Sequence
atgc intronic sequence ATGC exonic sequencegtaggttgcctttcttccatcaaaccatcgttttactagttacttggttgcacccaactcgtactagatccatggttatgttaatcaataccctttcctcttttgggttttatgtagGCTCTACCATTCTCAGATTCTTTGAAGTTTCTTTGCTACATGAAAGACTGGAGTTTAATTCCCGAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G21540.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G21540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G37050.1 (Glycine max), 3'ss of exon 7
gtaggttgcctttcttccatcaa--accatcgttttactagttacttggttgcacccaactcgtactagatc--catggttatgt-taatcaataccctttcctcttttgggttttatgtagGCTCTACCATTCTCAGATTCTTTGAAGTTTCTTTGCTACATGAAAGACTGGAGTTTAATTCCCGAAAAG
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----------tttcatgtagaagtggcaaaagtacgacca-ctagaaaatggtagctaacttttttttaattgtaaacattatgtctaatttgtaccattcc-----------tttatgcagGCTTTACCATTTTCAGATGCTTTGAAGCTTCTGTCGTACTTGAAAGACTGGACTTCATACTCTGATAAG
upper sequence: AT3G21540.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G34360.1 (Glycine max), 3'ss of exon 9
gtaggttgcctttcttccatcaaaccatcgttttactagttacttggttgcacccaactcgtactag-atccatggttatgttaatcaataccctttcctct--tttgggt------tttatgtagGCTCTACCATTCTCAGATTCTTTGAAGTTTCTTTGCTACATGAAAGACTGGAGTTTAATTCCCGAAAAG
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--------------------------tttcatgtagaagtggctcaagtacaaccaccagaaaatggtagctatacttttttaaattgtaagcattatgtctaatttgtaccattcctttatgcagGCTTTACCATTTTCAGATGCTTTGAAGCTTCTGTCGTACTTGAAAGACTGGACTTCATACTCTGATAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actagatccatggttatgttaatcaataccctttcctcttttgggttttatgtagGCTCTACCATTCTCAGATTCTTTGAAGTTTCTTTGCTACATGAAAGACTGGAGTTTAATTCCCGAAAAG
tgttaat putative branch site (score: 3)
ccctttcctcttttgg putative PPT
ttatgttaatcaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggttgcctttcttccatcaaaccatcgttttactagttacttggttgcacccaactcgtactagatccatggttatgttaatcaataccctttcctcttttgggttttatgtagGCTCTACCATTCTCAGATTCTTTGAAGTTTCTTTGCTACATGAAAGACTGGAGTTTAATTCCCGAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG