Sequence
atgc intronic sequence ATGC exonic sequencegtaaagaaagattgaacctatgaagtttgagtttgttcccctttagattgtggtttcaatctctcatttccccgggaattaattgaaaattttcttgtgtcttgatcatgaacagATGTTTAGAAGAAGGAGCTGAAGAGTTTTTCTTGAAACCAGTAAGATTGGCTGATCTTAACAAGTTGAAACCTCATATGATGAAAACAAAGTTGAAGAAC
Basic information
species | Arabidopsis thaliana |
transcript | AT3G57040.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G57040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA19G31320.2 (Glycine max), 3'ss of exon 4
gtaaagaaagattgaacctatgaagtttgagtttgttcccctttagattgtggtttcaatctctcatttccccgggaattaattgaaaattttcttg-tgtcttgatcatg---aacagATGTTTAGAAGAAGGAGCTGAAGAGTTTTTCTTGAAACCAGTAAGATTGGCTGATCTTAACAAGTTGAAACCTCATATGATGAAAACAAAGTTGAAGAAC
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-----gtaagaaggaga----aatatttcagtactttttttaaaaaaataaaataa-aattccctatgaacatttttatgacgtgaaattctgatgaatatctcaaactggcaaaacagATGTTTGGAGGAAGGAGCAGAAGAATTTTTCTTGAAGCCTGTGAGGCTGTCAGATTTAAACAAGCTTAAACCCCATATGAAGAAAACCAAGTTGAAAGAT
upper sequence: AT3G57040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA03G28570.1 (Glycine max), 3'ss of exon 4
gtaaagaaagattgaacctatgaagtttgagtttgttcccctttagattgtggtttcaatctctcatttccccgggaattaattgaaaattttcttg-tgtcttgatcatg---aacagATGTTTAGAAGAAGGAGCTGAAGAGTTTTTCTTGAAACCAGTAAGATTGGCTGATCTTAACAAGTTGAAACCTCATATGATGAAAACAAAGTTGAAGAAC
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gtaa-gaaaga--gaact------atttctgtactttctttatttatttattttttttacctgtgaacattttt---atgaagtgaaattctgattaatatctgaaactggcaaaacagATGTTTGGAGGAAGGAGCCGAAGAATTTTTCTTGAAGCCTGTGAGGTTGTCAGATTTGAACAAGCTTAAACCCCACATGAAGAAAACCAAGTTCAAAGAT
upper sequence: AT3G57040.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv08s0007g05390.t01 (Vitis vinifera), 3'ss of exon 4
gtaaag---aaagattgaacctatgaagtttgagtttgttccccttta---gattgtggtttcaatctctcatttccccg-ggaattaattgaaaattttcttgtgtcttgatcatgaacagATGTTTAGAAGAAGGAGCTGAAGAGTTTTTCTTGAAACCAGTAAGATTGGCTGATCTTAACAAGTTGAAACCTCATATGATGAAAACAAAGTTGAAGAAC
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gtaaaactcaaaaacaagaattgggaattcctttccaattcctttccatggaaacacaatctggaagactgattctcaggtgaaattgactaaa--------tgggtgct-atcatta-cagATGCTTAGAAGAAGGAGCAGAAGAATTTTTTCTGAAACCAGTTCAGATATCAGATGTGAATCGGCTTAAACCTCATATGATGAAAGCCAAAAGTAAGGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctcatttccccgggaattaattgaaaattttcttgtgtcttgatcatgaacagATGTTTAGAAGAAGGAGCTGAAGAGTTTTTCTTGAAACCAGTAAGATTGGCTGATCTTAACAAGTTGAAACCTCATATGATGAAAACAAAGTTGAAGAAC
aattaattgaaaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagaaagattgaacctatgaagtttgagtttgttcccctttagattgtggtttcaatctctcatttccccgggaattaattgaaaattttcttgtgtcttgatcatgaacagATGTTTAGAAGAAGGAGCTGAAGAGTTTTTCTTGAAACCAGTAAGATTGGCTGATCTTAACAAGTTGAAACCTCATATGATGAAAACAAAGTTGAAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC