Sequence
atgc intronic sequence ATGC exonic sequence...tgaaatctgacttagattactaatggttacaaattcgattcctacactgaatctattaaaatccaggaatatgctaagtttgcaattaatcatgtttcagACAGCATTGATGCAAGCTTGTAGATACGGACATTGGGAAGTTGTGCAAACTCTTCTGCTTTTCCGATGCAAT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G07270.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA16G32090.1 (Glycine max), 3'ss of exon 2
tgaaatctgacttagattactaatggttacaaattcgattcctaca-ctgaatcta--ttaaaatccaggaatatgctaagtttgcaattaatcatgtttcagACAGCATTGATGCAAGCTTGTAGATACGGACATTGGGAAGTTGTGCAAACTCTTCTGCTTTTCCGATGCAAT
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tgttgctttccttttatgcatgtttatgatgcact-gattcagaaatcagaatatggcttactaaatgagattttggtttgttt-tgattcttgat-ttgaagACTGCTTTGATGCAAGCTTGTAGATATGGTCATTGGGAAGTTGTGCAGACCCTTCTGCTCTTCAGATGCAAT
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G26560.1 (Glycine max), 3'ss of exon 2
tgaaatctgacttagattactaatggttacaaattcgattcctacactgaatctattaaaatccaggaatatgctaagtttgcaattaatcatgtttc--agACAGCATTGATGCAAGCTTGTAGATACGGACATTGGGAAGTTGTGCAAACTCTTCTGCTTTTCCGATGCAAT
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atgcatgttgctttgcttttttatgcatgtgtatgatgcactgattcagaatatggcttactaaatgagatt--ttggtttgctttgatccttgatttgaagACCGCTTTGATGCAAGCTTGTAGATATGGACATTGGGAAGTTGTACAGACCCTTCTGCTCTTCAAATGCAAT
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA10G38270.1 (Glycine max), 3'ss of exon 2
---tgaaatctgacttagattactaatggttacaaattcgattcctacactga-atctattaaaatccaggaatatgctaagtttgcaattaatcatgtttc--agACAGCATTGATGCAAGCTTGTAGATACGGACATTGGGAAGTTGTGCAAACTCTTCTGCTTTTCCGATGCAAT
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tcaatggatctgatgtaaatt--caatagaagcatgataaaatgaagctttattagctatactaatttgataatatg----gtttgcattgacccttgatttgaagACGGCGTTGATGCAAGCTTGTAGATATGGGCATTGGGAGGTTGTACAAACACTTCTACTCTTCAGATGCAAT
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA20G29590.1 (Glycine max), 3'ss of exon 2
---tgaaatctgacttagatt--actaatggttacaaattcgattcctacactgaatctattaaaatccaggaatatgctaagtttgcaattaatcatgtttc--agACAGCATTGATGCAAGCTTGTAGATACGGACATTGGGAAGTTGTGCAAACTCTTCTGCTTTTCCGATGCAAT
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tcaatggatctgatgtcaattcaatagaagcatgataacatgaagctt-tattagctatactaa--tttgataatatg----gtttgcattgatccttgatttgaagACCGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAGGTTGCACAGACACTTTTACTCTTCAGATGCAAT
upper sequence: AT5G07270.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv16s0100g00690.t01 (Vitis vinifera), 3'ss of exon 3
------tgaaatctgacttagattactaatggttacaaattcgatt--cctacactgaatctattaaaatccaggaatatgctaagtttgcaattaatcatgtttcagACAGCATTGATGCAAGCTTGTAGATACGGACATTGGGAAGTTGTGCAAACTCTTCTGCTTTTCCGATGCAAT
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cgtagaaataatctgattgtcttctttttagagcaaagaattgatggatctgtgttgaatctg-----attgtggactggtttttgtttgtaattg--tat-ttgaagACGGCATTGATGCAAGCTTGTAGATATGGGCATTGGGAAGTTGTTCAGACTCTACTGCTCTTCAGATGCAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.actgaatctattaaaatccaggaatatgctaagtttgcaattaatcatgtttcagACAGCATTGATGCAAGCTTGTAGATACGGACATTGGGAAGTTGTGCAAACTCTTCTGCTTTTCCGATGCAAT
aattaat putative branch site (score: 3)
aattaatcatgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaaatctgacttagattactaatggttacaaattcgattcctacactgaatctattaaaatccaggaatatgctaagtttgcaattaatcatgtttcagACAGCATTGATGCAAGCTTGTAGATACGGACATTGGGAAGTTGTGCAAACTCTTCTGCTTTTCCGATGCAAT
tgaaatc
- - - - - - - - - - - - - - -caaattc
- - - - - - - - - - - - - - - - - - - - - - - ctgaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatcca