Sequence
atgc intronic sequence ATGC exonic sequencegtctgtagtctcctcataagaagaatgctttatgtacttactacttactctaaaccctaaatctgaaatcttattcgttttgtttcttattgagcagGAAACACTAATACATTGGCTGGTAATGTACCTCCAAAGGCTAATCTTGGTGATTTGAGGGGACTAGCAGGCGGGTTGAACGGGCTAAACAGCTCGGCGAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G54190.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G54190.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G35050.2 (Glycine max), 3'ss of exon 3
gtctgtagtctcctcataagaagaatgctttatgtacttactacttactctaaaccc--taaatctgaaatcttattcgttttgtttcttattgagcagGAAACACTAATACATTGGCTGGTAATGTACCTCCAAAGGCTAATCTTGGTGATTTGAGGGGACTAGCAGGCGGGTTGAACGGGCTAAACAGCTCGGCGAT
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-------gtctagt--tcattagcatgtttattgtgagttccagttcttatcacaccattaggttgcatttcttatgctgattgtgtgt-attcaacagGGAACACAAACACATTGGCTGGTAATGTACCTCCCAAGGCTAACCTTGGTGACTTGAGGGGACTTCAGGGTGGTTTGAATGGGCTAAACAGCTCAGCCAT
upper sequence: AT5G54190.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA06G38160.1 (Glycine max), 3'ss of exon 3
----------gtctgtagtctcctcataagaagaatgctttatgtacttactacttactctaaaccctaaatctgaaatcttattcgttttgtttcttattgagcagGAAACACTAATACATTGGCTGGTAATGTACCTCCAAAGGCTAATCTTGGTGATTTGAGGGGACTAGCAGGCGGGTTGAACGGGCTAAACAGCTCGGCGAT
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ataatgcattgttagtaattctttttatagtgaacctttatttgtattgaaggttt---ttaggattcatat---aggtgctgatgattttgtaaat-atcaaacagGAAACACCAACACATTGGCTGGAAATGTGCCACCCAAGGCTAACCTTGGTGACATGAGGGGACTAGCTGGAGGCTTGAATGGGCTAAACACTTCAGCCAT
upper sequence: AT5G54190.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv19s0014g03160.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------gtctgtagtctcctcataagaagaatgctttatgtacttactacttactctaaaccctaa-atctgaaatcttattcgttttgtttcttattgagcagGAAACACTAATACATTGGCTGGTAATGTACCTCCAAAGGCTAATCTTGGTGATTTGAGGGGACTAGCAGGCGGGTTGAACGGGCTAAACAGCTCGGCGAT
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gtactgcaattaatcaggacaaatatgattcatgtaaaatagaagtaccactgaatttcatgatgagttcaatacaaatttgtcatataaatgtactaagtatgctattccttctataaaatgaatcagGGAACACAAATACCTTGGCTGGAAATGTGCCTCCAAAGGCCAACCTTGGGGACTTGAGGGGAATGGCAGGAGGTCTAAATGGGCTGAACAGCTCAGCCAT
upper sequence: AT5G54190.2 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv12s0059g00270.t01 (Vitis vinifera), 3'ss of exon 3
-------------gtctgtagtctcctcataagaagaatgctttatgtacttactac-ttactctaaaccctaaatctgaaatcttattcgttttgtttcttattgagcagGAAACACTAATACATTGGCTGGTAATGTACCTCCAAAGGCTAATCTTGGTGATTTGAGGGGACTAGCAGGCGGGTTGAACGGGCTAAACAGCTCGGCGAT
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gtggtgtgtgtagatccaaacctctaacaaaaccagaaagccagagagagttgatacattaagcaagacacatgatctaaa-----------tctgcaactgatgtttcagGAAACACAAACACCTTGGCTGGAAATGTGCCCCCAAAGGCTAACCTGGGGGATCTAAGGGGACTTGCTGGAGGATTGAATGGGATAAACGGCTCACCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttactctaaaccctaaatctgaaatcttattcgttttgtttcttattgagcagGAAACACTAATACATTGGCTGGTAATGTACCTCCAAAGGCTAATCTTGGTGATTTGAGGGGACTAGCAGGCGGGTTGAACGGGCTAAACAGCTCGGCGAT
ttcgttttgtttctt CT-rich tract
ttttgtttcttatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgtagtctcctcataagaagaatgctttatgtacttactacttactctaaaccctaaatctgaaatcttattcgttttgtttcttattgagcagGAAACACTAATACATTGGCTGGTAATGTACCTCCAAAGGCTAATCTTGGTGATTTGAGGGGACTAGCAGGCGGGTTGAACGGGCTAAACAGCTCGGCGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC