Sequence
atgc intronic sequence ATGC exonic sequencegtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATGGTAAAACAGTAGATAAAGTGTCTGTCTCGCCGTTCAATA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G01230.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G01230.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G31380.1 (Glycine max), 3'ss of exon 6
gtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATGGTAAAACAGTAGATAAAGTGTCTGTCTCGCCGTTCAATA
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---------------ttctttatttgaatttcaactacatgcgctgcttgctttgttttggtaagctactttt-tatttatttt-gtgaacccccctctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG---------------------------------------
upper sequence: AT5G01230.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA13G31350.1 (Glycine max), 3'ss of exon 1
gtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttcc--ggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATGGTAAAACAGTAGATAAAGTGTCTGTCTCGCCGTTCAATA
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------------------tttatttgaatttcaactacatgcgttgcttgctttgttttggtaagctactttt-tatttattttgtgaacccccctcttctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG---------------------------------------
upper sequence: AT5G01230.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA15G07970.2 (Glycine max), 3'ss of exon 6
gtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgt-gt-ttgtttccatgg-cttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATGGTAAAACAGTAGATAAAGTGTCTGTCTCGCCGTTCAATA
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---------------acttgtttgctggaggcttct-----ttttcccatcaattaaattatcctcaatgactattgtattatgtttgtgaacccctcttctttggcttgatttgttcagGTCATTAGACATTTTGATGGTTGCAAGGCTGACCTAGTTGTGTGTGATGGTGCGCCTGATG---------------------------------------
upper sequence: AT5G01230.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0007g01960.t01 (Vitis vinifera), 3'ss of exon 5
gtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATGGTAAAACAGTAGATAAAGTGTCTGTCTCGCCGTTCAATA
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------gtatttgtgtgctattttaaatcatttttgctctcagtttttggctgtgtaaaaatgat--atatctgacattatccttat---ttatcatcttc--tgttcttc----agGTCATTAGGCATTTTGATGGATGCAAGGCTGACCTGGTTGTGTGTGATGGTGCTCCTGATG---------------------------------------Mapped 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|164218939|gb|ES095525.1|ES095525EST: ACATAACTAATGCTCGGACTGCTGAAGTG GTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGT
genomic: ACATAACTAATGCTCGGACTGCTGAAGTGgtaaaatttc ... ttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATGGTAAAACAGTAGATAAAGTGTCTGTCTCGCCGTTCAATA
ggcttac putative branch site (score: 3)
ccttttccggtgtttt CT-rich tract
ttttttttcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaatttctcgactcctatctcataaatttttctacatctctttcttcctctttaattatgcttcaagtttgtgtttgtttccatggcttaccttttccggtgttttttttcaagGTCATTAGACACTTTGACGGCTGCAAAGCGGACCTGGTTGTCTGTGATGGTGCTCCAGATGGTAAAACAGTAGATAAAGTGTCTGTCTCGCCGTTCAATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG