Sequence
atgc intronic sequence ATGC exonic sequencegtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttcatgtccattataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os02g32110.1 (Oryza sativa), 3'ss of exon 2
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctg-cttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttcatgtccattataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
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gtaatgatatattggtttatttgtcttct--tacctgccaagtccttgtcactgttgtagctagtcatgattttagttccacaatagttttaagaaata-ggtagctcaggatagatcctacctttagtcc---ctatctattctgaaactgcatatgcaatggttatatgtcttt----------acagGAAGAGAAAGCTATTGAGCGTGGGATACTTCCATTGCTCCGCCGTGCCACATTGGTTCAAACTTTTGGACAGAAGAACCATGTGTGCTTGAAGGAGGGTT
upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 2
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttcatgtccattataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
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------------------------------------------------------------------------------ttaatcatcta-ccctgattggcaccttctatcatactttgtgcccacattctctttg---------gttatttcagcgtattgatcttttgcttctgtt-attgtttcagGAAGAAAAGGCAATTGGACGTGGAATCCTCCCATTGCTTCAGCGTGCCACCCTGGTTCAGACCTTTGGACAAAAGAACCATGTCTGCTTGAAGGACGGCT
upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os04g32670.1 (Oryza sativa), 3'ss of exon 2
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttg-gatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcaga-gaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttcatgtccattata--------acagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
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----gtgtgtgctaattcccttggcatctcacattt----ggatttgtctgtgtgtaattctctttctgatttcattgtttactttgg-agtttggacatacccttttagatgtcaacgctaaggataaaacattattttgaccttttctactcacaagttctgaagtagtgttattaactgttgtatactatttgtagGAAGAAAAAGCTATTGAGCGTGGAATTCTACCGTTGCTGCAACGTGCTACGTTGGTCCAAACATTTGGACAGGAGAACCATGTTTGCTTAAAAGAGGGTT
upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 2
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttcatgtccattataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
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---------------------------------------------------------------------------tttagtagaaaaaaccactcactaaatttccaattga---ctactgttactgtctgtt--tcaatatcttgatattt-ctgtaacaagtacttcaa--------actgtaccagGAAGAGAAAGCCATTGGACGGGGAATCCTTCCCTTGCTTCAGCGTGCTACGTTGGTTCAGACCTTTGGACAGAAGAACCATGTCTGCCTGAAGGATGGGT
upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 2
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttcatgtccatt-ataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
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gtaagaaattt-agtgtaccgtttta------attttgctattttcatcactat---tagttctattaagaat----tcaaacaaattgtgtggtgtttggtg----agaaggaccttggatt----ttattcttcaatatgtacatggat-attgtaacatgcacttttatcatgtttttccgttccagGAAGAGAAGGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGACAGAGGAATCATGTGTGCTTGAAAGAGGGCT
upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 2
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcat---tattcactttcactgggcctctgttcatgtccatt-ataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
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------------------gtaagaaatttagtgtacc---attttaattttgttatttaaatcact---attagttcttttaagaattcaaacaaattttgtggtttttggtgacaa--ggaccatggattccactattaaagatgtacatggatattgtaacatgcacttttatcatgtttttttgttccagGAAGAGAAAGCAATTGAAAGAGGAATTCTTCCATTGCTTCAGCGTGCTACCTTGGTTCAAACATTTGGGCAGAGGAATCATGTGTGCTTGAAAGAGGGCT
upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 2
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactg-gcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggc-ctctgttcatgtccattataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
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-------------------------gtacaagatttttc-acatatcactgttagt----tttacttaagtat----ttgaaccaattatatgctgtcttgagaagtaacaaagaaaagcagtttagatgtaggataccta--tccaaaagtaacacataacatgcattttattcat-tattttgttctagGAAGAGAAGGCAATTGAAAGAGGGATTCTTACACTACTACGGCGTGCTACCTTGGTTCAAACATTTGGACAGAGAAATCATGTGTGCTTGAAAGAGGGCT
upper sequence: Vv17s0000g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttc-atgtcc-attataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
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--------------------------------------------------------------------------------------ttgatggagcagaaaattttcacgag---ccgtgacaacaaagatttgtgcctgtgat-actgctaaccta-gctgatctcttgttttgtgtttgactgtggcagGAAGAGAAGGCAATAGGAAGAGGAATACTACCCTTGCTTCAACGAGCTACACTGGTGCAGACATTTGGACAAAGGAATCATGTTTGCTTGAAAGAAGGTTMapped 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|110702747|gb|EE078988.1|EE078988EST: ATCACTTTTTTGTAGTGCCCCATGACTTTGGGGCGTGCTTCCATTACCAA GAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACC
genomic: ATCACTTTTTTGTAGTGCCCCATGACTTTGGGGCGTGCTTCCATTACCAAgtaagaaact ... attataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACC
EST:
gi|110718481|gb|EE095362.1|EE095362EST: ATCACTTTTTTGTAGTGCCCCATGACTTTGGGGCGTGCTTCCATTACCAA GAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACC
genomic: ATCACTTTTTTGTAGTGCCCCATGACTTTGGGGCGTGCTTCCATTACCAAgtaagaaact ... attataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcctaaactcattattcactttcactgggcctctgttcatgtccattataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
tcctaaa putative branch site (score: 2)
attataaca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaaacttcaatttcttttgtcacccagtactcccccacattcattcgtttggatagtctgcttgaatgtgctcttgaaccaactggcccagatttagtttttcagagaggcctctggctagtgtcttttcttcctaaactcattattcactttcactgggcctctgttcatgtccattataacagGAAGAGAAAGCTATTGAAAGAGGAATTCTTCACTTGCTCCAGCGTGCCACCTTGGTTCAAACTTTTGGACAACGGAATCATGTTTGCTTGAAAGAAGGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG