Sequence
atgc intronic sequence ATGC exonic sequenceGTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCTTTCCCGCTTCCCACCCCGCCTAGATCCGAAGACGAGgttagcctcttcactgaaaaatgtgtgacaattaaacccctgattagtcactaatccctcttggaaatctttgattag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G20540.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G066672_T01 (Zea mays), 5'ss of exon 4
---GTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCTTTCCCGCTTCCCACCCCGCCTAGATCCGAAGACGAGgttag----cctcttcactgaaaaatgtgtgacaattaaacccct------gattagtcactaatccctcttggaa-atctttgattag-----------------------------------------------------------------------------
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ATGGTGGGCTGAAAACTATGACAAAGTTATGGAACTTTACAATGTGCAGAAGTTTAATC---AAACTGTCCCTCTCCCAGCTACCCCAAAATCTGAAGATGAGgtgaggaggccactcaatttgtttatctgttttttttaaaataattcaaggggctacacaccagttcctcacgcaacattctttctctctgtaccaatagctacagacatattttctttatgactggactgatacatcgttcgatgacatttgcttcttcccatag
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA09G07930.1 (Glycine max), 5'ss of exon 2
GTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCTTTCCCGCTTCCCACCCCGCCTAGATCCGAAGACGAGgttagcctcttcactgaaaa-atgtgtgacaattaaacccctgat--tagtcactaatccctcttgg---aaatctttgattag-----------------
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GTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTGCAAAGGCTTAATCGTCAAGCTTTCCCTCTTCCAACTCCGCCTAGATCTGAAGACGAGgt-aacttctgaatttacgctgtgtgaactgtttgtaatttggaatgtagatacagacgtgtggtggtgcaaataccaacgctgactttattctagtccta
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA15G18980.1 (Glycine max), 5'ss of exon 2
GTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCTTTCCCGCTTCCCACCCCGCCTAGATCCGAAGACGAGgttagcctcttcactga----------aaaatgtgtgacaattaaacccctgattagtcac-taatccctcttgg---aaatctttgattag---------
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GTGGGCAGAGAACTATGACAAGGTGATGGAACTTTACAATGTTCAAAGGCTTGATCGCCAAGCTTTCCCTCTTCCAACTCCACCAAGGTCTGAAGACGAGgt-aacttctgaatttatgtagcttctagacattgttatgtaaaattttgtaatcgtctgcatcatgttacttgacccaaatgtttattttgggcaatttt
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA13G16800.1 (Glycine max), 5'ss of exon 4
GTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCTTTCCCGCTTCCCACCCCGCCTAGATCCGAAGACGAGgttagcctcttcactgaaaaatgtgtgacaat-----taaacccctgattagtcacta---atccctcttggaaatctttgattag--------------
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GTGGGCAGAGAACTACGACAAAGTTATGGAACTTTACAATGTTCAAAGGTTTAACCGCCAAGCATTTCCTCTTCCAACGCCACCAAGATCTGAAGATGAGgtaatttgggtagcttatacacatgtaaaaacatatacaatttactaattggctgctgcatattactcggggcaatgcttaggccgttcaattcatacaa
upper sequence: AT5G20540.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA17G05900.1 (Glycine max), 5'ss of exon 3
GTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCTTTCCCGCTTCCCACCCCGCCTAGATCCGAAGACGAGgttagcctcttcactgaaaaatgtgtgacaat-----taaacccctgattagtcacta-atccctcttgga--aatctttgattag--------------
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GTGGGCAGAGAACTACGACAAGGTTATGGAACTTTACAATGTTCAAAGGTTTAACCGCCAAGCATTTCCTCTTCCAACGCCTCTAAGATCTGAAGATGAGgtaatttgggtagcttatacacatgtaaaaacatatacaatttactaattggctgctgcatgttacttggggcaatgcataggccgttcaattcctatatMapped 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|125250295|gb|EL264380.1|EL264380EST: CCGCCAAGCTTTCCCGCTTCCCACCCCGCCTAGATCCGAAGACGAG AATGCAAAAGTGGAGTACCATCCAGAAGACACTCCTGCAACACCGCCTCTA
genomic: CCGCCAAGCTTTCCCGCTTCCCACCCCGCCTAGATCCGAAGACGAGgttagcctct ... ctttgattagAATGCAAAAGTGGAGTACCATCCAGAAGACACTCCTGCAACACCGCCTCTA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTGGGCAGATAACTATGACAAAGTAATGGAACTTTACAATGTTCAAAAACTAAGCCGCCAAGCTTTCCCGCTTCCCACCCCGCCTAGATCCGAAGACGAGgttagcctcttcactgaaaaatgtgtgacaattaaacccctgattagtcactaatccctcttggaaatctttgattag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA