Sequence
atgc intronic sequence ATGC exonic sequence...ttatcgaaatcttaatcgattgatccacctagatcacctaaagttcttatgttcgctgtagtagatgtgaccttaactagttccgagtttagttgtgcagAGTGAGCTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTCACTTCGAAA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G38780.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G38780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA11G12160.1 (Glycine max), 3'ss of exon 4
ttatcgaaatcttaatcg-attgatccac-ctagatcacctaaagttcttatgttcgctgtagtagatgtgacct-taactagttccgagtttagttgtgcagAGTGAGCTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTCACTTCGAAA
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---ttgaacttttaaatgtaatgacatatactctagcagggaaactagagaaaaaatatatatttggaggaatatatgcatgagattaatcatgtctgtgcagAGTGAGCTTCATGGATTAGCTGCTTTGCAGTGGTCGATTTGTCAAGACTCCCTCAGTAG
upper sequence: AT2G38780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA12G04370.1 (Glycine max), 3'ss of exon 5
ttatcgaaatcttaatcgattgatccac-ctagatcacctaaagttcttat-gttcgctgtagtagatgtgacct-taactagttccgagtttagttgtgcagAGTGAGCTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTCACTTCGAAA
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---ttaacttttaaatgtaatgacatatactctagcagggaaactagagagagaaaaaaatatttggaggaatatgtgcatgagattaatcatgtctgtgcagAGTGAGCTCCATGGATTAGCTGCTTTGCAGTGGTCGATTTGTCAAGACTCCCTCAGTAG
upper sequence: AT2G38780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0139g00280.t01 (Vitis vinifera), 3'ss of exon 4
----------ttatcgaaatcttaatcgattgatccacctagatcacctaaagttcttatgttcgctgtagtagatgtgaccttaactagttccgagtttagttgtgcagAGTGAGCTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTCACTTCGAAA
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ggggttgttattatacaaatttttctttagtg-tagagaataattacacaagatttttg----ctcttttatttatttcatttcatatgttt----gtttt-ttgtgtagAGTGAACTTCATGGATTAGCTGCTTTGCAGTGGTCTATTTGTCTAGATTCACTCAGCGG
upper sequence: AT2G38780.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv13s0019g01030.t01 (Vitis vinifera), 3'ss of exon 4
ttatcgaaatcttaatcgatt-gatccacctagatcacctaaagttcttatgttcgctgtagtagatgtgaccttaactagttccgagt-----ttagttgtgcagAGTGAGCTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTCACTTCGAAA
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-----gaggttgttattattcagatttttctttggtgtggagaataattatacaagattta-tgttcttttatttatttcatttcatatgtttgttgtttgtgcagAGTGAACTTCATGGATTAGCTGCTTTGCAGTGGTCTATTTGTCTAGATTCACTCAGCAGMapped 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|125234373|gb|EL248458.1|EL248458EST: GCCATACTATGAAAAGGTCATGGAGAAAATAGTTTTCAAG AGTGAGCTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTCA
genomic: GCCATACTATGAAAAGGTCATGGAGAAAATAGTTTTCAAGgtaatttctg ... agttgtgcagAGTGAGCTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTCA
EST:
gi|124917124|gb|EH990998.1|EH990998EST: ATGGAGAAAATAGTTTTCAAG AGTGAGCTTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTC
genomic: ATGGAGAAAATAGTTTTCAAGgtaatttctg ... agttgtgcagAGTGAGC-TTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttatgttcgctgtagtagatgtgaccttaactagttccgagtttagttgtgcagAGTGAGCTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTCACTTCGAAA
ccttaac putative branch site (score: 3)
ttaacta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatcgaaatcttaatcgattgatccacctagatcacctaaagttcttatgttcgctgtagtagatgtgaccttaactagttccgagtttagttgtgcagAGTGAGCTTCATGGACTAGCGGCTTTGCAGTGGTCTATTTGTCAGGATTCACTTCGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - cgaaatc
- - - - - - - - - - - - ccaccta
- - - - - - - - - - - - - - - - - -acctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -accttaa