Sequence
atgc intronic sequence ATGC exonic sequencegtaagaagaatagtggcattcacgcggataaatgttattttgtttttagctatgtactaatgttatacttgaaacatttctcctcagGTGACGCTAGCTGCCCTTGGAGAGATATTTGAAGCGGCACGTGCCATTATGAGTTGGCTTGGTGATTGTGCAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G24120.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G24120.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA06G24890.1 (Glycine max), 3'ss of exon 6
----------gtaagaagaatagtggcattcacgcggataaatgttattttgtttttagctatgtact---aatgttatacttgaaacatttctcctcagGTGACGCTAGCTGCCCTTGGAGAGATATTTGAAGCGGCACGTGCCATTATGAGTTGGCTTGGTGATTGTGCAAAG
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cttatacattctatcaggtttcttaatgcattcaaattctcttatcattctggttcatatcaggtagtttgatcaacattttcaaacttaatttctatagGTGACATTGGCTGCCCTTGGAGAAGTTTTTGAAGCTGCACGTGGCATTATGGGTTGGCTTGGAGATTGTGCAAAG
upper sequence: AT2G24120.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA04G24350.1 (Glycine max), 3'ss of exon 8
----------gtaagaagaatagtggcattcacgcggataaatgttattttgtttttagctatgtact---aatgttatacttgaaacatttctcctcagGTGACGCTAGCTGCCCTTGGAGAGATATTTGAAGCGGCACGTGCCATTATGAGTTGGCTTGGTGATTGTGCAAAG
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cttatgcattccatcaggttttttgatgtattcaaatgctcttatcattctggttattattaggaagtttgattgacattttcaaacttaatttctgtagGTGACATTGGCTGCCCTTGGAGAAGTTTTTGAAGCTGCACGTGGCATCATGGGTTGGCTTGGGGATTGTGCAAAG
upper sequence: AT2G24120.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: GLYMA17G07940.1 (Glycine max), 3'ss of exon 13
-----gtaagaagaatagtg---gcattcacgcggataaatgttattttgtttttag-ctatgtactaatgttatacttgaaacattt----ctcctcagGTGACGCTAGCTGCCCTTGGAGAGATATTTGAAGCGGCACGTGCCATTATGAGTTGGCTTGGTGATTGTGCAAAG
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aatatatgagtggaaatgcatgtgaaccaacatgcaaagacatgcttatacaataaatctgctttcttgtcttatattttatactcttatcattctatagGTGACATTAACTGCGCTTGGAGAAATTTTTGGTGCTGCACGTGTCATTATGGGTTGGCTTGGTGATTGTGCAAAG
upper sequence: AT2G24120.2 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv11s0037g00630.t01 (Vitis vinifera), 3'ss of exon 13
-------gtaagaaga---atagtggcattcacgcggataaatgttattttgtttttagctatgtactaatgttatacttgaaa-----catttctcctcagGTGACGCTAGCTGCCCTTGGAGAGATATTTGAAGCGGCACGTGCCATTATGAGTTGGCTTGGTGATTGTGCAAAG
|| | | | | | | || | | | | ||||| ||| | | | | | | ||| | ||| ||| |||||||| | ||||| |||||||||||||| |||| ||||||| ||||||| |||||||||||| ||||||||
tgtatccatatgtaattttacatttgaatcttcttcttctctctctctctctcttttatttatttttt--tttcccattcaaaattttccctttttccatagGTGACGTTGGCTGCTCTTGGAGAGATATTCCAAGCTGCACGTGACATTATGGCTTGGCTTGGTGAATGTGCAAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttattttgtttttagctatgtactaatgttatacttgaaacatttctcctcagGTGACGCTAGCTGCCCTTGGAGAGATATTTGAAGCGGCACGTGCCATTATGAGTTGGCTTGGTGATTGTGCAAAG
tactaat putative branch site (score: 1)
catttctcctc putative PPT
ttttgttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagaagaatagtggcattcacgcggataaatgttattttgtttttagctatgtactaatgttatacttgaaacatttctcctcagGTGACGCTAGCTGCCCTTGGAGAGATATTTGAAGCGGCACGTGCCATTATGAGTTGGCTTGGTGATTGTGCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG