Sequence
atgc intronic sequence ATGC exonic sequencegtaagatccttatctcttgtcaaatcaaataactaaggaccaaaactaaagaagcttataaatcgcgtttggtttcagATAAGAAGAACGAGAACAAGAAAGTGGCTGTCAACGATTTCTTGCCATCAGAGAGTGCACATGAAGCTATTCAGTACTCCAT
Basic information
species | Arabidopsis thaliana |
transcript | AT2G46860.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G015418_T01 (Zea mays), 3'ss of exon 7
--------------------------gtaagatccttatctcttgtcaa--atcaaataactaaggaccaaaactaaagaagcttataaatcgcgtttggttt-cagATAAGAAGAACGAGAACAAGAAAGTGGCTGTCAACGATTTCTTGCCATCAGAGAGTGCACATGAAGCTATTCAGTACTCCAT
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gtacgcaccatttcgtctccaaatctgtctgattttttttttctttctatgatcgtagcgctacggtt---gctttgaaatccatttcacatgtatttaatttgcagACAAGAAGAACGAGAACAAGGAGGTTGCTGTGAACGATTTCTTGCCACCAACTACTTCCCTGGAGGCCATTCAACACTCAAT
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G026470_T02 (Zea mays), 3'ss of exon 4
-------------------------------------------------gtaagatccttat----ctcttgtcaaatcaaataactaaggaccaaaactaaagaagc-----ttataaatcgcgtttgg------tttcagATAAGAAGAACGAGAACAAGAAAGTGGCTGTCAACGATTTCTTGCCATCAGAGAGTGCACATGAAGCTATTCAGTACTCCAT
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gtacgcgcttgctctctctctacatatatctcgctgctccgtgatgctcgctaggtttccgcgcggtccttgctggatcggacg-ctcctcccttcaactgaccgtgtggttgttttgtttcctgctctggccaaattccagACAAGAAGAACGAGAACAAGGAGGTGGCCGTCAACGACTTCCTGCCCGCCGCCGCTGCCCGCGAAGCCATCCAGTACTCCAT
upper sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: EFJ33440 (Selaginella moellendorffii), 3'ss of exon 6
gtaagatccttatctcttgtcaaatcaaataactaaggaccaaaactaaagaa--gcttataaatcgcgtttggtttcagATAAGAAGAACGAGAACAAGAAAGTGGCTGTCAACGATTTCTTGCCATCAGAGAGTGCACATGAAGCTATTCAGTACTCCAT
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---gtatccttttgtgccggctgtgtgagcgtgttggaattttctctctttgtctgctttctttaactggagggagtcagACAAGAAGAACGAGAACAAGACCGTGGCTGTGAACGACTTCCTGCCAGCAGAAAACGCCGTGCAGGCGATCCAGCATTCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcaaataactaaggaccaaaactaaagaagcttataaatcgcgtttggtttcagATAAGAAGAACGAGAACAAGAAAGTGGCTGTCAACGATTTCTTGCCATCAGAGAGTGCACATGAAGCTATTCAGTACTCCAT
aactaaa putative branch site (score: 2)
ttataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagatccttatctcttgtcaaatcaaataactaaggaccaaaactaaagaagcttataaatcgcgtttggtttcagATAAGAAGAACGAGAACAAGAAAGTGGCTGTCAACGATTTCTTGCCATCAGAGAGTGCACATGAAGCTATTCAGTACTCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC