Sequence
atgc intronic sequence ATGC exonic sequencegtttgtctcttactctttaactcttatttaatgttacatttggcttttgtatcttttaatccacagcatgataatgtcttctttatatactaacagaagactaaatttgctattttatttgctaatgatagGGAAGTGAAGCTAGAGCAGAAAAGGTTGAAGGAGAAAATGAAGGAATTCAATAAAAAGGAAGCCAAATTTTATGGAAACATGTTTGCGAAACTAA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G25230.2 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G25230.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv00s0769g00010.t01 (Vitis vinifera), 3'ss of exon 11
------gtttgtctcttactctttaa-ctcttatttaatgttac--atttg---gcttttgtatcttttaat--ccacagcatgat------------aatgtcttctttat-----------atactaacagaagactaaattt--gctattt-tatttgctaatgatagGGAAGTGAAGCTAGAGCAGAAAAGGTTGAAGGAGAAAATGAAGGAATTCAATAAAAAGGAAGCCAAATTTTATGGAAACATGTTTGCGAAACTAA-----
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gtatcagattatatcttgcctcttgatctgatttccaatgtgacgaacttgcatgatctaaaataatataattacaatacaatgattgaaattgtcacaacatgtccattaataaggtagtagatcccaactgaggaaagaattataactattaatgtttgtttaaaacagGGATGTAAAGCTGGAGTATAGAACTTTAAAGGAAAAAATGAAGGAGTACAATAAGAAAGAGGCCAAATTCTATGGCAACATGTTTGCAAGGATGAACAAG
upper sequence: AT3G25230.2 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv00s0958g00020.t01 (Vitis vinifera), 3'ss of exon 7
------gtttgtctcttactctttaa-ctcttatttaatgttac--atttg---gcttttgtatcttttaat--ccacagcatgat------------aatgtcttctttat-----------atactaacagaagactaaattt--gctattt-tatttgctaatgatagGGAAGTGAAGCTAGAGCAGAAAAGGTTGAAGGAGAAAATGAAGGAATTCAATAAAAAGGAAGCCAAATTTTATGGAAACATGTTTGCGAAACTAA-----
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gtatcagattatatcttgcctcttgatctgatttccaatgtgacgaatttgcatgatctaaaataatataattacaatacaatgattgaaattgtcacaacatgtccattaataaggtagtagatcccaactgaggaaagaattataactattaatgtttgtttaaaacagGGATGTAAAGCTGGAGTATAGAACTTTAAAGGAAAAAATGAAGGAGTACAATAAGAAAGAGGCCAAATTCTATGGCAACATGTTTGCAAGGATGAACAAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|164003585|gb|ES198248.1|ES198248EST: CCCTTGAAATCGATCCCAACAACAG GGAAGTGAAGCTAGAGCAGAAAAGGTTGAAGGAGAAAATGAAGGAATTCAA
genomic: CCCTTGAAATCGATCCCAACAACAGgtttgtctct ... ctaatgatagGGAAGTGAAGCTAGAGCAGAAAAGGTTGAAGGAGAAAATGAAGGAATTCAA
EST:
gi|124711958|gb|EH803360.1|EH803360EST: TTGGCCGAGTTTGATGTCAAGAAGGCCCTTGAAATCGATCCCAACAACAG GGAAGTGAAGCTAGAGCAGAAAAGGTTGAAGGAGAA
genomic: TTGGCCGAGTTTGATGTCAAGAAGGCCCTTGAAATCGATCCCAACAACAGgtttgtctct ... ctaatgatagGGAAGTGAAGCTAGAGCAGAAAAGGTTGAAGGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttctttatatactaacagaagactaaatttgctattttatttgctaatgatagGGAAGTGAAGCTAGAGCAGAAAAGGTTGAAGGAGAAAATGAAGGAATTCAATAAAAAGGAAGCCAAATTTTATGGAAACATGTTTGCGAAACTAA
actaaatttgctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtctcttactctttaactcttatttaatgttacatttggcttttgtatcttttaatccacagcatgataatgtcttctttatatactaacagaagactaaatttgctattttatttgctaatgatagGGAAGTGAAGCTAGAGCAGAAAAGGTTGAAGGAGAAAATGAAGGAATTCAATAAAAAGGAAGCCAAATTTTATGGAAACATGTTTGCGAAACTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA