Sequence
atgc intronic sequence ATGC exonic sequencegtagtgtatgtttggaattactagattttatggcttttgaatatcatctagtttgtgctatctaatgtatgtatgtagtagttacatctttgagtggacacaaaggcatagatctcagggactttcactaatttagggaaaatggaatgacatttttggataacagATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTTTCAGCAGCATCCTATCCAGATCTCAAGGAGCAAGCGCCTGTTAGTGTTC
Basic information
species | Arabidopsis thaliana |
transcript | AT2G31810.3 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G13290.1 (Glycine max), 3'ss of exon 5
gtagtgtatgtttggaattactagattttatggcttttgaatatcatctagtttgtgctatctaatgtatgtatgtagtagttacatctttgagtggacacaaaggcatagatctcagggactttcactaatttagggaaaatggaatgacatttttggataacagATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTTTCAGCAGCATCCTATCCAGATCTCAAGGAGCAAGCGCCTGTTAGTGTTC
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----------------gttggaaagttcaat------tgagtacccaacaaatt----tccttaacttttgtatcttgt--ccactttgttgag----cattatattgtaaggctgtgcaaagtttactaattc-gttattattggatgatgtaactatact-tagATTGCATTAAGAAGGGAAAAGATGGGTGCATCTGCTCCATTTTGGCGGTATTCAGCTGCTTCTTATCCAGATCTTGAAGGAAGAACACCTGTGAATGCCA
upper sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G30130.1 (Glycine max), 3'ss of exon 5
gtagtgtatgtttggaattactagattttatggcttttgaatatcatctagtttgtgctatctaatgtatgtatgtag-tagttacatctttgagtggacacaaaggcatagatctcagggactttcactaatttagggaaaatggaatgacatttttggataacagATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTTTCAGCAGCATCCTATCCAGATCTCAAGGAGCAAGCGCCTGTTAGTGTTC
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----------------------------------gttggaa----agctcaattgaa-tacctaacaaatttccttaactttttatcttgtctattttgttgagcattataaggctgtacaaaatttactaattc-gttattattggatgatgtaactatact-tagATTGCATTAAGAAGGGAAAAGATGGGTGCATCTGCTCCATTTTGGCGGTATTCAGCTGCTTCTTATCCAGATCTTGAAGGAAGAACACCTGTTAATGCCC
upper sequence: AT2G31810.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv05s0094g01110.t01 (Vitis vinifera), 3'ss of exon 5
gtagtgtatgtttggaattactagattttatggcttttgaatatcatctagtttgtgctatctaatgtatgtatgtagtagttacatctttgagtggacacaaaggcatagatctcagggactttcacta-atttagggaaaatggaatgacatttttggataacagATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTTTCAGCAGCATCCTATCCAGATCTCAAGGAGCAAGCGCCTGTTAGTGTTC
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-------------------gttggatgtt-tccctttgaaatac-------tttataatatct------ttcagacatttattttctcttctcatg-attcatcttcagaatccttttgagcatgcatttcatgtatcagtgactgaa--actttttcttgttgtagATTGCCTTGAGAAGGGAAAAAATGGGCGAGTCTGCTCCATTTTGGCGATTTTCAGCATCTTCATATCCTGATCTTGAAGGAGAAATTCCAGAAAACACTTMapped 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|164052616|gb|ES160398.1|ES160398EST: GTAAGGACAGGAAAG ATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTT
genomic: GTAAGGACAGGAAAGgtagtgtatg ... tggataacagATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTT
EST:
gi|301501257|gb|HO206797.1|HO206797EST: AAAGAAATTTGAAAAAGTTTCAGATCAGAGAGATTGTAAGGACAGGAAAG ATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTT
genomic: AAAGAAATTTGAAAAAGTTTCAGATCAGAGAGATTGTAAGGACAGGAAAGgtagtgtatg ... tggataacagATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTT
EST:
gi|125059377|gb|EL128054.1|EL128054EST: AAAGAAATTTGAAAAAGTTTCAGATCAGAGAGATTGTAAGGACAGGAAAG ATAGCACTGAGAAGGGAAAAGATGGGTGCAACTG
genomic: AAAGAAATTTGAAAAAGTTTCAGATCAGAGAGATTGTAAGGACAGGAAAGgtagtgtatg ... tggataacagATAGCACTGAGAAGGGAAAAGATGGGTGCAACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctcagggactttcactaatttagggaaaatggaatgacatttttggataacagATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTTTCAGCAGCATCCTATCCAGATCTCAAGGAGCAAGCGCCTGTTAGTGTTC
cactaat putative branch site (score: 2)
cattttt putative PPT
actaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagtgtatgtttggaattactagattttatggcttttgaatatcatctagtttgtgctatctaatgtatgtatgtagtagttacatctttgagtggacacaaaggcatagatctcagggactttcactaatttagggaaaatggaatgacatttttggataacagATAGCACTGAGAAGGGAAAAGATGGGTGCAACTGCTCCATTTTGGCGATTTTCAGCAGCATCCTATCCAGATCTCAAGGAGCAAGCGCCTGTTAGTGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG