Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttgcaatgtttctcagttgcttttcattttccaatctcttttatttttctggattctgtatttgatgatatcgcatcttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G01750.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G01750.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA05G34560.1 (Glycine max), 3'ss of exon 3
gta-tgtttgcaatgtttctcagttgcttttcattttccaatctcttttatttttctggattctgtatttgatgatatcgcatcttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
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gtaatgcttgaagcctctatcaa--gcttagtgagaggtaaattttttaggttacgtgg----tgtgtttaataaactgggtatttcttgcagAATCTTGAAATAAAGAAAATCAATGATGAAAAAAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
upper sequence: AT2G01750.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G09390.1 (Glycine max), 3'ss of exon 3
gtatgtttgcaatgtttctcagttgcttttcattttccaatctcttttatttttctggattctgtatttgatgatatcgcatcttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
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gtatttcttgaag---cctccatcaacttt-agtaaatagtcattttcccaggt-taggtggtatgttttctgaattaaatatttctggcagAATCTTGAAATAAAAAAAATCAACGATGAAAAGAAGGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCACGCTGCCCAGAAAG
upper sequence: AT2G01750.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA08G05100.1 (Glycine max), 3'ss of exon 3
gta-tgtttgcaatgtttctcagttgcttttcattttccaatctcttttatttttctggattctgtatttgatgatatcgcatcttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
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gtaatgcttgaagcctctatcaa--gcttagcgaggagtaaatttctgaggttacgtgg--tgtgtttttactaaactggatatttcttgcagAATCTTGAAATAAAGAAAATTAATGATGAAAAGAAAGCATCGATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTCGAAGGGTCCATGCTGCTCAGAAGG
upper sequence: AT2G01750.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA07G26540.1 (Glycine max), 3'ss of exon 3
gtatgtttgcaatgtttctcagttgcttttcattttccaatctcttttatttttctggattctgtatttgatgatatcgcat-cttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
|||| |||| ||| | ||| | | || ||| | | | | | | ||| ||| |||| || || | ||||| |||||||| || ||||| ||||| ||||| | || |||||||||||||| ||||| || |||||||||||| ||||||| |||||||| || || |
gtat---tgcatgaagcctctatcaacttt-aggaaatagtcattttcccaggt-taggtggtatgttttctga-atcgaatatttctggcagAATCTTGAAATTAAAAAAATCAACGATGAAAAGAAAGCATCAATGGCAGCTCAGTTTGCAGCTGAAGCCACTCTTAGAAGGGTCCATGCTGCCCAGAAAG
upper sequence: AT2G01750.2 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv01s0011g05790.t01 (Vitis vinifera), 3'ss of exon 3
gtatgtttgcaatgtttctcagttgcttttcattttccaatctc--ttttatttttctggattctgta-tttgatgatatcgcat-cttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
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-----------gtattgcatgaaacccttccatttttctttataagttttgtgtgtgtgtgttttgcagttttgtcctaacaattgttttttgcagAATCTCGAGATCAAGAAAATCAATGATGAAAAGAAGGCCTCCATGGCTGCTCAATTTGCAGCAGAAGCCACTCTTAGAAGGGTTCATGCTGCGCAGAAGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caatctcttttatttttctggattctgtatttgatgatatcgcatcttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
atttgat putative branch site (score: 5)
tcttgtc putative PPT
tcttttatttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttgcaatgtttctcagttgcttttcattttccaatctcttttatttttctggattctgtatttgatgatatcgcatcttgtcacagAACCTTGAAATCAAGAAAATAAACGAAGAAAAAAGGGCTTCAATGGCAGCTCAATTTGCTGCAGAAGCCACTCTTCGAAGGGTTCATGCTGCTCAAAAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT