Sequence
atgc intronic sequence ATGC exonic sequence...tgtgcttctaaatttataaacttttagtcaatttcttctttgactagagtctcatcccagagtattgcttagccttgacttatgtgatacattttataagAGGAATTTGTGGCACATTCTGCTGCTGTTAATTGTCTTAAGATTGGGAGGAAGTCCTCCAGGGTTCTCGTTACAGGCGGAGAAGATCACAAGGTTAATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G08390.1 |
intron # | 2 |
splice site | 3' |
intron type | U12 (go to U12 genes for details) |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA19G00890.1 (Glycine max), 3'ss of exon 2
--------------------------------------------------------------tgtgcttctaaatttataaacttttagtcaatttcttctttgactagagtctcatcccagagtattgcttagccttgacttatgt-gatacattttata-agAGGAATTTGTGGCACATTCTGCTGCTGTTAATTGTCTTAAGATTGGGAGGAAGTCCTCCAGGGTTCTCGTTACAGGCGGAGAAGATCACAAGGTTAATCT
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gtatccttcatctcttgtctgtctgtgctttacattttgtttgatctatctatgcactcgcccttcattttctatctgcagatctctctctactttgttattatgttagagtctt-tctttgtgtgtgtgtgtgacttggctggccttgacgagttatgtccagAGGAATTTGTAGCACATGCTTCTACTGTCAATTGCCTCAAGATTGGACGGAAATCATCCAGGGTTCTTGTCACTGGAGGTGAAGATCACAAGGTCAATCT
upper sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA05G09360.1 (Glycine max), 3'ss of exon 2
--------------------------------tgtgcttctaaatttataaacttttagtcaatttcttctttgactagagtctcatcccagagtattgcttagccttgactta-----tgtgat---------acattttata---agAGGAATTTGTGGCACATTCTGCTGCTGTTAATTGTCTTAAGATTGGGAGGAAGTCCTCCAGGGTTCTCGTTACAGGCGGAGAAGATCACAAGGTTAATCT
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gtatccttcatctcttgtttgtctgtgctttacattttgtttgatctatgcacttgccctccattttctatctgcagatctctctctctctctctctctctctctctctacttggtgtgtgtgacttggccttgacgagttatgtccagAGGAATTTGTAGCACATGCTTCTACCGTCAATTGCCTCAAGATTGGACGGAAATCATCCAGGGTTCTTGTCACTGGAGGTGAAGATCACAAGGTCAATCT
upper sequence: AT5G08390.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 1
tgtgcttctaaatttataaacttttagtcaatttcttctttgactagagtctcatcccagagtattgcttagccttgacttatgtgatacattttataagAGGAATTTGTGGCACATTCTGCTGCTGTTAATTGTCTTAAGATTGGGAGGAAGTCCTCCAGGGTTCTCGTTACAGGCGGAGAAGATCACAAGGTTAATCT
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tctgcagatcccttctctacccttgcttcacagcatttgttattttgaattttgaatttttacttctcgagaaaattccttgaccacggtttttgaacagAGGAATTTGTAGCACACTCTTCCAGTGTAAACTGTCTCAAGATTGGGAGGAAGTCATCCAGGGTTCTTGTCACCGGTGGAGAAGATCACAAGGTGAATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagtctcatcccagagtattgcttagccttgacttatgtgatacattttataagAGGAATTTGTGGCACATTCTGCTGCTGTTAATTGTCTTAAGATTGGGAGGAAGTCCTCCAGGGTTCTCGTTACAGGCGGAGAAGATCACAAGGTTAATCT
agccttgac putative branch site
tgatacattttataa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgtgcttctaaatttataaacttttagtcaatttcttctttgactagagtctcatcccagagtattgcttagccttgacttatgtgatacattttataagAGGAATTTGTGGCACATTCTGCTGCTGTTAATTGTCTTAAGATTGGGAGGAAGTCCTCCAGGGTTCTCGTTACAGGCGGAGAAGATCACAAGGTTAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA