Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttttttttcacccttcctctgcttattacatgaaagttgggatgattttcactaaatttggtagctagccaggtgaggtcatctaagagtttttttccttgccttttttgcagGTTGTTAATCCATTTACCAAATATCCTTTATCAAGAAATATTCAGAGACTTTTCATTTATCTCT
Basic information
species | Arabidopsis thaliana |
transcript | AT3G54830.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G54830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA16G08770.1 (Glycine max), 3'ss of exon 4
gtaagtttttttttttcacccttcctctgcttattacatgaaagttgggatgattttcactaaatttggtagctagccaggtgaggtcatctaagagtttttttccttgcctttttt-gcagGTTGTTAATCCATTTACCAAATATCCTTTAT-CAAGAAATATTCAGAGACTTTTCATTTATCTCT-----------------------------------
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--------------attattctcatactatggcttaattcagtattagcata----ttattaatgtt--ttattaaccatataaa--taaccaagatttttatgtgttacttttttttgcagGTGGTTAATCCATTTACCAAATATCCTTTATACATAAGAGCATGCATGTCATTATACATACCATGGAAAATGTCATTCAACATAAGGAATGGCTTTGTTT
upper sequence: AT3G54830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA02G19430.1 (Glycine max), 3'ss of exon 6
gtaagtttttttttttcacccttcctctgcttattacatgaaagttgggatgattttcactaaatttggtagctagccaggtgaggtcatctaagagtttttttccttgccttttttgcagGTTGTTAATCCATTTACCAAATATCCTTTATCAAGAAATATTCAGAGACTTTTCATTTATCTCT
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-ctagtttgagttgttaacctaatttatattcaccatat-----tgtgaataatttttatcag---tcataaatttctatcttta-ttatcttgtggtttgatt-----------ttgcagGTGGTTAATCCATTTACCAAATATCCTTCAT-ATGCGCC-------------------------
upper sequence: AT3G54830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA10G15130.1 (Glycine max), 3'ss of exon 5
gtaagtttttttttttcacccttcctctgcttattacatgaaagttgggatgattttcactaaatttggtagctagccaggtgaggtcatctaagagtttttttccttgccttttttgcagGTTGTTAATCCATTTACCAAATATCCTTTATCAAGAAATATTCAGAGACTTTTCATTTATCTCT
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-------tgagttgttaacctaatctatatatatcaccatattattgatat--tttttaatcagtcatataaattgcta---------attttattatcatgtggtttga---ttttgcagGTGGTTAATCCATTTACCAAATATCCTTCAT-ATGCGTC-------------------------
upper sequence: AT3G54830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G32260.1 (Glycine max), 3'ss of exon 8
gtaagtttttttttttcacccttcctctgcttattacatgaaagttgggatgattttcactaaatttggtagctagccaggtgaggtcatctaagagtttttttccttgcctttttt-gcagGTTGTTAATCCATTTACCAAATATCCTTTATCAAGAAATATTCAGAGACTTTTCATTTATCTCT
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--------------attattctcatactatggcttaattcagtatcagcata----ttattaatgtt--ttattaaccatataaa--taaccaagatttttatctgttacttttttttgcagGTGGTTAATCCATTTACCAA--------------------------------------------
upper sequence: AT3G54830.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv13s0019g04660.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtttttttttttcacccttcctctgcttattac-atgaaagttgggatgattttcactaaatttggtagctagccaggtgaggtcatctaagagtttttttccttgccttttttgcagGTTGTTAATCCATTTACCAAATATCCTTTATCAAGAAATATTCAGAGACTTTTCATTTATCTCT
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---------------gcagatgcaacaaaattattgctacctatgttgtaaatcacttcttccactataatattg---cagtttctttgatctatatatcctgtttgtt----cttttgcagGTAGTTAACCCTTTTACCAAATATCCTTTTTCTA-ATATAATTAGA---TTTTCAG-------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggtagctagccaggtgaggtcatctaagagtttttttccttgccttttttgcagGTTGTTAATCCATTTACCAAATATCCTTTATCAAGAAATATTCAGAGACTTTTCATTTATCTCT
tttttttccttgcctt CT-rich tract
agttttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttttttttcacccttcctctgcttattacatgaaagttgggatgattttcactaaatttggtagctagccaggtgaggtcatctaagagtttttttccttgccttttttgcagGTTGTTAATCCATTTACCAAATATCCTTTATCAAGAAATATTCAGAGACTTTTCATTTATCTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA