Sequence
atgc intronic sequence ATGC exonic sequencegtaaaagaacaacttttactgtccaatgcttgtcatctaaaaaatggggtttttgtttttaatattcttctgttgatagGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT1G72330.2 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os10g25130.1 (Oryza sativa), 3'ss of exon 11
gtaaaagaacaacttttactgtccaatgcttgtcatctaa-aaaatggggtttttgtttttaatattcttctgttgatagGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT
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--gtaaatacgatgat--ctgtt---ttcttattttctattggcactggattctcaaaaggattttcttgctgacaacagGATATTATGGTGAATGTGGCAAAAGAGGAGGCTACATGGAGATTACTGGCTTCAGTGCTCCAGTTAGAGAGCAGATCTACAAAGTGGCGTCAGTGAACTT
upper sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: LOC_Os03g08530.1 (Oryza sativa), 3'ss of exon 10
gtaaaagaacaacttttactgtccaatgcttgtcatctaaaaaatggggtttttgttttta-atattctt----ctgttgatagGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT
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gtgaaatcccatcatccgcctttct---ttctccaagtacattgtaactccttaccacatagatatttttttgcctgccatcagGATATTACGGAGAGTGTGGCAAGAGAGGCGGTTACATGGAGGTCACTGGCTTCAGCACTCCAGTTAGAGAACAACTCTACAAAATTGCATCTGTTAACTT
upper sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G088064_T02 (Zea mays), 3'ss of exon 3
gtaaaagaacaacttttactgtccaat--gcttgtcatctaaaaaatggggtttttgtttttaatattcttctgttgatagGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT
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gtaaatttatataaccagctactttatctgccttttggccaagtaactggcttatccaaaacattttgttgctgcaaccagGATACTATGGAGAGTGTGGTAAAAGAGGAGGGTACATGGAGATTACTGGCTTCAGTGCTCCAGTAAGAGAGCAGATCTACAAGATAGCTTCAGTGAACCT
upper sequence: AT1G72330.3 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 11
-----------------gtaaaa--gaacaacttttactgtccaatgcttgtcatctaaaaaatggggtt---tttgtttttaatattcttctgttgat---agGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT
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gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgctggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aatgcttgtcatctaaaaaatggggtttttgtttttaatattcttctgttgatagGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT
ttttaat putative branch site (score: 3)
ttcttctgtt CT-rich tract
tttttgtttttaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaagaacaacttttactgtccaatgcttgtcatctaaaaaatggggtttttgtttttaatattcttctgttgatagGATATTATGGAGAATGTGGAAAAAGAGGAGGTTACATGGAGGTTACTGGATTCACTTCTGATGTAAGAGAACAGATATACAAAATGGCTTCTGTGAATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA