Sequence
atgc intronic sequence ATGC exonic sequencegttaggactcttttgttaattatctagttagtgcttgttatgtgaaaatgcatagattctaaaagcattcaatcctatttgtttatggtgccaaagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os08g14460.3 (Oryza sativa), 3'ss of exon 6
----------------------------gttaggactcttttgttaa--ttatctagttagtgcttgttatgtgaaaatgc----atagattctaaaagcattca-atcctatttgtttatggtgcca--aagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG
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gtagaattgccatgccatagtcttatttttttagatcaatctgttcatcttgcttgcttactttgttttcggagaagttattaatgtgtatactgatgggaccaatatcttgctttctaattttctttttaagCAAGTACGTACCCAGCAAATTCATGAAATGAAGAAAAAAGAGAAAGAATACATCAAATTGCAG
upper sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 6
---------------------------------gttaggactcttttgttaattatctagttagtgc-ttgttatgtgaaaatgcatagattctaaaagcattc-aatcctatttgtttatggtgccaaagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG
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gttagactgccttattttattccttcgagtatcatcctaaccatagcat-gtttattttgttattgcattgatatttggtgatg-aggtatgttgaacctgtcctgaccttctttggttcttctgc--aagCAAGTACGCACCCAGCAAATTCATGAAATGAAGAAGAAAGAGAAAGAATACATAAAGTTGCAG
upper sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 6
-------gttaggactcttttgttaat----tatctagttagtgct-tgttatgtgaaaatgcatagat-tctaaaagcattcaatcctatttgtttatggtgccaaagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG
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gttagaagtttgatctctttgcttattgtggcgtcttgtttggatgaccctacttcaaaatggataagcctctgactcttgtgaatttgactattgaatggtgttaaagCAAGTAAAGACTCAACAAATGCATGAGATGAAGAAGAAGGAAAAGGAATACATAAAGTTGCAG
upper sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 6
-------gttaggactcttttgttaattat------ctagttagtgcttgttatgtgaaaatgcataga--ttctaaaagcattcaatcctatttgtttatggtgccaaagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG
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gttagaagtttgatcttctttgcttattgtggcgtcttgtttggatgaccctacttcaaaatggataaagcctctgactcttgtgaatttgactcttgaatggtgttaaagCAAGTAAAGACTCAACAAATGCATGAGATGAAGAAGAAGGAAAAAGAATACATAAAGTTGCAG
upper sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 6
gttaggactcttttgttaattatctagttagtgcttgttatgtgaaaatgcatagattctaaaagcattcaatcctatttgtttatggtgccaaagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG
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gtctgattgtgtttgctcttggattaactactttatcttagaggaaattgtactgatgatggattctctgcatttcttct-tttatttctgaatagCAAGTGAAGGCTCAACAGATACACGAAATGAAGAAAAAGGAGAAGGATTACATTAAGTTGCAG
upper sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S47_178V6.2 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------gttaggactcttttgttaattat-ctagttagtgcttgttatgt-gaaaatgcatag-attctaaaagc-------attcaatcctatttgttt-atggtgccaa-------agCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG
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gtgggtagacaatcttcttactgtcttgatttggagctaagacactcttgaaacacatgcttgttttgtcttgatatcttgcatttccttagtacgctagcagcctattatatacaacctaatctattttacgggttcgattctttcagCAAGTGAAGACTCAGCAGATGCACGAGTTAAAGAAGAAAGAGAAGGAATACATCAAGTTGCAGMapped 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|294964330|gb|GW838133.1|GW838133EST: AATTGCAGCAGGAGCGGGATGAATTGCAAAGGATGGTTATTGGTAATCAG CAAGTGAGGACTCAACAAATTCATGAAATGAAGAAAAAAGAGAAGGAATAC
genomic: AATTGCAGCAGGAGCGGGATGAATTTCAAAGGATGGTTATTGGTAATCAGgttaggactc ... ggtgccaaagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaaaatgcatagattctaaaagcattcaatcctatttgtttatggtgccaaagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG
ttctaaa putative branch site (score: 2)
tatttgtttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttaggactcttttgttaattatctagttagtgcttgttatgtgaaaatgcatagattctaaaagcattcaatcctatttgtttatggtgccaaagCAAGTGAGGACTCAACAAATTCATGAGATGAAGAAAAAAGAGAAGGAATACATAAAATTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA