Sequence
atgc intronic sequence ATGC exonic sequencegttattccttttctgctaataattattctttggattatcttggtattagacagttcatgggaagacaagtgtttaattttcttgtatatatatcttcatgcttttcagGTTTTGAATGGACTAGAGGCAGCAACAAATATCGTTGATGACATGGATGAATGGTTAGGAATATTCAACATTAAACTTAGACACATGAGGGAAGACATTG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G47550.2 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA04G03710.1 (Glycine max), 3'ss of exon 7
gttattccttttctgctaataattattctttggattatcttggtattagacagttcatgggaagacaagtgt-ttaattttcttgtatatatatcttcatgcttttcagGTTTTGAATGGACTAGAGGCAGCAACAAATATCGTTGATGACATGGATGAATGGTTAGGAATATTCAACATTAAACTTAGACACATGAGGGAAGACATTG
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-----cttcactttacaaatcattgtgtttctcgtcat-tagttatttaaaa--ttattttaacatgtttttatgaagtggttcatactaataatct-gtgcctggcagGTGTTGCAAGGGCTTGAAGCAGCATCAAATTGCGTGGAAGACATGGATGAATGGTTAGGCATGTTCAATGTAAAGCTTCGACACATGAGGGAAGATATTG
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0001g11700.t01 (Vitis vinifera), 3'ss of exon 7
gttattccttttctgctaataattattctttggattatcttggtattagacagttcatgggaagacaagt-gtttaattttcttgtatatatatcttcatgcttttcagGTTTTGAATGGACTAGAGGCAGCAACAAATATCGTTGATGACATGGATGAATGGTTAGGAATATTCAACATTAAACTTAGACACATGAGGGAAGACATTG
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------tcatgtatgttaacaagtga-caatagtgcgtattatttatgaagtcctc-taaagtggcatctagtctggttttttagtg-gttgatttgtttgtttttcagGTACTGCAAGGCCTCGAGACAGCTACAAATTGTGTTGATGATATGGATGAATGGTTAGGCATTTTCAATGTGAAACTTAGACACATGAGAGAGGATATTG
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ12163 (Selaginella moellendorffii), 3'ss of exon 7
gttattccttttctgctaataattattctttggattatcttggtattagacagttcatgggaagaca-agtgtttaattttcttgtatatatatcttcatgcttttcagGTTTTGAATGGACTAGAGGCAGCAACAAATATCGTTGATGACATGGATGAATGGTTAGGAATATTCAACATTAAACTTAGACACATGAGGGAAGACATTG
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---------------------------------------------gtaaatc-ttcaaagaacaatatagtgctggctgtgtttaca-aca-atcgttatatggtatagGTTCTTAGACGTTTGAATAATGCGTCAGAAGCGGTCGAAGACATGGATGAATGGCTAGGAATATTTAACGTCAAGCTTAGGCACATGCGGGAAGACATCG
upper sequence: AT1G47550.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: EFJ29370 (Selaginella moellendorffii), 3'ss of exon 7
gttattccttttctgctaataattattctttggattatcttggtattagacagttcatgggaagaca-agtgtttaattttcttgtatatatatcttcatgcttttcagGTTTTGAATGGACTAGAGGCAGCAACAAATATCGTTGATGACATGGATGAATGGTTAGGAATATTCAACATTAAACTTAGACACATGAGGGAAGACATTG
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---------------------------------------------gtaaatt-ttcaaagaacaatatagtgttggctgtgtttaca-aca-atcgttatatggtatagGTTCTTAGACGTTTGAATAATGCGTCAGAAGCGGTCGAAGACATGGATGAATGGCTAGGAATATTTAACGTCAAGCTTAGGCACATGCGGGAAGACATCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttcatgggaagacaagtgtttaattttcttgtatatatatcttcatgcttttcagGTTTTGAATGGACTAGAGGCAGCAACAAATATCGTTGATGACATGGATGAATGGTTAGGAATATTCAACATTAAACTTAGACACATGAGGGAAGACATTG
gtttaat putative branch site (score: 4)
tcttcatgcttttc putative PPT
tttaattttcttgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttattccttttctgctaataattattctttggattatcttggtattagacagttcatgggaagacaagtgtttaattttcttgtatatatatcttcatgcttttcagGTTTTGAATGGACTAGAGGCAGCAACAAATATCGTTGATGACATGGATGAATGGTTAGGAATATTCAACATTAAACTTAGACACATGAGGGAAGACATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA