Sequence
atgc intronic sequence ATGC exonic sequencegtaatgtcagtttatcttgtctaaaataacggtgatcttgtgctaacttttacttacattttcaaattcatgcagGGAAATTTATCTGGGCAAAGGCAAGGGCAGCCTGTTCTTATCACCAGACTTGAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G25540.2 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G25540.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os09g13610.1 (Oryza sativa), 3'ss of exon 9
---------------------gtaatgtcagtttatcttgtctaaaataacggtgatcttgtgctaacttttac----ttacattttcaaattcatg-cagGGAAATTTATCTGGGCAAAGGCAAGGGCAGCCTGTTCTTATCACCAGACTTGAG
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tgtctcaagttgcctatgttgatgatactggtatcatcagtc-aatatatgatttgtttgttgtggatgcataatatgtaatgtttctatttttatttcagGGAACTTTATCTGGGCAAAGGCAAGGACAACCTGTATTTATCTGTAAACTTGAA
upper sequence: AT1G25540.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os09g13610.3 (Oryza sativa), 3'ss of exon 9
---------------------gtaatgtcagtttatcttgtctaaaataacggtgatcttgtgctaacttttactt----acattttcaaattcatg-cagGGAAATTTATCTGGGCAAAGGCAAGGGCAGCCTGTTCTTATCACCAGACTTGAG----------------------------------------------
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tgtctcaagttgcctatgttgatgatactggtatcatcagtc-aatatatgatttgtttgttgtggatgcataatatgtaatgtttctatttttatttcagGGAACTTTATCTGGGCAAAGGCAAGGACAACCTGTATTTATCTGTAAACTTGAAGTAAGTTTCTGTTTGTTGGATGAATTGTCTGTGACTCCGACTATTA
upper sequence: AT1G25540.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G138178_T01 (Zea mays), 3'ss of exon 9
-----------------gtaatgtcagtttatcttgtc-taaaataacggtgatcttgtgctaacttttacttacattttcaaattcat-------gcagGGAAATTTATCTGGGCAAAGGCAAGGGCAGCCTGTTCTTATCACCAGACTTGAG
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tatctaatccccttggagggcccatggttgctgctgccgcagctcctccgtgggcctccttagaccctgacatgatgtttgccatttatctgtatttcagGGAACTTTATCTGGCCAAAGGCAAGGACAGCCTGTAATAATTTGTAAACTCGAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaaaataacggtgatcttgtgctaacttttacttacattttcaaattcatgcagGGAAATTTATCTGGGCAAAGGCAAGGGCAGCCTGTTCTTATCACCAGACTTGAG
tacttac putative branch site (score: 1)
ttttacttacattttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgtcagtttatcttgtctaaaataacggtgatcttgtgctaacttttacttacattttcaaattcatgcagGGAAATTTATCTGGGCAAAGGCAAGGGCAGCCTGTTCTTATCACCAGACTTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG