Sequence
atgc intronic sequence ATGC exonic sequence...aacaatgtagatagtgatttgttattttacatgctgctttccatgctggctttgaatctctatattggtctaatgtaaaattatattatttcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0013g01540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os07g30790.1 (Oryza sativa), 3'ss of exon 2
aacaatgtagatagtgatttgttattttacatgctgctttccatgctggctttgaatctctatattggtctaa--tgtaaaattatattattt--catatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT
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---cat-taactgcatacctgttttggtaactgtttgtttcatttccatctttttatgcttaagatatactgggtcggcaatttctgacattttccttttacagTTTTTCAGTTGGAGAAAACATTTAAAACAACATTTTCATTACTTGTTCTCCATATGTGGCTTATTCTACGTCGCTTGAAAGAAGAAGGGAAGGATGGTGT
upper sequence: Vv16s0013g01540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G18850.1 (Glycine max), 3'ss of exon 3
-------aacaatgtagatagtgatttgttattttacatgctgctttccatgctggctttgaatctctatattggtctaatgtaaaattatattatttcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT
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attgagtaatcatggcgtgggaggagtttaatttgtattagtgctcatcaaactagtgtttgatcttt-tagcattctaa------acttcttcctgctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTACTTCATATGTGGTTATGTTTGCGTCGCTTGAAGCAAGAGGGAAATGAGGGTGT
upper sequence: Vv16s0013g01540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G06170.1 (Glycine max), 3'ss of exon 2
-------aacaatgtagatagtgatttgttattttacatgctgctttccatgctggctttgaatctctatattggtctaatgtaaaattatattatttcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT
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atcgagtaatcatggtatgggaggagtttgatttgtattactgctcatcaaactagtgtttgatct-tgtagcattctaa------acttcttccttctgcttgcagTGTTTAACTTGGAGAAAACATTCAAAACAACATTCTCTTTACTTGTGCTTCATATGTGGTTCTGTTTGCGTCGCTTGAAGCAAGAGGGAAAGGAGGGTGT
upper sequence: Vv16s0013g01540.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G51220.1 (Arabidopsis thaliana), 3'ss of exon 2
aacaatgtagatagtgatttgttattttacatgctgctttccatgctggctttgaatctctatattg-gtctaatgtaaa-----attatattatttcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT
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---------gtactttatttggtttccaacacaacttttgcaaacagagttatgtatttacattttgtgctttgtttatatatcgggtgctctgtctctgctgcagTATTCAACTTGGAGAAAACATTCAAAATAACGTATTCGCTGCTTGTCCTTCATATGTGGCTTGTTTTACGCCGCTTGAAGGAAGATGGACAGGAAGGTGTMapped 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|110685949|gb|EE063114.1|EE063114EST: GGTATACCGGCGAATTGCTTCACAAGTTGATAAACCTGCCATATATAATG CATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTC
genomic: GGTATACCGGCGAATTGCTTCACAAGTTGATAAACCTGCCATATATAATGgtgagttttt ... tcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTC
EST:
gi|26257759|gb|CA808822.1|CA808822EST: GGTATACCGGCGAATTGCTTCACAAGTTGACAAACCTGCCATATATAATG CATTTAACTTGGAGAAAACCTTTAAAACAACATTTCCTCTGCTTATACTTC
genomic: GGTATACCGGCGAATTGCTTCACAAGTTGATAAACCTGCCATATATAATGgtgagttttt ... tcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctggctttgaatctctatattggtctaatgtaaaattatattatttcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT
gtctaat putative branch site (score: 3)
ttatttc putative PPT
tatattggtctaatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacaatgtagatagtgatttgttattttacatgctgctttccatgctggctttgaatctctatattggtctaatgtaaaattatattatttcatatgcagCATTTAACTTGGAGAAAACCTTTAAAACAACATTTTCTCTGCTTATACTTCATATGTGGCTTTGCTTACGCCGCTTGAAAGAAGATGGAAAGGAAGGTGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- caatgta
- - - - - - - - - - - - - - acatgct
- - - - - - - - - - - - - - - - - - - - ccatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatta