Sequence
atgc intronic sequence ATGC exonic sequencegtatttttttagtcatgtatcttatatggttctttgtgagttagaacttagaagtgaggattaatcttgttgtcaaaaatgttttatagACTGTCCAACACAACGCATATGATCAAGATCCATATGCAAAGGAGTTTGGCATGAACATAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43810.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA10G38770.1 (Glycine max), 3'ss of exon 9
-gtatttttttagtcatgtatcttatatggttctttgtgagttagaacttag--aagtgaggatta-----atcttgttgtcaaaaatgttttat----agACTGTCCAACACAACGCATATGATCAAGATCCATATGCAAAGGAGTTTGGCATGAACATAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAG
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tatattctcttaactacatgacactgtcggggcttcat-agtaatgatttgtttattttatttttatttgtatgtggtggtggtgggggtcataccaacagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCGG
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA20G28970.1 (Glycine max), 3'ss of exon 9
gtatttttttagtcatgt---atcttatatggttctttgtgagttagaacttagaagtgaggatta-----atcttgttgtcaaaaatgttttata----gACTGTCCAACACAACGCATATGATCAAGATCCATATGCAAAGGAGTTTGGCATGAACATAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAG
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-tattctcttaactacatgacactgttggggattcatagtaatgatttgtttattttttatttttatttgtatgtggtggtggttggggtcatacaagcagACCGTTCAACATAATGCTTATGATCAAGATCCTTATGCAAAGGAATTTGGAATTAAAATCAGTGAAAAGCTAGCTTCTGTTGAAGCACGAATTCTTCCTG
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA02G00510.1 (Glycine max), 3'ss of exon 8
---gtatttttttagtcatgtatcttatat----ggttctttgtgagttagaacttagaagtgagg-attaatcttgt-tgtcaaaaatgttttat--agACTGTCCAACACAACGCATATGATCAAGATCCATATGCAAAGGAGTTTGGCATGAACATAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAG
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tttatatcttcacaaacaaataatatatatccatgatattctagaagctaaacaataaagttgtgtcatcaaattaacatttcaattttgcttcatgcagACCATTCAGCACAATGCTTATGGTCAAGATCCTTATGCAAAGGAATTTGGGATTAAAATTAGTGAAAAGCTAGCTTCTGTAGAAGCGCGAATTCTCCCTG
upper sequence: AT5G43810.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv05s0020g04190.t01 (Vitis vinifera), 3'ss of exon 8
-----------gtatttttttagtcatgtatcttatatggttctttgtg-agttagaacttagaagtgaggattaatcttgttgtcaaaaatgttttatagACTGTCCAACACAACGCATATGATCAAGATCCATATGCAAAGGAGTTTGGCATGAACATAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAG
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tgtttgatcttggattgacatgattctgtgatgtttttgggtcttggtttagtttgagctaataacatcttatgctttttaaacttcaaaaaataac-cagACGGTTCAACATAATGCTTATGATCAAGATCCATATGCAAAGGAGTTTGGGATCAAAATCAGTGAAAAATTAGCTTCTGTTGAGGCTCGGATTCTTCCTGMapped 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|164058295|gb|ES120186.1|ES120186EST: TGAAAGTTACATGCCAAAGGCCGAGGGACAGAGAAAACGATATTTTGCGG ACTGTCCAACACAACG
genomic: TGAAAGTTACATGCCAAAGGCCGAGGGACAGAGAAAACGATATTTTGCGGgtattttttt ... tgttttatagACTGTCCAACACAACG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgagttagaacttagaagtgaggattaatcttgttgtcaaaaatgttttatagACTGTCCAACACAACGCATATGATCAAGATCCATATGCAAAGGAGTTTGGCATGAACATAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAG
gattaat putative branch site (score: 3)
tcaaaaatgttttata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttttttagtcatgtatcttatatggttctttgtgagttagaacttagaagtgaggattaatcttgttgtcaaaaatgttttatagACTGTCCAACACAACGCATATGATCAAGATCCATATGCAAAGGAGTTTGGCATGAACATAAGCGAAAAGTTAGCTTCTGTTGAAGCTCGTATTCTTCCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC