Sequence
atgc intronic sequence ATGC exonic sequence...tcaccacattctctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 1
---tcaccacattctctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
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gtttcactgtataattgatt-ttaccatccactggtcttcatctttcctaccatgttgtagcctttaatgttttttgtttc-ttatgatgg-gcctattgcagCTGGAGTTCCATTGGAGAATATTCTATATCTTGGAGGTCCTAACATTGCATCTGAGATATATAACAAAGAATATGCAAATGCTCGCATATGTGGAGCTGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 2
------tcaccacattctctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
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ttaacggccgagtgttcatgcttggttttactt--cttaactgttttgaattatatccttccaattt----atttctgcaatttatatttgttttgttttctgcagCGGGGGTTCCATTGGAAAACATTCTTTATCTTGGAGGCCCTAACATTGCTTCAGAAATTTACAATAAAGAATATGCAAATGCTCGTATATGTGGAGCTGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
tcaccacat-tctctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttct-ttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
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--gacatgcatttatgtgatattaactttcgttgacccaacctattccttcccttgttttattcaaattacaactaattcagcattttaaaataaattgcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 1
--tcaccacattctctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttctttgcctcattattatattgtgct-ttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
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ttttaccgaactgatactaacaccctgctctttatctcaattctgtatactatactgt---tggtttgcttttgtggttgttgatcatggattcttactgcagCTGGAGTTCCCTTGGAGAACATTCTATATCTTGGAGGCCCAAACATTGCTTCTGAGATTTATAACAAAGAATATGCGAATGCTCGCATATGTGGAGCTGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 2
tcaccacattc-tctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttctt-tgcctcattatta--tattg-tgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
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-----agatacatatatatgctcaatgcttcctcctaatctccaagtatttgttgtcccctctttgattttgtatgatttattatggactattggtataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 2
tcaccacattc---tctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
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gcatctggttgaaacgtataaacagttttt-ttctgcttaatgcttggcctgcttatttgagatcagcagtaca--gactgatttttaaggaatgcattgcagCTGGAGTTCCAACTGAAAATATACTCTATCTTGGAGGACCAAACATCGCCTCGGAAATTTATAACAAAGAATATGCAAACGCTCGAATCTGTGGATCCAA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 1
-----------tcaccacattctctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
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gaaaaaaaatcttgatattctttctggagttcttattt-ttgtaatggtacatgacatccatgtttaattaaactcccatcgttgcctgattt----------ctttgcagCTGGCGTTCCCTTGGACAGCATCCTTTATCTTGGAGGACCGAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAATGCTCGGATATGTGGGGCAGA
upper sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G01380.1 (Glycine max), 3'ss of exon 1
-------tcaccacattctctgtagtttttatttgtcctaattgatgccaccttttttattttactttc-tccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
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gaatttttaattcagtttaattttgttggcatgt-ttatagtttatactaactaaatgattttttttccatccccttcactgtctc-------tatcatgttttgtagCTGGAGTCCCCATTGAGAACATCCTTTACCTTGGAGGTCCTAACATTGCCTCAGAAATTTACAACAAGGAATATGCAAACGCTAGGATATGTGGGGCAGAMapped 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|33403903|gb|CF209530.1|CF209530EST: GGAGCCAGAACCCCGTATTATAACTCCCACTCAAATGATCAATAGGGCAA CTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCT
genomic: GGAGCCAGAACCCCGTATTATAACTCCCACTCAAATGATCAATAGGGCAAgtaagaattc ... tgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttttattttactttctccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
tcattattatattgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcaccacattctctgtagtttttatttgtcctaattgatgccaccttttttattttactttctccacttctttgcctcattattatattgtgctttgcagCTGGAGTTCCCATGGAGAATATTCTCTATCTTGGTGGACCGAATATTGCCTCAGAAATTTACAACAAGGAATACGCTAATGCTCGCATATGTGGAGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
-caccaca
- - - - - ctctgta