Sequence
atgc intronic sequence ATGC exonic sequencegtttgtgattagcttaagagatacttagcttacgtttaatcatcggtcttaatttcttgattatcattttttgtgttaaagGTTTTAGAGGTTCGTCCTGTGATAGACTGGAACAAAGGAAGAGCGGTCGAGTTTCTATTAGAATCTCTCG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G12430.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G12430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os10g40555.1 (Oryza sativa), 3'ss of exon 7
-------------gtttgtgattagcttaagagatacttagcttacgtttaatcatcggtcttaatttcttgattatcattttttgtgttaaagGTTTTAGAGGTTCGTCCTGTGATAGACTGGAACAAAGGAAGAGCGGTCGAGTTTCTATTAGAATCTCTCG------------------------------
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gtaaggaatatacacaaccgcacagctgtttcgaagcactggttaagtaccattgttgtatttgtttttaattcaactgcgctcttgaattcagGTTCTTGAGGTTCGACCTGTGATAGACTGGAACAAGGGGAAAGCTGTGGAATTTTTGCTGGAGTCACTTGGACTATGTGGGAAAGAAGATGTTCTTCCTA
upper sequence: AT4G12430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G14780.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------------------------------------------------------------gtttgtgattagcttaagagatacttagcttacgtttaatcatcgg--tcttaatttcttgattatcattttttg-tgttaaagGTTTTAGAGGTTCGTCCTGTGATAGACTGGAACAAAGGAAGAGCGGTCGAGTTTCTATTAGAATCTCTCG
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gtatgtatgacgagcattcttaattggaaaatagacactttgttcttagcataatttttaaacattttatgatagttactaatttataactttagtaactcgatattcaagtttgttcaagcactccatagtgta-attcaattagctacatcataaatatctcttccctatgttttggtgtggtagGTTTTAGAAGTTCGTCCTGTGATTGATTGGAATAAAGGAAAAGCTGTTGAATTTTTACTTGAATCTCTAG
upper sequence: AT4G12430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv00s0233g00030.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------gtttgtgattagctta-agagatacttagc--ttacgtttaatcatcggtcttaatttcttgattatcattttttgtgttaaagGTTTTAGAGGTTCGTCCTGTGATAGACTGGAACAAAGGAAGAGCGGTCGAGTTTCTATTAGAATCTCTCG
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gtaatattttctccctgaacacccttgcatatttttcctcaagatatggagattttaggcagtggttcttattagtaaatttcatcaacttcatatgttcttcccatgctta-gGTTTTAGAGGTCCGTCCTGTGATTGACTGGAACAAGGGGAAAGCAGTTGAATTTCTTCTCGAATCACTTG
upper sequence: AT4G12430.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv02s0154g00110.t01 (Vitis vinifera), 3'ss of exon 7
------------------------------gtttgtgattagctta-agagatacttagc--ttacgtttaatcatcggtcttaatttcttgattatcattttttgtgttaaagGTTTTAGAGGTTCGTCCTGTGATAGACTGGAACAAAGGAAGAGCGGTCGAGTTTCTATTAGAATCTCTCG
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gtaatattttctccctgaacacccttgcatatttttcctcaagatatggagattttaggcagtggttcttattagtaaatttcatcaacttcatatgttctttccatgctta-gGTTTTAGAGGTCCGTCCTGTAATTGACTGGAACAAGGGGAAAGCAGTTGAATTTCTTCTCGAATCACTTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcttacgtttaatcatcggtcttaatttcttgattatcattttttgtgttaaagGTTTTAGAGGTTCGTCCTGTGATAGACTGGAACAAAGGAAGAGCGGTCGAGTTTCTATTAGAATCTCTCG
tcatttttt CT-rich tract
ttaatttcttgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtgattagcttaagagatacttagcttacgtttaatcatcggtcttaatttcttgattatcattttttgtgttaaagGTTTTAGAGGTTCGTCCTGTGATAGACTGGAACAAAGGAAGAGCGGTCGAGTTTCTATTAGAATCTCTCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA