Sequence
atgc intronic sequence ATGC exonic sequenceCAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTCTCCAGgtaccaaaccaaaccgtaaaaacatctttcaaaacttttgtttcttgatttgtggcatcataataaaaactatgtttgatttttaattcag
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54670.1 |
intron # | 16 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA12G16580.1 (Glycine max), 5'ss of exon 16
CAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTCTCCAGgtaccaaacca--aaccgtaaaaacatc-tttcaaaacttttgtttcttgatttgtggcatcataataaaaactatgtttgatttttaattcag------
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CAACAAAAGTTTATCATCACTGAGTGATGTTATATTCGCCTTAGCCAAGAAGGAGGATCATGTGCCATTCAGGAACTCAAAGCTTACATATCTCCTTCAGgtaatgcattattattctttcacatggcattccaaagaatttaatttaattgtcatgcatttccagtgtaaaatttcttgcattatcaaccaatcagaaa
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA06G41600.1 (Glycine max), 5'ss of exon 15
CAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTCTCCAGgtacca---aaccaaaccgtaaaaacatctttcaaaacttttgtttcttgatttgtggcatcataataaaaactatgtttgatttttaattcag-----------
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CAACAAAAGTTTATCATCACTGAGTGATGTTATATTTGCCTTAGCCAAGAAGGAGGACCATGTGCCATTCAGAAACTCAAAGCTTACATATCTGCTTCAGgtaatgcataattattctttcacatggcattctgaagattttaattgtca---tgcattatca--gtgtaattttttttgcactatcaatcgatcaaaactaatc
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA12G34330.1 (Glycine max), 5'ss of exon 15
CAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTCTCCAGgtaccaaaccaaaccgtaaaaacatctttcaaaactt----ttgtttcttgatttgtggcatcataataaaaactatgtttgatttttaattcag---------
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AAATAAAAGTCTGTCATCATTAAGTGATGTTATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTTACATACCTTCTTCAGgtg----attatattttgttcatatttttaaacattctttattatttagttactcactatattaaactcataataatgccagaattttcttaccttgcacaatc
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: GLYMA13G36230.1 (Glycine max), 5'ss of exon 16
CAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTCTCCAGgtaccaa------accaaaccgtaaaaacatctttcaaaacttt-tgtttcttgatttgtggcatcataataaaaactatgtttgatt--tttaattcag-
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AAATAAAAGTCTGTCATCATTAAGTGATGTAATATTTGCCTTGGCCAAGAAGGAGGATCATATCCCATTCAGGAACTCAAAGCTCACATACCTACTTCAGgtgattattttttgttcatattttaaaacattctttagtatttagttattctttatattaaac-tcataataatgccaaaattttcttagcttgatgaaaa
upper sequence: AT5G54670.1 (Arabidopsis thaliana), 5'ss of exon 16
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 5'ss of exon 15
CAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTCTCCAGgta------ccaaaccaaac-----cgtaaaaacatctttcaaaactttt--gtttcttgatttgtggcatcataataaaaactatgtttgatttttaattcag
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CAATAAGAGTCTGTCATCATTAAGTGATGTTATATTTGCCCTGGCAAAGAAGGAGGACCATGTACCATTTAGGAACTCAAAGCTTACGTATCTTCTTCAGgtaaatgctccgatttaggcagatatgaaaaaacgacaatcaaattttttaagaaaaatgatttgattgatttaggtatacatc----ttgaccttgtgttcatMapped 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|164174254|gb|EL996416.1|EL996416EST: AAAGCTCACATATCTTCTCCAG CCTTGCTTAGGCGGTGACGCAAAGACGCTAATGTTTGTGAACATTGCACCG
genomic: AAAGCTCACATATCTTCTCCAGgtaccaaacc ... tttaattcagCCTTGCTTAGGCGGTGACGCAAAGACGCTAATGTTTGTGAACATTGCACCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAACAAAAGTTTGTCGTCGCTAGGCGATGTCATATTCGCCTTAGCAAAGAAAGAAGATCATGTACCATTCCGAAACTCAAAGCTCACATATCTTCTCCAGgtaccaaaccaaaccgtaaaaacatctttcaaaacttttgtttcttgatttgtggcatcataataaaaactatgtttgatttttaattcag
- - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA