Sequence
atgc intronic sequence ATGC exonic sequencegtgttgtatgcgttgttcaactttgagattcaaagttcccttatgtaagatcattgtgtgcaattcttaaaaacgatttgactggtttctttcagGGTCACCCTTGGTTTAGAGGCACAGAATGGGGAAAATTGTATCAAATGAAAGCTGCCTTTATTCCCCAAGTTAATGATGAGTTGGACACCCAAAATTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G14350.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA10G32480.1 (Glycine max), 3'ss of exon 8
gtgttgtatgcgttgttcaactttgagattcaaagttcccttatgtaagatcattgtgtgcaattcttaaaaacgatttgactggtttctttcagGGTCACCCTTGGTTTAGAGGCACAGAATGGGGAAAATTGTATCAAATGAAAGCTGCCTTTATTCCCCAAGTTAATGATGAGTTGGACACCCAAAATTTTG
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gtgttgtg-gtgt-gttcttttctgaattctataatttactt-tgggttacagttacatattaacaacataactggttggtcta-ttatttccagGCTCACCCATGGTTTAAAGGTATTGAATGGGACAAATTGTACCAAATGAAAGCTGCTTTTATTCCTGAGGTTAATGATGAATTAGATACTCAAAATTTTG
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA20G35110.1 (Glycine max), 3'ss of exon 8
gtgttgtatgcgttgttcaactttgagattcaaagttcccttatgtaagatcattgtgtgcaattcttaaaaacgatttgactggtttctttcagGGTCACCCTTGGTTTAGAGGCACAGAATGGGGAAAATTGTATCAAATGAAAGCTGCCTTTATTCCCCAAGTTAATGATGAGTTGGACACCCAAAATTTTG
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gtgttgtg-gtgt-gttcttttctgaattctataatttactt-tgggttacagttgcatattaactgcataactggccggtcta-ttatttccagGCGCACCCATGGTTTAAAGGTATTGAATGGGACAAATTGTACCAAATTAAAGCTGCTTTTATTCCTGAGGTTAATGATGAATTAGATACTCAAAATTTTG
upper sequence: AT4G14350.3 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 3'ss of exon 8
gtgttgtatgcgttgttcaactttgagattcaaagttcccttatgtaagatcattgtgtgcaattcttaaaaacg-atttgactggtttctttcagGGTCACCCTTGGTTTAGAGGCACAGAATGGGGAAAATTGTATCAAATGAAAGCTGCCTTTATTCCCCAAGTTAATGATGAGTTGGACACCCAAAATTTTG
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gtgttgtgtggtgtgttcaattctgaattactggatttggtt---cacaatggaattacaaagtgaggaataatgtggttggctctgtaaattcagGCTCACCCCTGGTTTGAAGGTGTTGACTGGGACAAATTGTATCAAATTGAAGCTGCATTTATTCCTGAGGTCAATGATGAGTTAGATACCCAAAACTTTGMapped 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|116396686|gb|EG439278.1|EG439278EST: TATGCAATGTTGAACAAAGGCTTGGAACAAAAGGAGCAGATGAAATTAAG GGTCACCCTTGGTTTAGAGGCACAGAATGGGGAAAATTGTATCAAATGAAA
genomic: TATGCAATGTTGAACAAAGGCTTGGAACAAAAGGAGCAGATGAAATTAAGgtgttgtatg ... tttctttcagGGTCACCCTTGGTTTAGAGGCACAGAATGGGGAAAATTGTATCAAATGAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgtaagatcattgtgtgcaattcttaaaaacgatttgactggtttctttcagGGTCACCCTTGGTTTAGAGGCACAGAATGGGGAAAATTGTATCAAATGAAAGCTGCCTTTATTCCCCAAGTTAATGATGAGTTGGACACCCAAAATTTTG
atttgac putative branch site (score: 4)
tttctttc putative PPT
aattcttaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttgtatgcgttgttcaactttgagattcaaagttcccttatgtaagatcattgtgtgcaattcttaaaaacgatttgactggtttctttcagGGTCACCCTTGGTTTAGAGGCACAGAATGGGGAAAATTGTATCAAATGAAAGCTGCCTTTATTCCCCAAGTTAATGATGAGTTGGACACCCAAAATTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC