Sequence
atgc intronic sequence ATGC exonic sequencegtactcggttgaacctaagtatccatatgatttaagtaataatcaatggaattgctctatactttttatgcttgccatatcagGTCCTGCATTGGTTACAACCAAGGACATTGGAGATGCTGTTACTTTGCTACAATCAATGACTGGTTCAACATTTGATAGCAGCCAGCTCGTTTTCACTGC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39280.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 10
gtactcggttgaacctaagtatccatatgatttaagtaataat-------caatggaattgctctatactttttatgcttgccatatc----agGTCCTGCATTGGTTACAACCAAGGACATTGGAGATGCTGTTACTTTGCTACAATCAATGACTGGTTCAACATTTGATAGCAGCCAGCTCGTTTTCACTGC
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gtact-ggctgaaaatgtttaatggaaaaagtaaactagcaatgcttaagccatgcatatgctc-acagaacttaatttcatcatgtcttgtagGTCCTGCGTTGGTAACAACAAAGGATGCTGGAGATGCAGTTACTTTACTTCAGTCGTTGGCTGGCTCCACATTTGATAGCAGTCAGCTTGTACTGACAGC
upper sequence: AT2G39280.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 10
----------------------gtactcggttgaacctaagtat---ccatatgatttaagtaataatcaatggaattgctctatactttttatgcttgccatatc------agGTCCTGCATTGGTTACAACCAAGGACATTGGAGATGCTGTTACTTTGCTACAATCAATGACTGGTTCAACATTTGATAGCAGCCAGCTCGTTTTCACTGC
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gtactgggtaaaagacatttaattaccgtgatattcttcaggataatcaacatggatttaatacta-tgtagggtatctttttacagaatgtaattttgttcagtctcttgtagGACCTGCTTTGGTTACCACTAAGGATGCTGGAGATGCAGTTACTCTGCTGCAGTCACTGGCTGGCTCAACATTTGATAGCAGTGAACTTGTCTTGACTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatttaagtaataatcaatggaattgctctatactttttatgcttgccatatcagGTCCTGCATTGGTTACAACCAAGGACATTGGAGATGCTGTTACTTTGCTACAATCAATGACTGGTTCAACATTTGATAGCAGCCAGCTCGTTTTCACTGC
aagtaataatcaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactcggttgaacctaagtatccatatgatttaagtaataatcaatggaattgctctatactttttatgcttgccatatcagGTCCTGCATTGGTTACAACCAAGGACATTGGAGATGCTGTTACTTTGCTACAATCAATGACTGGTTCAACATTTGATAGCAGCCAGCTCGTTTTCACTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC