Sequence
atgc intronic sequence ATGC exonic sequence...gaacacctgcatgtgggcccacagctttgtgtatattctgagcctgtggatctgctttatgctttgccagctgtttcctaaccagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g03460.1 (Oryza sativa), 3'ss of exon 2
-gaacacctgcatgtgggcc-cacagctttgtgtatattctgagcctgtggatctgctttatgctttgccag-------------ctgtttcctaaccagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA
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ggttcataaaaagttgagcagcaaagtttttaccagttcaagagtttgtactgttaaatttcactatagcaagcgaataggattcctcttgcttatgcagTATGTGTTTTGCCAGAAATTGCATACAGTTGGCCAATACTTCTTGGTGGGCAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATTTCTATTAGTAG---------------
upper sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G053711_T05 (Zea mays), 3'ss of exon 2
gaacacctgcatgtgggccc--acagctttgtgtatattctgagcctgtggatctgctttatgctttgccagctgtttcctaac-cagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA
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-atttttattattgaagtccttacaaggtcatgt-cgttct-agtgtttctatttctttgctaccagtaggaccctctcctgatatacagcgtatcttggcagGCATAGCATACAATTGGCCAATTCTTCTTGGTGGACAAGCTCACTGGACAGTTGGACTTGTAGCAACCTTGATGGCTATTAGTAGCATCATTGCTGCTGA
upper sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G30030.2 (Glycine max), 3'ss of exon 4
gaacacctgcatgtgggcccac-agctttgtgtatattctgagcctgtggatctgctttatgctttgccagctgtttcctaaccagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA
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-tatattagtatttatattcattagcataattttaaactccctattttctatgtagcttgaattaggacctgtatgttcttaatagattattattttgtagAAATAGGAGCAACATGGCCTATACTCCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGTAACTTTGATTACCATAAGCAGCGTAATTGCAGCTGA
upper sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G06190.1 (Glycine max), 3'ss of exon 3
gaacacctgcatgtgggcccacagctttgtgtatattctgagcctgtggatctgctttatgctttg--ccag---ctgtttcctaaccagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA-
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------atatattattatttatattcattagcataattttgaactccctattttctctgtggcttgaattaggccctatgtccttaatagattattattttgtaggAATAGGAGCAACATGGCCTATACTTCTTGGTGGCCAAGCTCATTGGACAGTTGGTCTTGTGGCAACTTTGATTACCATAAGCAGCGTTATTGCAGCGGAT
upper sequence: Vv15s0048g00240.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G45150.2 (Arabidopsis thaliana), 3'ss of exon 3
--gaacacctgcatgtgggccc-----acagcttt---gtgtatatt-ctgagcctgtgga-tctgctttatgctttgccagctgtt-tcctaaccagggttattt---------ttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA
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gcaagctctcgccttttctcctcttttatatctctaaagttcagattattgaggccaagctctctgctttgtcctacttcagatgtccttttgaccagttttttttcctattgtttctatagGTATCGGAAGGACATGGCCAATTCTTCTTGGTGGTCAAGCTCATTGGACAGTTGGACTTGTGGCAACATTGATTTCTTTCAGCGGTGTAATTGCGACAGAMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|110699872|gb|EE077264.1|EE077264EST: TTTCTGGGTTAAGCTTCGATGTGGTTTAGCAGCTCCTGCCTTAAACACCA GAATAGGAACAGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAG
genomic: TTTCTGGGTTAAGCTTCGATGTGGTTTAGCAGCTCCTGCCTTAAACACCAgtaagaagtg ... tttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtggatctgctttatgctttgccagctgtttcctaaccagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA
tcctaac putative branch site (score: 1)
ttattttt putative PPT
ttattttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaacacctgcatgtgggcccacagctttgtgtatattctgagcctgtggatctgctttatgctttgccagctgtttcctaaccagggttatttttggtagGAATAGGAACGGCTTGGCCTTTTCTTCTTGGTGGTCAAGCTCATTGGACAGTGGGTCTTGTGGTAACCTTGATTTCTATCAGCAGTATAATTGCAGCAGA
- - -cctgcat
- - - - - - - - gcccaca
- - - - - - - - - - - - - - - - - - - - - - - - - -ctgcttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttg