Sequence
atgc intronic sequence ATGC exonic sequence...tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 17
tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
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-----------gtgccccctgt---tctgctaattattg--tactctgcaac---tcaggcctca-gaatc----tgaagataacccttttatttgc-agTGTGGCACGTTTCTTGGAATCACGGGGCATGTTGGAAGAAGCCCTTGAGATAGCAACAGACTCTAATTACAGATTTGACTTGGCCGTGCAGCTTGGTCGG
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G141587_T02 (Zea mays), 3'ss of exon 17
tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
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--------------------gtgctcaatgtcatggt-aattattgtagtatcaagtcaggtt-tagcat----agaaacataacctttctttttgc-agTGTGGCGCGTTTCTTGGAATCACGGGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAACTTGGTCGA
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G124886_T01 (Zea mays), 3'ss of exon 17
tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
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---------------------gtgctgaatgacatggtaattattgtgt--taaatcaggttta--gcatggaaacataa----cttttctctttgc-agTGTGGCACGTTTCTTGGAATCACGTGGAATGTTGGAGGAAGCCCTCGAGATAGCAACTGACACTAATTACAGATTTGACCTGGCTGTGCAGCTTGGTCGA
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 17
----tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
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gtttattcaaatttcagagtt-cagtcttcggatctgaagttttgtaattagtg--ctaatatattacctgcatcctaatcaaaatacttgattttatgg-tagTGTGGCTCATTTTCTGGAATCACGAGGTATGATAGAAGATGCCCTTGAAGTAGCTACTGACCCTGACTACAGATTTGATCTAGCAATACAGCTTGGAAAA
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 6
----tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
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tctatctgca-tatggtgttttcttggctttcattttcaatgtttggtgctcagatgtcacatatatcctaattgcaattttttac--ttgtttttac-actagTGTGGCTCGTTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGTAGCTACTGACCCTGACTATAGGTTTGATCTAGCCATACAGCTTGGAAGA
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 17
------tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
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tgtttattcaaatttcagagttcagtcatcg-gatttgaagtttggtaatagtgg----taatatattacctgaatcctaatcaaaattcttgattttatgg-tagTGTGGCTCATTTCCTTGAATCACGAGGGATGATAGAAGATGCTCTTGAAGTAGCTACTGACCCTGAGTACAGATTTGATCTATCAATACAGCTTGGAAAA
upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 17
tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagtt-gtttgaatt---gctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
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--tctatctgcatatggtgttttcttggatttcattttcaatgtttggtg--ctccgatgtcacatacatcctaattgcaattctttacttgtttttacaccagTGTGGCTCATTTCCTGGAATCACGAGGGATGATAGAGGATGCTCTTGAAGTAGCTACCGACCCTGACTATAGGTTTGATCTAGCCATACAGCTTGGAAGAMapped 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|110728301|gb|EE103751.1|EE103751EST: GAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAG TGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGT
genomic: GAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttct ... gaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGT
EST:
gi|161716849|gb|FC068107.1|FC068107EST: GAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAG TGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGT
genomic: GAACGGGCCAATGAACTTTTACCTTCAATTCCCAAAGAACATCATAATAGgtaaatttct ... gaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
tgctaat putative branch site (score: 2)
taataagaaaagtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgaacttttatacccgctgaaaatgaaacaaagatgaattattttgcagtcttttaagtttcttgcatgctaataagaaaagttgtttgaattgctagTGTGGCTCGTTTCTTGGAATCACGGGGTATGATAGAGGATGCCCTGGAAGTAGCTACTGACCCTGATTACCGATTTGAGCTAGCAATGCAGCTTGGCAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - tacccgc
- - - - - - - - - - gaaaatg
- - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - tgcagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa