 5.04 12.4 16.4 11.6 5.79 6.65 6.21 6.65 13.3 4.10 4.39 4.39 1.26 5.79 10.8 1.45 7.64 4.39 1.10 5.79 2.35 9.41 5.04 2.19 8.19 2.35 2.52 1.91 8.19 7.13 5.04 10.8 18.8 1.26 3.10 4.10 9.41 4.71 10.1 7.64 7.64 6.21 5.40 5.04 0.89 3.10 2.19 1.91 4.39 13.3 8.19 4.39 9.41 2.35 1.02 0.09 2.19 0.42 7.13 5.40 5.79 1.55 7.64 2.90 10.8 4.71 5.79 49.7 6.65 7.64 3.33 2.05 1.26 0.59 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 ARMC2 5' 3' encoded on plus strand of chromosome 6 from 109,060,487 to 109,295,675 50 152 3 u 5800 8378 2924 3398 1446 1099 2087 809 2228 1801 3000 4035 4835 3649 3865 a [NM] 50 152 1 1 t 5800 1187 8378 2924 3398 1446 1099 2087 809 2228 1801 3000 4035 4835 3649 3865 b 220 8378 2924 3398 c 1 152 157 68 s d-u 1351 q 4835 142 n 6 152 1 l 86 55 vb 1 4035 4835 3649 3865 e 6 152 7 r 5800 f 152 2 vc 5800 1187 1169 g 5800 1169 h 50 8 o 949 i 2228 1801 k 50 152 7 2 p 8378 1711 m 9 4035 4835 3649 j 7 55 va 10kb 0 197 bp exon 7568 bp [gt-ag] intron 6 GenBank accessions 44 RNA-seq supporting reads 44 Neuroblastoma 128 bp exon 756 bp [gt-ag] intron 9 GenBank accessions 143 RNA-seq supporting reads 18 UHR pooled cells 12 Brain 6 Blood 107 Neuroblastoma (also 1 Primates bodymap) 102 bp exon 102 bp exon 8546 bp [gt-ag] intron 1 GenBank accession 2 RNA-seq supporting reads 2 Neuroblastoma (also 1 Primates bodymap) 169 bp exon 1 accession 169 bp exon 133 bp exon 5678 bp [gt-ag] intron 22 GenBank accessions 5778 RNA-seq supporting reads 458 UHR pooled cells 392 Brain 1053 Blood 3846 Neuroblastoma 29 Other (also 647 Primates bodymap) 261 bp exon 261 bp exon 3713 bp [gt-ag] intron 31 GenBank accessions 16246 RNA-seq supporting reads 1228 UHR pooled cells 1179 Brain 3108 Blood 10632 Neuroblastoma 99 Other (also 3623 Primates bodymap) 73 bp exon 10552 bp [gt-ag] intron 30 GenBank accessions 13314 RNA-seq supporting reads 1073 UHR pooled cells 1129 Brain 2171 Blood 8879 Neuroblastoma 62 Other (also 1708 Primates bodymap) 172 bp exon 7147 bp [gt-ag] intron 18 GenBank accessions 8360 RNA-seq supporting reads 408 UHR pooled cells 763 Brain 2170 Blood 4979 Neuroblastoma 40 Other (also 1977 Primates bodymap) 208 bp exon 18116 bp [gt-ag] intron 15 GenBank accessions 2909 RNA-seq supporting reads 173 UHR pooled cells 146 Brain 1020 Blood 1557 Neuroblastoma 13 Other (also 1613 Primates bodymap) 77 bp exon 5150 bp [gt-ag] intron 12 GenBank accessions 3386 RNA-seq supporting reads 270 UHR pooled cells 195 Brain 951 Blood 1951 Neuroblastoma 19 Other (also 2128 Primates bodymap) 99 bp exon 4437 bp [gt-ag] intron 6 GenBank accessions 1440 RNA-seq supporting reads 128 UHR pooled cells 164 Brain 348 Blood 779 Neuroblastoma 21 Other (also 1662 Primates bodymap) 176 bp exon 6493 bp [gt-ag] intron 6 GenBank accessions 1093 RNA-seq supporting reads 71 UHR pooled cells 107 Brain 284 Blood 611 Neuroblastoma 20 Other (also 1131 Primates bodymap) 103 bp exon 1333 bp [gt-ag] intron 6 GenBank accessions 2081 RNA-seq supporting reads 188 UHR pooled cells 215 Brain 631 Blood 1012 Neuroblastoma 35 Other (also 2957 Primates bodymap) 224 bp exon 15529 bp [gt-ag] intron 6 GenBank accessions 803 RNA-seq supporting reads 73 UHR pooled cells 88 Brain 147 Blood 475 Neuroblastoma 20 Other (also 1078 Primates bodymap) 146 bp exon 8666 bp [gt-ag] intron 7 GenBank accessions 2221 RNA-seq supporting reads 198 UHR pooled cells 231 Brain 476 Blood 1274 Neuroblastoma 42 Other (also 2169 Primates bodymap) 100 bp exon 16033 bp [gt-ag] intron 7 GenBank accessions 1794 RNA-seq supporting reads 150 UHR pooled cells 221 Brain 329 Blood 1084 Neuroblastoma 10 Other (also 1447 Primates bodymap) 319 bp exon 8220 bp [gt-ag] intron 6 GenBank accessions 2994 RNA-seq supporting reads 266 UHR pooled cells 277 Brain 395 Blood 2016 Neuroblastoma 40 Other (also 1206 Primates bodymap) 123 bp exon 319 bp [gt-ag] intron 9 GenBank accessions 4026 RNA-seq supporting reads 447 UHR pooled cells 523 Brain 379 Blood 2623 Neuroblastoma 54 Other (also 1167 Primates bodymap) 114 bp exon 2052 bp [gt-ag] intron 12 GenBank accessions 4823 RNA-seq supporting reads 506 UHR pooled cells 625 Brain 590 Blood 3048 Neuroblastoma 54 Other (also 939 Primates bodymap) 133 bp exon 667 bp [gt-ag] intron 11 GenBank accessions 3638 RNA-seq supporting reads 376 UHR pooled cells 462 Brain 439 Blood 2307 Neuroblastoma 54 Other (also 1318 Primates bodymap) 161 bp exon 8216 bp [gt-ag] intron 12 GenBank accessions 3853 RNA-seq supporting reads 339 UHR pooled cells 543 Brain 464 Blood 2465 Neuroblastoma 42 Other (also 1660 Primates bodymap) 1116 bp exon 36 accessions, NM_032131.4 some from testis (seen 13 times) lung (4), breast carcinoma (2) multiple sclerosis lesions (2) tongue, tumor tissue (2) capped 5' end, 5 accessions Validated 3' end, 4 accessions Validated 3' end, 3 accessions 1116 bp exon 32 bp exon 7568 bp [gt-ag] intron 6 GenBank accessions 44 RNA-seq supporting reads 44 Neuroblastoma 128 bp exon 128 bp exon 756 bp [gt-ag] intron 9 GenBank accessions 143 RNA-seq supporting reads 18 UHR pooled cells 12 Brain 6 Blood 107 Neuroblastoma (also 1 Primates bodymap) 102 bp exon 6592 bp [gt-ag] intron 1 GenBank accession (also 1 Primates bodymap) 274 bp exon 274 bp exon 1121 bp [gt-ag] intron 1 GenBank accession 1 accession 66 bp exon 131 bp exon 5678 bp [gt-ag] intron 22 GenBank accessions 5778 RNA-seq supporting reads 458 UHR pooled cells 392 Brain 1053 Blood 3846 Neuroblastoma 29 Other (also 647 Primates bodymap) 261 bp exon 14338 bp [gt-ag] intron 4 GenBank accessions 1183 RNA-seq supporting reads 138 UHR pooled cells 232 Brain 113 Blood 687 Neuroblastoma 13 Other (also 806 Primates bodymap) 172 bp exon 7147 bp [gt-ag] intron 18 GenBank accessions 8360 RNA-seq supporting reads 408 UHR pooled cells 763 Brain 2170 Blood 4979 Neuroblastoma 40 Other (also 1977 Primates bodymap) 208 bp exon 208 bp exon 18116 bp [gt-ag] intron 15 GenBank accessions 2909 RNA-seq supporting reads 173 UHR pooled cells 146 Brain 1020 Blood 1557 Neuroblastoma 13 Other (also 1613 Primates bodymap) 77 bp exon 5150 bp [gt-ag] intron 12 GenBank accessions 3386 RNA-seq supporting reads 270 UHR pooled cells 195 Brain 951 Blood 1951 Neuroblastoma 19 Other (also 2128 Primates bodymap) 99 bp exon 4437 bp [gt-ag] intron 6 GenBank accessions 1440 RNA-seq supporting reads 128 UHR pooled cells 164 Brain 348 Blood 779 Neuroblastoma 21 Other (also 1662 Primates bodymap) 176 bp exon 6493 bp [gt-ag] intron 6 GenBank accessions 1093 RNA-seq supporting reads 71 UHR pooled cells 107 Brain 284 Blood 611 Neuroblastoma 20 Other (also 1131 Primates bodymap) 103 bp exon 1333 bp [gt-ag] intron 6 GenBank accessions 2081 RNA-seq supporting reads 188 UHR pooled cells 215 Brain 631 Blood 1012 Neuroblastoma 35 Other (also 2957 Primates bodymap) 224 bp exon 15529 bp [gt-ag] intron 6 GenBank accessions 803 RNA-seq supporting reads 73 UHR pooled cells 88 Brain 147 Blood 475 Neuroblastoma 20 Other (also 1078 Primates bodymap) 146 bp exon 8666 bp [gt-ag] intron 7 GenBank accessions 2221 RNA-seq supporting reads 198 UHR pooled cells 231 Brain 476 Blood 1274 Neuroblastoma 42 Other (also 2169 Primates bodymap) 100 bp exon 16033 bp [gt-ag] intron 7 GenBank accessions 1794 RNA-seq supporting reads 150 UHR pooled cells 221 Brain 329 Blood 1084 Neuroblastoma 10 Other (also 1447 Primates bodymap) 319 bp exon 8220 bp [gt-ag] intron 6 GenBank accessions 2994 RNA-seq supporting reads 266 UHR pooled cells 277 Brain 395 Blood 2016 Neuroblastoma 40 Other (also 1206 Primates bodymap) 123 bp exon 319 bp [gt-ag] intron 9 GenBank accessions 4026 RNA-seq supporting reads 447 UHR pooled cells 523 Brain 379 Blood 2623 Neuroblastoma 54 Other (also 1167 Primates bodymap) 114 bp exon 2052 bp [gt-ag] intron 12 GenBank accessions 4823 RNA-seq supporting reads 506 UHR pooled cells 625 Brain 590 Blood 3048 Neuroblastoma 54 Other (also 939 Primates bodymap) 133 bp exon 667 bp [gt-ag] intron 11 GenBank accessions 3638 RNA-seq supporting reads 376 UHR pooled cells 462 Brain 439 Blood 2307 Neuroblastoma 54 Other (also 1318 Primates bodymap) 161 bp exon 8216 bp [gt-ag] intron 12 GenBank accessions 3853 RNA-seq supporting reads 339 UHR pooled cells 543 Brain 464 Blood 2465 Neuroblastoma 42 Other (also 1660 Primates bodymap) 426 bp exon 3 accessions, some from amygdala (seen 2 times) embryonic stem (once) capped 5' end, 1 accession Validated 3' end, 1 accession 426 bp exon 127 bp exon 5403 bp [gt-ag] intron 4 GenBank accessions 216 RNA-seq supporting reads 5 UHR pooled cells 39 Brain 18 Blood 152 Neuroblastoma 2 Other (also 11 Primates bodymap) 261 bp exon 261 bp exon 3713 bp [gt-ag] intron 31 GenBank accessions 16246 RNA-seq supporting reads 1228 UHR pooled cells 1179 Brain 3108 Blood 10632 Neuroblastoma 99 Other (also 3623 Primates bodymap) 73 bp exon 10552 bp [gt-ag] intron 30 GenBank accessions 13314 RNA-seq supporting reads 1073 UHR pooled cells 1129 Brain 2171 Blood 8879 Neuroblastoma 62 Other (also 1708 Primates bodymap) 172 bp exon 7147 bp [gt-ag] intron 18 GenBank accessions 8360 RNA-seq supporting reads 408 UHR pooled cells 763 Brain 2170 Blood 4979 Neuroblastoma 40 Other (also 1977 Primates bodymap) 208 bp exon 18116 bp [gt-ag] intron 15 GenBank accessions 2909 RNA-seq supporting reads 173 UHR pooled cells 146 Brain 1020 Blood 1557 Neuroblastoma 13 Other (also 1613 Primates bodymap) 77 bp exon 5150 bp [gt-ag] intron 12 GenBank accessions 3386 RNA-seq supporting reads 270 UHR pooled cells 195 Brain 951 Blood 1951 Neuroblastoma 19 Other (also 2128 Primates bodymap) 450 bp exon 12 accessions, some from testis (seen 8 times) eye (once), retinoblastoma (once) Validated 3' end, 1 accession 450 bp exon 140 bp exon 19994 bp [gt-ag] intron 1 GenBank accession (also 3 Primates bodymap) 128 bp exon 756 bp [gt-ag] intron 9 GenBank accessions 143 RNA-seq supporting reads 18 UHR pooled cells 12 Brain 6 Blood 107 Neuroblastoma (also 1 Primates bodymap) 102 bp exon 102 bp exon 21784 bp [gt-ag] intron 1 GenBank accession 156 RNA-seq supporting reads 4 UHR pooled cells 11 Brain 20 Blood 121 Neuroblastoma (also 27 Primates bodymap) 164 bp exon 71873 bp [gt-ag] fuzzy intron 1 GenBank accession 67 RNA-seq supporting reads 19 Brain 4 Blood 43 Neuroblastoma 1 Other 210 bp exon 1 accession from stomach adenocarcinoma 210 bp exon 21 bp uORF 2155 bp exon 2155 bp exon 2155 bp exon 2155 bp exon Sequence gap 2164 bp 20 accessions, some from carcinoid (seen 4 times) eye (4), lung (4), cerebellum (3) retina (2) Validated 3' end, 3 accessions 1693 bp exon 1156 bp exon 1156 bp exon 1156 bp exon 24799 bp [gt-ag] intron 2 GenBank accessions 1349 RNA-seq supporting reads 116 UHR pooled cells 120 Brain 167 Blood 929 Neuroblastoma 17 Other (also 145 Primates bodymap) 6 accessions, some from brain (seen 2 times) hippocampus (once), multiple sclerosis lesions (once) substantia nigra (once) capped 5' end, 2 accessions Validated 3' end, 1 accession 74 bp exon 102 bp exon 102 bp exon 2052 bp [gt-ag] intron 12 GenBank accessions 4823 RNA-seq supporting reads 506 UHR pooled cells 625 Brain 590 Blood 3048 Neuroblastoma 54 Other (also 939 Primates bodymap) 133 bp exon 9044 bp [gt-ag] intron 2 GenBank accessions 140 RNA-seq supporting reads 8 UHR pooled cells 24 Brain 13 Blood 94 Neuroblastoma 1 Other (also 2 Primates bodymap) 177 bp exon 2 accessions, some from breast (seen 2 times) 177 bp exon 164 bp exon 94 bp [gt-ag] intron 2 GenBank accessions 4 RNA-seq supporting reads 2 UHR pooled cells 2 Neuroblastoma 128 bp exon 128 bp exon 756 bp [gt-ag] intron 9 GenBank accessions 143 RNA-seq supporting reads 18 UHR pooled cells 12 Brain 6 Blood 107 Neuroblastoma (also 1 Primates bodymap) 102 bp exon 8509 bp [gt-ag] intron 1 GenBank accession 206 bp exon 1 accession 206 bp exon 124 bp exon 3097 bp [gt-ag] intron 1 GenBank accession 85 RNA-seq supporting reads 26 UHR pooled cells 5 Blood 54 Neuroblastoma (also 9 Primates bodymap) 112 bp exon 2469 bp [gt-ag] intron 2 GenBank accessions 53 RNA-seq supporting reads 16 UHR pooled cells 4 Brain 12 Blood 21 Neuroblastoma (also 39 Primates bodymap) 261 bp exon 261 bp exon 3713 bp [gt-ag] intron 31 GenBank accessions 16246 RNA-seq supporting reads 1228 UHR pooled cells 1179 Brain 3108 Blood 10632 Neuroblastoma 99 Other (also 3623 Primates bodymap) 47 bp exon 1 accession from testis capped 5' end, 1 accession 47 bp exon 14 bp exon 14 bp exon 644 bp [gt-ag] intron 1 GenBank accession (also 2 Primates bodymap) 123 bp exon 319 bp [gt-ag] intron 9 GenBank accessions 4026 RNA-seq supporting reads 447 UHR pooled cells 523 Brain 379 Blood 2623 Neuroblastoma 54 Other (also 1167 Primates bodymap) 114 bp exon 2052 bp [gt-ag] intron 12 GenBank accessions 4823 RNA-seq supporting reads 506 UHR pooled cells 625 Brain 590 Blood 3048 Neuroblastoma 54 Other (also 939 Primates bodymap) 133 bp exon 667 bp [gt-ag] intron 11 GenBank accessions 3638 RNA-seq supporting reads 376 UHR pooled cells 462 Brain 439 Blood 2307 Neuroblastoma 54 Other (also 1318 Primates bodymap) 161 bp exon 8216 bp [gt-ag] intron 12 GenBank accessions 3853 RNA-seq supporting reads 339 UHR pooled cells 543 Brain 464 Blood 2465 Neuroblastoma 42 Other (also 1660 Primates bodymap) 276 bp exon 1 accession from brain from medulla 276 bp exon 159 bp exon 159 bp exon 94 bp [gt-ag] intron 2 GenBank accessions 4 RNA-seq supporting reads 2 UHR pooled cells 2 Neuroblastoma 128 bp exon 128 bp exon 756 bp [gt-ag] intron 9 GenBank accessions 143 RNA-seq supporting reads 18 UHR pooled cells 12 Brain 6 Blood 107 Neuroblastoma (also 1 Primates bodymap) 102 bp exon 7987 bp [gt-ag] intron 4 GenBank accessions 3 RNA-seq supporting reads 3 Neuroblastoma 1 accession 728 bp exon 110 bp exon 5678 bp [gt-ag] intron 22 GenBank accessions 5778 RNA-seq supporting reads 458 UHR pooled cells 392 Brain 1053 Blood 3846 Neuroblastoma 29 Other (also 647 Primates bodymap) 261 bp exon 3713 bp [gt-ag] intron 31 GenBank accessions 16246 RNA-seq supporting reads 1228 UHR pooled cells 1179 Brain 3108 Blood 10632 Neuroblastoma 99 Other (also 3623 Primates bodymap) 73 bp exon 10552 bp [gt-ag] intron 30 GenBank accessions 13314 RNA-seq supporting reads 1073 UHR pooled cells 1129 Brain 2171 Blood 8879 Neuroblastoma 62 Other (also 1708 Primates bodymap) 284 bp exon 1 accession from adrenal gland 284 bp exon 85 bp exon 85 bp exon 756 bp [gt-ag] intron 9 GenBank accessions 143 RNA-seq supporting reads 18 UHR pooled cells 12 Brain 6 Blood 107 Neuroblastoma (also 1 Primates bodymap) 102 bp exon 8462 bp [gt-ag] intron 1 GenBank accession 1 RNA-seq supporting reads 1 UHR pooled cells 140 bp exon 1 accession 140 bp exon 98 bp exon 5678 bp [gt-ag] intron 22 GenBank accessions 5778 RNA-seq supporting reads 458 UHR pooled cells 392 Brain 1053 Blood 3846 Neuroblastoma 29 Other (also 647 Primates bodymap) 261 bp exon 14338 bp [gt-ag] intron 4 GenBank accessions 1183 RNA-seq supporting reads 138 UHR pooled cells 232 Brain 113 Blood 687 Neuroblastoma 13 Other (also 806 Primates bodymap) 90 bp exon 7229 bp [gt-ag] intron 3 GenBank accessions 1166 RNA-seq supporting reads 62 UHR pooled cells 114 Brain 265 Blood 721 Neuroblastoma 4 Other (also 24 Primates bodymap) 136 bp exon 1 accession from brain from frontal lobe 136 bp exon 62 bp exon 5678 bp [gt-ag] intron 22 GenBank accessions 5778 RNA-seq supporting reads 458 UHR pooled cells 392 Brain 1053 Blood 3846 Neuroblastoma 29 Other (also 647 Primates bodymap) 261 bp exon 3713 bp [gt-ag] intron 31 GenBank accessions 16246 RNA-seq supporting reads 1228 UHR pooled cells 1179 Brain 3108 Blood 10632 Neuroblastoma 99 Other (also 3623 Primates bodymap) 73 bp exon 10552 bp [gt-ag] intron 30 GenBank accessions 13314 RNA-seq supporting reads 1073 UHR pooled cells 1129 Brain 2171 Blood 8879 Neuroblastoma 62 Other (also 1708 Primates bodymap) 90 bp exon 7229 bp [gt-ag] intron 3 GenBank accessions 1166 RNA-seq supporting reads 62 UHR pooled cells 114 Brain 265 Blood 721 Neuroblastoma 4 Other (also 24 Primates bodymap) 260 bp exon 2 accessions, some from brain (seen once) 260 bp exon 197 bp exon 7568 bp [gt-ag] intron 6 GenBank accessions 44 RNA-seq supporting reads 44 Neuroblastoma 128 bp exon 128 bp exon 7450 bp [gt-ag] intron 1 GenBank accession 7 RNA-seq supporting reads 7 Neuroblastoma 1461 bp exon 1 accession 1461 bp exon 148 bp exon 5664 bp [gt-ag] intron 4 GenBank accessions 945 RNA-seq supporting reads 48 UHR pooled cells 122 Brain 79 Blood 691 Neuroblastoma 5 Other (also 13 Primates bodymap) 261 bp exon 261 bp exon 3713 bp [gt-ag] intron 31 GenBank accessions 16246 RNA-seq supporting reads 1228 UHR pooled cells 1179 Brain 3108 Blood 10632 Neuroblastoma 99 Other (also 3623 Primates bodymap) 73 bp exon 10552 bp [gt-ag] intron 30 GenBank accessions 13314 RNA-seq supporting reads 1073 UHR pooled cells 1129 Brain 2171 Blood 8879 Neuroblastoma 62 Other (also 1708 Primates bodymap) 136 bp exon 4 accessions, some from testis (seen 2 times) uterus (once) capped 5' end, 2 accessions 136 bp exon 351 bp exon 351 bp exon 24 bp uORF 351 bp exon 351 bp exon 8666 bp [gt-ag] intron 7 GenBank accessions 2221 RNA-seq supporting reads 198 UHR pooled cells 231 Brain 476 Blood 1274 Neuroblastoma 42 Other (also 2169 Primates bodymap) 100 bp exon 100 bp exon 16033 bp [gt-ag] intron 7 GenBank accessions 1794 RNA-seq supporting reads 150 UHR pooled cells 221 Brain 329 Blood 1084 Neuroblastoma 10 Other (also 1447 Primates bodymap) 189 bp exon 1 accession from adipose 189 bp exon 196 bp exon 7568 bp [gt-ag] intron 6 GenBank accessions 44 RNA-seq supporting reads 44 Neuroblastoma 128 bp exon 128 bp exon 756 bp [gt-ag] intron 9 GenBank accessions 143 RNA-seq supporting reads 18 UHR pooled cells 12 Brain 6 Blood 107 Neuroblastoma (also 1 Primates bodymap) 102 bp exon 7987 bp [gt-ag] intron 4 GenBank accessions 3 RNA-seq supporting reads 3 Neuroblastoma 1180 bp exon 1180 bp exon 225 bp [gt-ag] intron 2 GenBank accessions 3 accessions 147 bp exon 18 bp exon 18 bp exon 7147 bp [gt-ag] intron 18 GenBank accessions 8360 RNA-seq supporting reads 408 UHR pooled cells 763 Brain 2170 Blood 4979 Neuroblastoma 40 Other (also 1977 Primates bodymap) 208 bp exon 3577 bp [gt-ag] intron 1 GenBank accession 1710 RNA-seq supporting reads 57 UHR pooled cells 132 Brain 121 Blood 1399 Neuroblastoma 1 Other (also 12 Primates bodymap) 329 bp exon 3 accessions 329 bp exon 61 bp exon 2052 bp [gt-ag] intron 1 GenBank accession 8 RNA-seq supporting reads 4 Blood 3 Neuroblastoma 1 Other (also 3 Primates bodymap) 123 bp exon 319 bp [gt-ag] intron 9 GenBank accessions 4026 RNA-seq supporting reads 447 UHR pooled cells 523 Brain 379 Blood 2623 Neuroblastoma 54 Other (also 1167 Primates bodymap) 114 bp exon 114 bp exon 2052 bp [gt-ag] intron 12 GenBank accessions 4823 RNA-seq supporting reads 506 UHR pooled cells 625 Brain 590 Blood 3048 Neuroblastoma 54 Other (also 939 Primates bodymap) 133 bp exon 667 bp [gt-ag] intron 11 GenBank accessions 3638 RNA-seq supporting reads 376 UHR pooled cells 462 Brain 439 Blood 2307 Neuroblastoma 54 Other (also 1318 Primates bodymap) 143 bp exon 1 accession from bone marrow from from acute myelogenous leukemia 143 bp exon 109 bp exon 2822 bp [gt-ag] intron 1 GenBank accession 6 RNA-seq supporting reads 6 Neuroblastoma 112 bp exon 2469 bp [gt-ag] intron 2 GenBank accessions 53 RNA-seq supporting reads 16 UHR pooled cells 4 Brain 12 Blood 21 Neuroblastoma (also 39 Primates bodymap) 261 bp exon 261 bp exon 3713 bp [gt-ag] intron 31 GenBank accessions 16246 RNA-seq supporting reads 1228 UHR pooled cells 1179 Brain 3108 Blood 10632 Neuroblastoma 99 Other (also 3623 Primates bodymap) 73 bp exon 10552 bp [gt-ag] intron 30 GenBank accessions 13314 RNA-seq supporting reads 1073 UHR pooled cells 1129 Brain 2171 Blood 8879 Neuroblastoma 62 Other (also 1708 Primates bodymap) 5 bp exon 1 accession from testis capped 5' end, 1 accession 5 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 3738 bp 867 aa 176 bp 958 bp 2kb including Promoter 126059 bp 1kb
bAug10 2973 bp 702 aa 596 bp 268 bp 2kb including Promoter 125367 bp 1kb
cAug10 1368 bp 322 aa 170 bp 229 bp 2kb possibly including promoter 51449 bp 1kb
dAug10-unspliced 4547 bp 312 aa 532 bp 3076 bp 18 bp 2kb possibly including promoter 6012 bp 1kb
eAug10 821 bp 233 aa 118 bp 2kb 12719 bp 1kb
fAug10 728 bp 209 aa 98 bp 2kb 20671 bp 1kb
gAug10 585 bp 191 aa 9 bp 2kb 27830 bp 1kb
hAug10 746 bp 173 aa 224 bp 2kb 27918 bp 1kb
iAug10 618 bp 142 aa 191 bp 2kb including Promoter 20547 bp 1kb
jAug10 574 bp 120 aa 213 bp 2kb possibly including promoter 5664 bp 1kb
kAug10 640 bp 115 aa 295 bp 21 bp 2kb possibly including promoter 25339 bp 1kb
lAug10 600 bp 104 aa 221 bp 64 bp 2kb possibly including promoter 9959 bp 1kb
mAug10 555 bp 84 aa 298 bp 2kb 11279 bp 1kb
nAug10 412 bp 78 aa 173 bp 2kb 11508 bp 1kb
oAug10 1786 bp 63 aa 254 bp 1340 bp 2kb 16804 bp 1kb
pAug10 1753 bp 57 aa 253 bp 1326 bp 2kb 18289 bp 1kb
qAug10 1230 bp 46 aa 120 bp 969 bp 2kb including Promoter 26029 bp 1kb
rAug10 1117 bp 60 aa 933 bp 2kb 9954 bp 1kb
sAug10 744 bp 85 aa 294 bp 192 bp 2kb 115151 bp 1kb
tAug10 602 bp 57 aa 89 bp 339 bp 2kb 16639 bp 1kb
uAug10 596 bp 64 aa 337 bp 64 bp 2kb 17466 bp 1kb
vaAug10 560 bp 98 aa 264 bp 2kb including Promoter 20116 bp 1kb
vbAug10 544 bp 88 aa 279 bp 2kb including Promoter 9823 bp 1kb
vcAug10 327 bp 61 aa 139 bp 2kb 9545 bp 1kb

Gene neighbors and Navigator on chromosome 6q21 back to top
LACE1 C R P C FOXO3 D C I R P ARMC2 C R P R C6orf182 C R P FLJ37396 C R P CCDC162 D C R P C CCDC162.1 D C R P C C ZNF259P1 D C I R P SESN1 C 100kb 0 LACE1, 58 accessions, 8 variants wamame, 1 accession FOXO3, 429 accessions 11 variants ARMC2, 110 accessions 24 variants gleyjey, 12 accessions 3 variants C6orf182, 144 accessions 21 variants FLJ37396, 12 accessions 6 variants CCDC162, 7 accessions 3 variants klyjey, 4 accessions CCDC162.1, 26 accessions 8 variants loysporby, 1 accession slawgleyby, 1 accession sleegleyby, 2 accessions slergleyby, 1 accession pofly, 3 accessions teyplubu, 1 accession slorgleyby, 1 accession nartawby, 1 accession florspobu, 1 accession torplubu, 1 accession sloygleyby, 1 accession nawtawby, 1 accession smagleyby, 1 accession smugleyby, 1 accession tisiya, 1 accession smawgleyby, 10 accessions 2 variants smargleyby, 1 accession toyplubu, 1 accession spuvabo, 1 accession marsporby, 1 accession tosnobu, 14 accessions snugleyby, 2 accessions flawjey, 15 accessions snawgleyby, 1 accession sneegleyby, 1 accession sneygleyby, 1 accession vuplubu, 1 accession snoygleyby, 5 accessions spygleyby, 1 accession spugleyby, 2 accessions sparvabo, 1 accession glawspobu, 1 accession teytawby, 1 accession peyfly, 6 accessions speygleyby, 2 accessions spawvabo, 20 accessions ramame, 1 accession stagleyby, 2 accessions vytawby, 1 accession vutawby, 2 accessions porfly, 5 accessions stugleyby, 1 accession gleyspobu, 2 accessions mawayu, 1 accession glorspobu, 2 accessions stawgleyby, 7 accessions steegleyby, 7 accessions stergleyby, 3 accessions gloyspobu, 1 accession yanore, 5 accessions stoygleyby, 1 accession florjey, 5 accessions waplubu, 1 accession poyfly, 6 accessions klaspobu, 1 accession swygleyby, 1 accession swogleyby, 1 accession swawgleyby, 1 accession rafly, 2 accessions sweegleyby, 1 accession moysporby, 6 accessions sworgleyby, 1 accession kluspobu, 2 accessions glajey, 7 accessions werplubu, 1 accession swoygleyby, 1 accession chyplubu, 1 accession speevabo, 2 accessions rufly, 3 accessions klarspobu, 2 accessions boglorby, 2 accessions barglorby, 5 accessions bawglorby, 1 accession smeyjee, 2 accessions beyglorby, 3 accessions cheeplubu, 1 accession glyjey, 1 accession boyglorby, 1 accession daglorby, 1 accession glujey, 9 accessions smorjee, 1 accession duglorby, 1 accession doglorby, 1 accession darglorby, 1 accession cheyplubu, 2 accessions deeglorby, 1 accession derglorby, 1 accession kloyspobu, 1 accession reefly, 11 accessions blortawby, 1 accession deyglorby, 2 accessions plaspobu, 1 accession dorglorby, 1 accession doyglorby, 1 accession fyglorby, 1 accession narsporby, 2 accessions foglorby, 1 accession farglorby, 1 accession feeglorby, 1 accession ferglorby, 1 accession rorfly, 2 accessions blawplubu, 1 accession klawplubu, 1 accession forglorby, 2 accessions foyglorby, 1 accession gaglorby, 2 accessions glytawby, 1 accession glutawby, 1 accession guglorby, 1 accession goglorby, 1 accession garglorby, 1 accession geyglorby, 3 accessions jaglorby, 2 accessions glawjey, 5 accessions gloytawby, 1 accession skorplubu, 2 accessions jarglorby, 1 accession plytawby, 1 accession jeeglorby, 1 accession slaplubu, 1 accession smaplubu, 2 accessions skospobu, 1 accession joyglorby, 1 accession kuglorby, 2 accessions koglorby, 1 accession karglorby, 1 accession speyvabo, 2 accessions skerspobu, 1 accession sneyplubu, 1 accession spotawby, 1 accession gloyjey, 5 accessions spartawby, 1 accession sufly, 8 accessions sofly, 7 accessions laglorby, 4 accessions luglorby, 1 accession loglorby, 1 accession stytawby, 1 accession slawfloybu, 2 accessions snorplubu, 1 accession lerglorby, 1 accession snoyplubu, 1 accession peysporby, 2 accessions leyglorby, 2 accessions slorspobu, 1 accession loyglorby, 1 accession maglorby, 1 accession myglorby, 1 accession moglorby, 2 accessions swuplubu, 1 accession swytawby, 1 accession slogleyby, 4 accessions natawby, 1 accession peyplubu, 1 accession suplubu, 1 accession flawspobu, 1 accession koyome, 1 accession soplubu, 1 accession smygleyby, 1 accession glaspobu, 3 accessions smeegleyby, 1 accession sartawby, 1 accession glyspobu, 1 accession smergleyby, 1 accession smorgleyby, 1 accession smoygleyby, 1 accession snagleyby, 3 accessions snygleyby, 1 accession snogleyby, 5 accessions snergleyby, 2 accessions spagleyby, 1 accession spogleyby, 3 accessions gleespobu, 1 accession spawgleyby, 1 accession spergleyby, 1 accession sporgleyby, 4 accessions voplubu, 2 accessions storgleyby, 2 accessions veyplubu, 1 accession swugleyby, 1 accession swargleyby, 1 accession veytawby, 1 accession sweygleyby, 3 accessions ryfly, 4 accessions byglorby, 2 accessions chawplubu, 1 accession yunore, 30 accessions beeglorby, 1 accession berglorby, 3 accessions slafloybu, 1 accession borglorby, 1 accession dyglorby, 2 accessions dawglorby, 2 accessions zotawby, 1 accession plyspobu, 1 accession reyfly, 1 accession faglorby, 1 accession glarjey, 6 accessions sheyplubu, 1 accession pluspobu, 1 accession gyglorby, 1 accession kleeplubu, 1 accession gerglorby, 1 accession plawspobu, 2 accessions pleespobu, 1 accession jyglorby, 1 accession plorspobu, 1 accession rimame, 2 accessions rumame, 2 accessions, 2 variants spervabo, 1 accession klortawby, 1 accession smartawby, 1 accession royfly, 2 accessions skaspobu, 1 accession skyspobu, 1 accession jerglorby, 1 accession skuspobu, 1 accession slyplubu, 1 accession sleeplubu, 1 accession jeyglorby, 6 accessions snawplubu, 1 accession smeytawby, 1 accession jorglorby, 1 accession skawspobu, 1 accession kaglorby, 2 accessions kyglorby, 1 accession skeyspobu, 1 accession sporvabo, 1 accession korglorby, 1 accession lyglorby, 1 accession stoytawby, 3 accessions 2 variants sparplubu, 1 accession sleyspobu, 1 accession stuplubu, 2 accessions tasiya, 1 accession ZNF259P1, 1 accession SESN1, 339 accessions 15 variants jawglorby, 1 accession ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               2 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d-u, .e, .f, .g, .h, .i, .j, .k, .l, .m, .n, .o, .p, .q, .r, .s, .t, .u, .va, .vb, .vc 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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