Sequence
atgc intronic sequence ATGC exonic sequencegtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 2
gtaagggcctttgttttactatttattggtttctcaaatcttggct-ctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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----------------------------------------ttaacggccgagtgttcatgcttg-gttttac---ttcttaactgttttgaattatatccttccaa-------tttatttctgcaatttatatttgttttgt------tttctg--cagCGGGGGTTCCATTGGAAAACATTCTTTATCTTGGAGGCCCTAACATTGCTTCAGAAATTTACAATAAAGAATATGCAAATGCTCGTATATGTGGAGCTGA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 2
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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-------------------------------------gacatgcatttatgtgatattaactttcgtt---gacccaacctattcctt----cccttgttttattcaaa----ttacaacta--attcagcattttaaaataaatt--------gcagCTGGAGTTCCAACTGAGAATATACTATATCTTGGAGGCCCAAACATTGCCTCAGAGATTTATAACAAAGAATATGCAAATGCTCGAATCTGTGGGTCCAA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 1
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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--------------------------------------gtttcactgtataattgattt--taccatccactggtcttcatctttcctaccatgtt----------gtagccttta-----atgttttttgtttcttatg-atgggcctattg--cagCTGGAGTTCCATTGGAGAATATTCTATATCTTGGAGGTCCTAACATTGCATCTGAGATATATAACAAAGAATATGCAAATGCTCGCATATGTGGAGCTGA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 1
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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---------------------------------------------------ttttaccgaactgatactaacaccctgctctttatctcaattctgtatactatactgttggtttgcttttgtggttg-----ttgatcatggattcttactg--cagCTGGAGTTCCCTTGGAGAACATTCTATATCTTGGAGGCCCAAACATTGCTTCTGAGATTTATAACAAAGAATATGCGAATGCTCGCATATGTGGAGCTGA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 2
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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-------------------------------------------------gcatctggttgaaacgtataaacagtttttttctgctt---aatgcttggcctgctta----tttgagatcagcagtacagactgatttttaaggaatgcattg--cagCTGGAGTTCCAACTGAAAATATACTCTATCTTGGAGGACCAAACATCGCCTCGGAAATTTATAACAAAGAATATGCAAACGCTCGAATCTGTGGATCCAA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 2
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttt--tgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttc-tatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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------------------------------------agatacatatatatgctcaatgcttcctcctaatc-----tccaagtatttgttg------tcccct---------ctttgattttgtatgattta-----ttatggactattggtataatgcagCTGGAGTTCCATCAGAGAATATTCTTTATCTTGGCGGACCTAATATTGCTTCTGAAATTTACAACAAAGAATATGCAAATGCACGTATTTGTGGAGCTGA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G15900.1 (Glycine max), 3'ss of exon 1
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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-----------------------------------------agaatttat---ttgataccaaccaat-agaagctgata-atttagtagtatatctatttcta----------tattttctcattctcaac--tctttacaattcatactttgacagCTGGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCTCGAATATGCGGAGCAGA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA19G31730.1 (Glycine max), 3'ss of exon 1
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttt--tttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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-------------------------------------------------tcatctgattttttcttatcagagatc-atagccttct---aac-tatgcaataatatg----tttagtccttc--cctaattctttactctttgcgcccaaacttgacagCTAGAGTGCCTATGGAGAACATACTTTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATATGTGGAGCTGA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA03G28970.1 (Glycine max), 3'ss of exon 1
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaa-gccttttttatatatc-cttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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----------------------------------------------------aatactcttttttatttat---ttcatctgatttt----gtattatcataggtcatagccttc-ttaccatgcaataatatctattctttgcattgcaaacttgatagCTAGAGTGCCTATGGAGAACATACTCTATCTTGGTGGTCCAAATATTGCCTCAGAAATCTACAACAAGGAGTATGCCAATGCAAGAATCTGTGGAGCTGA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G33340.1 (Glycine max), 3'ss of exon 1
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaa---aagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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------------------------------------------------agaatttgtttgataacgaccaatggaagctggta-atttggtagtatatctattttta--------tctttcctcattctc-aactctttacaatgcatacttt---gacagCTGGAGTGCCTATGGAGAACATACTGTATCTTGGTGGTCCAAATATTGCCTCAGAAATATACAACAAGGAGTATGCCAATGCCCGAATTTGCGGAGATGA
upper sequence: Vv08s0007g09000.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G41540.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
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--------------------------------gtaagctttttcttcttccttttgctccttttatattgag----------tctattgacacaat---cttg--------cttagttttcttgaattggttcttactttggtgtttgtg----gtagCTGGTGTGCCGATTGACAATGTCCTGTATCTTGGTGGACCAAACATTGCTGCTGAAATTTACAACAAGGAATATGCCAATGCTAGAATCTGTGGAGCTGCMapped 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|349821528|gb|FQ408087.1|FQ408087EST: AGAACCCCTCCCACATATCATCACTCCCACACAAATGATTAACCGAGCAA CTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCT
genomic: AGAACCCCTCCCACATATCATCACTCCCACACAAATGATTAACCGAGCAAgtaagggcct ... tgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
tccttgct CT-rich tract
ttttttatatatcctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggcctttgttttactatttattggtttctcaaatcttggctctatgttttgtttcttgtgaattaaaagtccatatatttcttggaacatttgccttaagaagagcttttatttctatgatctaagccttttttatatatccttgctgggcagCTGGTGTAGCTATGGAAAACATTCTTTACCTTGGAGGACCAAACATTGCCTCAGAGATTTACAACAAGGAGTATGCGAATGCTCGAATATGTGGAGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA