Sequence
atgc intronic sequence ATGC exonic sequencegtaaggcttcttctgtgagaacttttcagctttaccatcaaagtttcctcttttgtgtacaatctacacaggatccttctttttgcaaggatgctgtgtaaagtctcatcttttttgttttgttattttaatgtatagATAGGCAGTCATTCTTGAACACATCCAAGTGGATTGAGGATGTTCGTACAGAGAGAGGTAGCGATGTCATCATTGTTCTGGTTGGTAACAAAACAGATCT
Basic information
species | Arabidopsis thaliana |
transcript | AT5G10260.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: AC166636.1_FGT008 (Zea mays), 3'ss of exon 3
gtaaggcttcttctgtgagaacttttcagctttaccatcaaagtttcctcttttgtgtacaatctacacaggatccttctttttgcaaggatgctgtgtaaagtctcatcttttttgttttgttattttaatgtatagATAGGCAGTCATTCTTGAACACATCCAAGTGGATTGAGGATGTTCGTACAGAGAGAGGTAGCGATGTCATCATTGTTCTGGTTGGTAACAAAACAGATCT
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------------cactagtaatcttttagcta-actattta--ttagatctagtgc-----atttaaaca----ccctctaaatataata-----gtatccagtctcatctc----atgtcgttcttttg-----cagACAGGCAGTCATTCTTGAACACGTCAAAGTGGATCGAGGAAGTAAACACGCAAAGAGGTGGAGACGTGCTCATCTTCCTCGTTGGAAATAAAACTGACCT
upper sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 3
gtaaggcttcttctgtgagaacttttcagctttaccatcaaagtttcctcttttgtgtacaatctacacaggatccttctttttgcaaggatgctgtgtaaagtctcatcttttttgttttgttattttaatgtatagATAGGCAGTCATTCTTGAACACATCCAAGTGGATTGAGGATGTTCGTACAGAGAGAGGTAGCGATGTCATCATTGTTCTGGTTGGTAACAAAACAGATCT
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---------------------------------ggcatccacatttagtgctt-acatg-aattcaaatctatccatatattatccacccaaacc-tacagtattctgaattgttcattaaatt--ttcactatgcagATCGGCAATCATTTCTGAACACGTCCAAGTGGATTGAGGAAGTGCGTACAGAACGAGGCACTGATGTCATTATTGTTCTTGTTGGGAATAAAACCGATCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaaggatgctgtgtaaagtctcatcttttttgttttgttattttaatgtatagATAGGCAGTCATTCTTGAACACATCCAAGTGGATTGAGGATGTTCGTACAGAGAGAGGTAGCGATGTCATCATTGTTCTGGTTGGTAACAAAACAGATCT
ttttaat putative branch site (score: 3)
tcttttttgttttgtt CT-rich tract
atcttttttgttttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggcttcttctgtgagaacttttcagctttaccatcaaagtttcctcttttgtgtacaatctacacaggatccttctttttgcaaggatgctgtgtaaagtctcatcttttttgttttgttattttaatgtatagATAGGCAGTCATTCTTGAACACATCCAAGTGGATTGAGGATGTTCGTACAGAGAGAGGTAGCGATGTCATCATTGTTCTGGTTGGTAACAAAACAGATCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG