Sequence
atgc intronic sequence ATGC exonic sequencegcaaagctccttctctgggtccttgatatcattctgttacacttgaatgcctatgatgctaagttttactattggatgtatattgatatctctgcttctttttgtgttcagTGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGTTGCGTGTGTTTTTCCTCATGGTGAGATAGATCCTGGACTGCAGACACAA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G43930.3 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G43930.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA03G32620.2 (Glycine max), 3'ss of exon 8
gcaaagctccttctctgggtccttgatatcattc-tgttacacttgaatgcctatgatgctaagttttactattggatgtatattgatatctctgcttctttttgtgttcagTGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGTTGCGTGTGTTTTTCCTCATGGTGAGATAGATCCTGGACTGCAGACACAA
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-----------catttggcattattacatcacaggcattatacttttttggat-tgaagtcagattgtatacttaatcagttagctgattcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGTGGTAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATATAGAAGCAGATCCAGGATTACAAACTCCA
upper sequence: AT5G43930.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 8
gcaaagctccttctctgggtccttgatatcattc-tgttacacttgaatgcctatgatgctaagttttactattggatgtatattgatatctctgcttctttttgtgttcagTGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGTTGCGTGTGTTTTTCCTCATGGTGAGATAGATCCTGGACTGCAGACACAA
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-----------catttggcattattacattacaggcattatgcttttttggat-tgaagtcagattatatacttaatcggttagctgactcaatggaatttgccctttgcagTGAAATGGGTGCTCATTTTTCACCATGCGGTAGATTTTTAGCTGCCTGTGTTGCATGTATGCTTCCCCATATAGAAGCAGATCCAGGATTACAAACTCCA
upper sequence: AT5G43930.3 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 8
gcaaagctccttctctgggtccttgatatcattctgttacacttgaatgcctatgatgctaagtt-ttactattggatgtatattgatatctctgcttctttt-tgtgttcagTGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGTTGCGTGTGTTTTTCCTCATGGTGAGATAGATCCTGGACTGCAGACACAA
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----------atatcaagtatttgcatttcataaaatttctgccta--gcctgtcatccttgatccttgttacttatggtttagc-atatttatgacacaactgtgattccagTGAAATGGGTGCACATTTATCACCTTGTGGGAGATTTTTAGCTGCCTGTGTTGCATGTGTGCTTCCTCATTTGGAAGCTGATCCTGGATTGCAAACACAGMapped 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|116473290|gb|EG515882.1|EG515882EST: CTGAAATCCGACAGATGTCTATTTACAATACCGCATGCCGTCCTTTGCAG TGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGT
genomic: CTGAAATCCGACAGATGTCTATTTACAATACCGCATGCCGTCCTTTGCAGgcaaagctcc ... ttgtgttcagTGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctaagttttactattggatgtatattgatatctctgcttctttttgtgttcagTGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGTTGCGTGTGTTTTTCCTCATGGTGAGATAGATCCTGGACTGCAGACACAA
tattgat putative branch site (score: 3)
tctctgcttctttttg CT-rich tract
atgtatattgatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcaaagctccttctctgggtccttgatatcattctgttacacttgaatgcctatgatgctaagttttactattggatgtatattgatatctctgcttctttttgtgttcagTGAAATGGGAGCTCATTATTCGCCATGTGGGAGATATTTAGCGGCCTGTGTTGCGTGTGTTTTTCCTCATGGTGAGATAGATCCTGGACTGCAGACACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG