Sequence
atgc intronic sequence ATGC exonic sequence...gtgatcactcaaattattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagctcttgatgttacaatgcagAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAATGACGGTGCAAGATCTGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43430.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43430.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os04g10400.1 (Oryza sativa), 3'ss of exon 3
------------------------------------------------------------------------------gtgatcactcaaa-----ttattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgtt-ttgtttgtaacagctcttgatgttacaatgcagAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAATGACGGTGCAAGATCTGAAA
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gtatgttccatgaaacatttattttctttcttttagtttaatttaacaaggctagtacttcgattcttcataagcattgcgatcatttagtgatctctgtcacatagctggatctttgtattgcattgtggttttgagccaatttcagaaattgcctaaactattgtttgatttt-tgtgacagCACGGATTTGAGACTGAACCAACCAAGGTATGCAACATTGCCAAACATAATGAAGGCAAAATCAAAAGTCATCAAGAAAGTCACCCCCGAAGATCTGGAT
upper sequence: AT5G43430.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G34520.1 (Glycine max), 3'ss of exon 3
gtgatcactcaa-attattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagctcttga---tgttacaatgcagAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAATGACGGTGCAAGATCTGAAA
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-tttctatgtaatagtaattagtgatttaacaagtgtgtttttctccctccttttaa-aaccctttcttgatatgtga--attttgaaccttttcttcttgcagCACTGATCTGAGGCTGAACCAACCAAGGTATGCTACTCTTCCCAACATAATGAAAGCAAAGTCGAAACCCATAAAAAAATTCACTCCGGAGGAGTTGAAT
upper sequence: AT5G43430.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0049g00470.t01 (Vitis vinifera), 3'ss of exon 4
gtgatcactcaaattattaagca-aactagcaattaagctttaatagaaaggtgcaacaactct-tgttttgttt-gtaacagctcttgatgttaca------atgcagAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAATGACGGTGCAAGATCTGAAA
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---------cagaaagctgactgcaattatttgccataggctagcataaatgcaacttggctctgtgtttcatctcattacttgacctgatattttgtacctcatgcagCACTGATTTGAGACTGAACCAGCCTCGGTATGCAACACTCCCCAACATTATGAAAGCAAAATCGAAGGTAATAAAGAAGTTCACTCCACAGGAATTGAATMapped 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|86084487|gb|DR380246.1|DR380246EST: GTGGATGGAGGTCTTGAGACTCTTAATGTAGACTTACCCGCTGTGATAAC AACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAAT
genomic: GTGGATGGAGGTCTTGAGACTCTTAATGTAGACTTACCCGCTGTGATAACgtaagttcta ... tacaatgcagAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaaaggtgcaacaactcttgttttgtttgtaacagctcttgatgttacaatgcagAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAATGACGGTGCAAGATCTGAAA
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgatcactcaaattattaagcaaactagcaattaagctttaatagaaaggtgcaacaactcttgttttgtttgtaacagctcttgatgttacaatgcagAACTGATTTGAGGCTGAACCAACCAAGATATGCATCACTCCCTAACATAATGAAGGCAAAATCAAAGCCTATAAAGAAAATGACGGTGCAAGATCTGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - actcaaa
- - - - - - - - - aagcaaa
- - - - - - - - - - - - - - - - - - - - -aatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - gcaacaa