Sequence
atgc intronic sequence ATGC exonic sequencegtaattgaagttagttgccagtatattagttcttaacaatgactggattggaagtagttgctattatattttgttcatttttttttttatctctaatacttcagTTTTGACGAGTTCTTGATGGACATGAAGCAAAGCAAAAGGAAAAATATCCGACAGGAACGCAAAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT2G23390.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G23390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os04g36062.1 (Oryza sativa), 3'ss of exon 6
gtaattgaagttagtt-gccagtatattagttcttaacaatgactggattggaagtagttgctattatattttgttcatttttttttttatctctaatacttcagTTTTGACGAGTTCTTGATGGACATGAAGCAAAGCAAAAGGAAAAATATCCGACAGGAACGCAAAAAG
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-cagttgttgtttatccaaaagtttataaggttacatactgaactgcctatatagtaaat--caatatttaccaatctctttctgttcattcttt--tttcccagTTTTGACGAGTTTTTAATGGATTTGAAGCAACCCAAACGGAAGAATATCAGACAAGAACGTAAAAAG
upper sequence: AT2G23390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA07G40290.1 (Glycine max), 3'ss of exon 2
----gtaattgaagttagttgccagtatattagttctta-acaatgactggattggaagtagttgctattatattttgttcatttttttttttatctctaatacttcagTTTTGACGAGTTCTTGATGGACATGAAGCAAAGCAAAAGGAAAAATATCCGACAGGAACGCAAAAAG
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gtgagtcatccatgatattagattctactttgggggatggactgctactgctacccatcccattcccattaccatatagctttagacttttgctgttttatgttggcagTTTTGATGACTTCTTGATGGACATGAAGCAAAGTAAAAGAAAAAATATACGTCAAGAGCGCAAAAAG
upper sequence: AT2G23390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G00490.2 (Glycine max), 3'ss of exon 2
gtaattgaagttagttgccagtatattagttcttaacaatgactggattggaagta--gttgctattatattttgttcatttttttttttatctctaatacttcagTTTTGACGAGTTCTTGATGGACATGAAGCAAAGCAAAAGGAAAAATATCCGACAGGAACGCAAAAAG---------------------------------
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-------------gtgactcatccatc--ttattagctctttctattttggcagtcttgctgtttttacatatagctttagacttttgctgttttatgt-tgccagTCTTGATGACTTCTTGATGGACATGAAGCAAAGTAAAAGAAAAAATATACGTCAAGAGTGCAAAAAGGTTACAAACATTGATATGTGCAGGTTTTTTCAA
upper sequence: AT2G23390.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv12s0035g01750.t01 (Vitis vinifera), 3'ss of exon 6
gtaattgaagttagttgccagtatattagtt--cttaacaatgactggattggaagtagttgctattatattttgttcatttttttttt---tatctctaatacttcagTTTTGACGAGTTCTTGATGGACATGAAGCAAAGCAAAAGGAAAAATATCCGACAGGAACGCAAAAAG
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---------gtcaattttttatgtaatcacttacctctggacttcagtgcttattgtgtttagtttttctttttgtatatggcattgaaaaatattgtgagttttgcagTTTTGATGAGTTCTTGATGGACATGAAGCAAAGTAAAAGGAAAAATATTCGTCAAGAGCGCAAAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggaagtagttgctattatattttgttcatttttttttttatctctaatacttcagTTTTGACGAGTTCTTGATGGACATGAAGCAAAGCAAAAGGAAAAATATCCGACAGGAACGCAAAAAG
ctctaat putative branch site (score: 3)
ttttgttcattttttt CT-rich tract
tattatattttgttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgaagttagttgccagtatattagttcttaacaatgactggattggaagtagttgctattatattttgttcatttttttttttatctctaatacttcagTTTTGACGAGTTCTTGATGGACATGAAGCAAAGCAAAAGGAAAAATATCCGACAGGAACGCAAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA