Sequence
atgc intronic sequence ATGC exonic sequencegtactgtacgttatactttgattcagctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttagGGTGGGATTTACACTCTTCCAAGTCATTTATCATCTGAGGCTAGAGACCTGATCCCAAGGATGCTTATAGTTGACCCGGTGAAACGAATCACCATTCCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G29160.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 5
---gtactgtacgttatactttgattcagctaa-aagactcttcttaaatggattca--tatgtatgtgaagtaacttatcaaggtgttttttttctctttagGGTGGGATTTACACTCTTCCAAGTCATTTATCATCTGAGGCTAGAGACCTGATCCCAAGGATGCTTATAGTTGACCCGGTGAAACGAATCACCATTCCTG
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ttggatttacccattgcctatccctacaatcattgatgttaccggtaaacagatctagttttgcttctgatgtg---tacctcactaattactatttttatagGGTGGGATATACACTCTTCCTAGTCATCTATCACCTGGTGCTAGAGATTTGATACCAAGGATGCTTGTGGTGGATCCCATGAAGAGGATGACCATACCTG
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 6
gtactgtacgttatactttgattcagctaaaagactcttcttaaatggattcatatgt-atgtgaagtaac--ttatcaaggtgtttt------ttttctctttagGGTGGGATTTACACTCTTCCAAGTCATTTATCATCTGAGGCTAGAGACCTGATCCCAAGGATGCTTATAGTTGACCCGGTGAAACGAATCACCATTCCTG
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----tgt-tgtaatagatctttttgagaatcaga-taatccaaattggatttattcatcaaatgatgttatcatcaaaaagattttttcccatgtttttcatgtagGGTGGGATTTACACTCTTCCCAGTCATCTATCACCCGGTGCTAGAGATTTGATACCAGGGATGCTTGTGGTTGACCCTATGAGGAGAATGACCATACCTG
upper sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 5
------gtactgtacgttatac-tttgattcagctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttct-ctttagGGTGGGATTTACACTCTTCCAAGTCATTTATCATCTGAGGCTAGAGACCTGATCCCAAGGATGCTTATAGTTGACCCGGTGAAACGAATCACCATTCCTG
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gctcttatcctataaagagtacattttatcctatcaatcatatattattttctgagattaaaaatgtttgc-----tccataaacccatttcatttgtattttagGGTGGGATATATACTCTTCCTAGTCATTTATCAACTGGTGCTAGAGATCTGATCCCAAGGATGCTCATAGTTGACCCTATGAAGCGAATGACAATTCCTGMapped 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|124827681|gb|EH912547.1|EH912547EST: TTTTCAAGAAAATTAAG GGTGGGATTTACACTCTTCCAAGTTCATTTATACATCTGAGGCTAGAGACC
genomic: TTTTCAAGAAAATTAAGgtactgtacg ... ttctctttagGGTGGGATTTACACTCTTCCAAG-TCATTTAT-CATCTGAGGCTAGAGACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttagGGTGGGATTTACACTCTTCCAAGTCATTTATCATCTGAGGCTAGAGACCTGATCCCAAGGATGCTTATAGTTGACCCGGTGAAACGAATCACCATTCCTG
aagtaac putative branch site (score: 2)
tgttttttttctcttt putative PPT
ttttttttctcttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgtacgttatactttgattcagctaaaagactcttcttaaatggattcatatgtatgtgaagtaacttatcaaggtgttttttttctctttagGGTGGGATTTACACTCTTCCAAGTCATTTATCATCTGAGGCTAGAGACCTGATCCCAAGGATGCTTATAGTTGACCCGGTGAAACGAATCACCATTCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG