Sequence
atgc intronic sequence ATGC exonic sequencegtacgcacacattccttttgcaagatattgctttgctagttcttgacttgttctcttaagctctactacttggttagtgcaaagttcactctgctctcatcttgttatgcaagagctgcttaaaattttcttaacttaataatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G25050.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G25050.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G33930.1 (Glycine max), 3'ss of exon 6
gtacgcacacattccttttgcaagatattgctttgctagttcttgacttgttctcttaagctctactacttggttagtgcaaagttcactctgctctcatcttgttatgcaagagctgcttaaaattttcttaacttaataatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
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---------------------------------------------------aattttaaaccattcaa-ttagtcagaaaggaatgt-ctccaatcgcagagaaacatgccaatttataattgtattctcatgtgctaatcattgtc--tttcagTGTGCTGTGCTTGCATTGGATGATTCAGTATTGGATGTTGATCAAGTTGAGAACCTCATAAAATTCTCTCCAACCAAAGAAGAGATGGAAATGCTGAAG
upper sequence: AT2G25050.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv04s0008g06530.t01 (Vitis vinifera), 3'ss of exon 9
gtacgcacacattccttttgcaagatattgctttgctagttcttgacttgttctcttaagctctactacttggttagtgcaaagttcactctgctctcatcttgttatgcaagagctgcttaaaattttcttaacttaataatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
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-----------------------------------cttgtgtctgttcagcaattctagtcccagacacgtggtaagtaaacag---agtctgattagttctttct-------------ttcattctggcttgccttca-aatgttt---tacagAGCTCAGTCCTTGCCTTGGATGATTCAGCATTAGATGTTGATCAAGTTGATAACCTCATAAAGTTCTGTCCAACAAAAGAAGAGATTGAACTACTCAAG
upper sequence: AT2G25050.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ33545 (Selaginella moellendorffii), 3'ss of exon 6
gtacgcacacattccttttgcaagatattgctttgctagttcttgacttgttctcttaagctctactacttggttagtgcaaagttcactctgctctcatcttgttatgcaagagctgcttaaaattttcttaacttaataatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
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------------------------------------------------------------------------------------------------gtaagttgctctctacattatgc--aatgtggtttttacttccaactct-------cagAAAGCAATACTAGCGTTGGATGGGACGGTACTGGATGTTGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACGAAGGAGGAGATGGAAACGCTCAAG
upper sequence: AT2G25050.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ36895 (Selaginella moellendorffii), 3'ss of exon 6
gtacgcacacattccttttgcaagatattgctttgctagttcttgacttgttctcttaagctctactacttggttagtgcaaagttcactctgctctcatcttgttatgcaagagctgcttaaaattttcttaacttaataatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
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------------------------------------------------------------------------------------------------gtaagttgctctctacattatgc--aatgtggtttttacttc-caaccct------cagAAAGCAATACTAGCGTTGGATGGGACGGTACTGGATGTTGATCAGGTTGATAATCTGATCAAGTTTTGTCCAACGAAGGAGGAGATGGAAACGCTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgttatgcaagagctgcttaaaattttcttaacttaataatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
tcttt CT-rich tract
ttaaaattttcttaac 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacgcacacattccttttgcaagatattgctttgctagttcttgacttgttctcttaagctctactacttggttagtgcaaagttcactctgctctcatcttgttatgcaagagctgcttaaaattttcttaacttaataatctttggttacagAGTTCTGTTCTTGCTTTGGATGAGTCAGTGATAGATGTTGATCAAGTTGACAATCTAATAAAGTTTTGTCCAACAAAAGAAGAAGCAGAATTGCTCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC