Sequence
atgc intronic sequence ATGC exonic sequenceatatccttcactacataatgcttttgtatatatcgcttatacttgtcaacaaaagatattgtgataccttaacgtagctttacGTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G44270.1 |
intron # | 6 |
splice site | 3' |
intron type | U12 (go to U12 genes for details) |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os01g41565.1 (Oryza sativa), 3'ss of exon 6
-----atatccttcactacataatg-cttttgtat----atatcg-cttatact-tgtcaacaaaagatattgtgata-ccttaacgtagctttacGTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAAT
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gttatatatcctt-attatgcaatatcccatatattctcatgtgatcttatgctctatttatcaattgtatgttattatccttgaccctatgacacgtatgcatatttcaaaaagCTGGACTACTTCTCCACAGAAT
upper sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os02g52470.2 (Oryza sativa), 3'ss of exon 7
atatccttcactacataatgc----ttttgtat-atatcgc-ttatacttgtcaacaaaag----atattgtgataccttaacgtagctttacGTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAAT
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atatcctt-actatgcaatatcccatataatgtgatattatgctctattcatcaattgcacttttatgttattat-ccttgaccttatgacacGTATGCATATTTCAAAAAGCTGGACTACTTCTCCACAGAAT
upper sequence: AT2G44270.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G00350.3 (Glycine max), 3'ss of exon 1
---------------------------atatccttcactacataatgcttttgtatatatcgcttatacttgtc---aac-----aaaagatattgtgataccttaacgtagctttacGTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAAT------------------------
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gtatgcttatttcaagaagctcgattacttttccaccgaatgtaaccttcctttcttttcctcttattttcccctctaactgccaaacaaacatttcactctctctacaattccagGCATTTACTCTCCTAATGCATATCGAGGTTTTGCTCGCGAGTTCATCAAAGATTTGGAGAGAATCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatcgcttatacttgtcaacaaaagatattgtgataccttaacgtagctttacGTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAAT
taccttaac putative branch site
aaaagatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatccttcactacataatgcttttgtatatatcgcttatacttgtcaacaaaagatattgtgataccttaacgtagctttacGTATGCTTATTTCAAGAAGCTGGATTACTTCTCCACTGAAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA