Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G54080.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 6
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
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-------------------------------------------gta-agtgtttcacgtatctgtgtgtattttttttttccagttctcactctgctagctgcgacattttatcggaagggtat-tttaccagttgttcaagattatgcattttctttcttacccatatgtatttttt-ttccagAGATGCTAGGGTAATGTGGGATCAGAAAACTGGACGATCCAGAGGTTTTGGTTTTGTTTCTTTCAGAAATCAGCAG
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G008611_T01 (Zea mays), 3'ss of exon 7
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcaga-atct-ttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
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-------------------------------------------------gtaagcactgcctggctctcatctctcctccatttacttgtcattgt---tgaca-------ttttagcagagtggcttgct-acttgtgcagtacatgacatgtctatttactagtttagcttggtaacttttgcagAGATGCTAGTGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGATTTGGTTTTGTTTCTTTCAGGAACCAGCAG
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 6
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcaga-atct-ttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
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-------------------------------------------------gtaagcactgcctggctctcatctctcctccatttacttgtcattgt---tgaca-------ttttagcagagtggcttgct-acttgtgcagtacatgacatgtctatttaccagtttagcttggtaacttttgcagAGATGCTAGGGTTATGTGGGACCAGAAAACAGGACGATCCAGAGGGTTTGGTTTTGTTTCTTTCAGGAACCAGCAG
upper sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 6
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
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----------------------------------------------------------------------------------atatttgt-actgtctcccatgatagttgtacggtgtgttctatacaattgtgttggtaacttagcttggctcatcattt--tattttttctggcggctccagAGATGCTAGGGTTATGTGGGATCAGAAGACTGGGCGTTCAAGGGGATTTGGATTTGTTTCATTCCGTAATCAACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
atttaat putative branch site (score: 4)
aatctttgatttaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcttgtgcttggtcttctgattttagttactagctggttacaaaaatgaaaatcttgttacacaactacggtgtacgcatatatcactatgtgttacaagattttctttaatgattaagcttatttgtttaaacagtctatcagaatctttgatttaatatctatagTTCTTATTATAGGGACGCAAGAGTAATGTGGGACCAGAAAACTGGACGCTCAAGAGGCTTTGGTTTTGTTTCCTTCCGTAATCAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG