Sequence
atgc intronic sequence ATGC exonic sequencegtttttgtttctaatttactacatttgatggaatttgttttttgaaattgcggtttctcagttaatctctctgctctcgatttgctgagcaaaatgttgtctttttagatcactagttgagaatctagtgatcattgatcttgatttcatctatattcttagTACTTAGGGAAGTTAATGAGGTTGGTTTTATGAACAGGGATGCATATGGATTTTCTGTGAGGCCTCAGCATGTGCAAAGATACCGAGAATATGTTAATAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39280.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39280.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G44110.1 (Glycine max), 3'ss of exon 1
gtttttgtttctaatttactacatttgatggaatttgttttttgaaattgcggtttctcagttaatctctctgctctcgatttgctgagcaaaatgttgtctttttagatcactagttgagaatctagtgatcattgatcttgatttcatctatattcttagTACTTAGGGAAGTTAATGAGGTTGGTTTTATGAACAGGGATGCATATGGATTTTCTGTGAGGCCTCAGCATGTGCAAAGATACCGAGAATATGTTAATAT-------
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---------------------------------------------------------------------------------------------tctctgctgtttttgttttttttttta---tctgtttattattggatttttttatttttatttttttggaaattaatga-gtgtttggtgtgaacact--gaacagGGATGCCTATGGGTTTACTGTGAGGCCTCAGCACCTGCAAAGATACCGTGAATATGCTAACATTTACAAG
upper sequence: AT2G39280.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G38810.1 (Glycine max), 3'ss of exon 1
gtttttgtttctaatttactacatttgatggaatttgttttttgaaattgcggtttctcagttaatctctctgctctcgatttgctgagcaaaatgttgtctttttagatcactagttgagaatctagtgatcattgatcttgatttcatctatattcttagTACTTAGGGAAGTTAATGAGGTTGGTTTTATGAACAGGGATGCATATGGATTTTCTGTGAGGCCTCAGCATGTGCAAAGATACCGAGAATATGTTAATAT-------
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--------------------------------------------------------------------------------------------cagttaattattttgagtctct-gttgattttttttttatcttt--ttattgttggattc-tgttttt--tatttttggaaattaatgcgtgtt-tggtgtgaacagGGATGCCTATGGGTTTACTGTGCGGCCTCAGCACCTGCAAAGATACCGTGAATATGCTAACATTTACAAG
upper sequence: AT2G39280.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv13s0067g03420.t01 (Vitis vinifera), 3'ss of exon 1
gtttttgtttctaatttactacatttgatggaatttgttttttgaaattgcggtttctcagttaatctctctgctctcgatttgctgagcaaaatgttgtctttttagatcactagttgagaatctagtgatcattgatcttgatttcatctat-attcttagTACTTAGGGAAGTTAATGAG-GTTGGTTTTATGAACAGGGATGCATATGGATTTTCTGTGAGGCCTCAGCATGTGCAAAGATACCGAGAATATGTTAATAT-------
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-------------------------------------------------------------------------------------------gaatattg---atttgacttggt--ttgccatgttactggaactt--tgttgattttactactgagtgctgtgactgggaggaattaattggcattggtct---gaacagGGATGCATATGGATTTGCAGTCAGACCACAGCATTTACAAAGATACCGAGAATATGCTAATATCTACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcactagttgagaatctagtgatcattgatcttgatttcatctatattcttagTACTTAGGGAAGTTAATGAGGTTGGTTTTATGAACAGGGATGCATATGGATTTTCTGTGAGGCCTCAGCATGTGCAAAGATACCGAGAATATGTTAATAT
tcttgat putative branch site (score: 4)
tattctt putative PPT
atttcatctatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttttgtttctaatttactacatttgatggaatttgttttttgaaattgcggtttctcagttaatctctctgctctcgatttgctgagcaaaatgttgtctttttagatcactagttgagaatctagtgatcattgatcttgatttcatctatattcttagTACTTAGGGAAGTTAATGAGGTTGGTTTTATGAACAGGGATGCATATGGATTTTCTGTGAGGCCTCAGCATGTGCAAAGATACCGAGAATATGTTAATAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG