Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttaactctagtctactgagtgtatatatgtctgattgattcaagtccgctaagttcaaccagctgccatcacatttatctttctgcttgatatctatgttcttcttttcttttctggtcttttagtttcaacatctttagccgaacaataataatttgtactgttattacttgacatcttggcatcagAGATATGTGGGAGAAGTCAATGAATGGTCTGCTAAGCTTGGTTAAGAAATCAACACCTTTGTCGTTTACATATATCTGTGAGAAGAGTGGAAATTCTTTG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21160.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA08G23730.1 (Glycine max), 3'ss of exon 9
gtaagtttaactctagtctactgagtgtatatatgtctgattgattcaagtccgctaagttcaaccagctgccatcacatttatctttctgcttgatatctatgttcttcttttcttttctggtcttttagtttcaacatctttagccgaacaataataatttgtactgttattacttgacatcttggcatcagAGATATGTGGGAGAAGTCAATGAATGGTCTGCTAAGCTTGGTTAAGAAATCAACACCTTTGTCGTTTACATATATCTGTGAGAAGAGTGGAAATTCTTTG
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----------------------------------------------------------------------------------------ttaaggcatttcaattttcct-ttcacataaatattgaataagtgtaagtgtttttt----aacttctttttttcat-ctatttctttctggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGCCTGTCAAGTTTGATTAGGAGATCAACACCATCTTCTTTTACTTATATATGTGAGAAGAATGGAGGATCTCTC
upper sequence: AT3G21160.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA07G02290.1 (Glycine max), 3'ss of exon 8
gtaagtttaactctagtctactgagtgtatatatgtctgattgattcaagtccgctaagttcaaccagctgccatcacatttatctttctgcttgatatctatgttcttcttttcttttctggtctt---ttagtttcaacatctttagccgaacaataataatttgtactgttattacttgacatcttggcatcagAGATATGTGGGAGAAGTCAATGAATGGTCTGCTAAGCTTGGTTAAGAAATCAACACCTTTGTCGTTTACATATATCTGTGAGAAGAGTGGAAATTCTTTG
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---------------------------------------------------------------------------------------------agacatttcaatt-ttcctttcacataaaatattgaataagtgtaaatgttttt---taaccttttctttttccatccatttctttttggaatcttgaaaacagAGATATGTGGGAGAAATCAATGAAAGGTCTATCAAGTTTGATTAGGAGATCAACACCATCTTCATTTGCTTATATATGTGAGAAGAATGGAGGATCTCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttagccgaacaataataatttgtactgttattacttgacatcttggcatcagAGATATGTGGGAGAAGTCAATGAATGGTCTGCTAAGCTTGGTTAAGAAATCAACACCTTTGTCGTTTACATATATCTGTGAGAAGAGTGGAAATTCTTTG
acttgac putative branch site (score: 4)
aataataatttgtact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttaactctagtctactgagtgtatatatgtctgattgattcaagtccgctaagttcaaccagctgccatcacatttatctttctgcttgatatctatgttcttcttttcttttctggtcttttagtttcaacatctttagccgaacaataataatttgtactgttattacttgacatcttggcatcagAGATATGTGGGAGAAGTCAATGAATGGTCTGCTAAGCTTGGTTAAGAAATCAACACCTTTGTCGTTTACATATATCTGTGAGAAGAGTGGAAATTCTTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA