Sequence
atgc intronic sequence ATGC exonic sequenceGTTGAACAAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcggtttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaatgatttttttggggggttgtag
Basic information
species | Arabidopsis thaliana |
transcript | AT2G33350.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g32900.2 (Oryza sativa), 5'ss of exon 3
GTTGAACAAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcgg-------tttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaatg-atttttttggggggttgtag-----------------------------------------------------------
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-----TCAAGACCGTCCGCCTCTCCAACGAGGAGAGGAAGGAAAAGATCCACAGGTACATCAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAGATCAAGGTGAGgcaagaacttccaaattattcaaattcaaattcaaaat-atcacccccccccccaacccatatttcaaacgaatttcacctcaccgccgaccacgttactgacatctcagattttttttttaaaaaaaaaatctgcag
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g32900.1 (Oryza sativa), 5'ss of exon 3
GTTGAACAAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcgg-------tttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaatg-atttttttggggggttgtag-----------------------------------------------------------
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GAGCTTCAAGACCGTCCGCCTCTCCAACGAGGAGAGGAAGGAAAAGATCCACAGGTACATCAAGAAGAGGAACGAGAGGAATTTCAGCAAGAAGATCAAGgtgaggcaagaacttccaaattattcaaattcaaattcaaaat-atcacccccccccccaacccatatttcaaacgaatttcacctcaccgccgaccacgttactgacatctcagattttttttttaaaaaaaaaatctgcag
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os03g04620.4 (Oryza sativa), 5'ss of exon 3
GTTGAACAAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcggtttttattaaaccaaaccggacttaaccgt-tgttaaatgttgtcccaatgatttttttggggggttgtag-------
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CCCCTACAAAGGTGTGCGTCTAACAGCTGAACAGAGAAAGGAAAAGATCTCCAGGTACATAAAGAAAAGGAACGAAAGGAACTTCAGCAAAAAAATAAAGgt--aatattgaacatttcaa---gaacataactacatgcatcatcttaccaaatttattgtactgatgtaaaacaaaatgcag
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G21380.1 (Glycine max), 5'ss of exon 4
GTTGAACAAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcggtttttattaaaccaaaccggacttaaccgttgttaaatgttgtccca----atgatttttttggggggttgtag----------------------
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TACCTTGAAGGTTGGAAAACTCTCTGTTGAGCAGAGGAAGGAAAAGATTCATAGATACATGAAGAAGAGAAACGAAAGAAATTTCAGCAAGAAAATCAAGgtactacatctg--aacaccaacattaacaaacaaatttcaaatcttatactgttttacatgatttccaatctactgcatcaaccaagccttatgcatattt
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G26990.1 (Glycine max), 5'ss of exon 2
GTTGAAC--AAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcggtttttattaaaccaa----accggacttaaccgttgttaaatgttgtcccaatgatt-tttttggggggttgtag--------------------------------------------------------------------
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--TAACTTGAAAGTTGGAAAACTCTCTGTTGAGCAGAGGAAGGAAAAGATTCATAGATACATGAAGAAGAGAAATGAAAGAAATTTCAGCAAGAAAATCAAGgtactacatctga-acaccaacattaacaaacaaatttgaaatcttatattatgttatacatgatttccaatctattgcatcaatcaagccttgtgcatattttcaaaattcaactaatgatccaatgttttttaaaaaaaaaatgcag
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA20G34250.1 (Glycine max), 5'ss of exon 5
GTTGAACAAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcggt-----ttttattaaac--caaaccgg--acttaaccgttgttaaatgttgtcccaatgatttttttggggggttgtag----------------------------------------------------------------------------
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CTCCTTCAAGGTTGGAAAACTTTCTGTTGAGCAAAGGAAAGAAAAGATCAATAGATACATGAAGAAAAGAAATGAAAGAAACTTCAGCAAGAAAATTAAGgtacagtcaagctccttcccatcttcaaaacagccacatcatcaaacaaaattgaaatcttatcatgttacatatgcatatgcaaggtattccttgcttataaacaaccacttgttattgcatactttcaagttcaactaatgatgcaaccaaatatgcag
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G33390.1 (Glycine max), 5'ss of exon 2
GTTGAACAAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcg-----gtttttattaaac--caaaccggacttaaccgttgttaaatgt-tgtcccaatga---------tttttttggggggttgtag------------------------------
| ||| ||||||||||| || ||||||||||||||| ||||| ||| ||||||||||| || || ||||| || |||| ||||||||| ||||| | | || | | | |||| | | | || | | | ||| | | | || | |||| ||| || |
CTCCTTCAAGGTTGGAAAACTTTCTGTTGAGCAAAGGAAAGAAAAGATCAATAGATACATGAAGAAAAGAAATGAAAGAAACTTCAGCAAGAAAATTAAGgtacactcaagcttcttcccatcttcaaaacagccatatcatgttacatatgcatatgcttataaacaaccactttttattgcatactttcaagttcaactaatgatgaaaccaaatatgcag
upper sequence: AT2G33350.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv05s0049g01830.t01 (Vitis vinifera), 5'ss of exon 3
GTTGAACAAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgtt-------------cggtttttattaaaccaaaccggacttaaccgttgttaa---------atgttgtcccaa---tgatttttttggggggttgtag------------------------
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CACTTTCAAGGTTGGAAAACTCTCTGTGGAGCAAAGGAAAGAGAAGATCCATAGATACATGAAGAAAAGGAACGAGAGGAATTTCAGCAAGAAAATCAAGgttatctctctctctctcgttcttctgctatcattttacattcagatcatgtataggcatacgtatgataacttaaactttattttcttactaaatgttagaaaaatataataataataatgcagMapped 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|116378841|gb|EG421433.1|EG421433EST: GTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAG TATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGA
genomic: GTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcggtttt ... ggggttgtagTATGCGTGTAGGAAAACATTGGCAGATAGTCGACCAAGAGTTAGAGGAAGA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GTTGAACAAAGTTGGAAAACTCTCCCCTGAGCAAAGGAAAGAGAAGATTCGTAGGTACATGAAGAAGAGGAACGAAAGGAATTTCAACAAGAAAATCAAGgttcggtttttattaaaccaaaccggacttaaccgttgttaaatgttgtcccaatgatttttttggggggttgtag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA