Sequence
atgc intronic sequence ATGC exonic sequencegttagcacacaaactatctgaccctcgacttggattttcttctgcagTTTGTCCAACTACATTGAAACGGATATGCAGGCAACATGGGATCATGAGGTGGCCATCTCGTAAGATTAACAAAGTGAACAGGTCACTAAGGAAAATACA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G43500.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G43500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os11g16290.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------------------------------------------------------------------------------------------------gttagcacacaaactatctgaccctcgacttggattttcttctgcagTTTGTCCAACTACATTGAAACGGATATGCAGGCAACATGGGATCATGAGGTGGCCATCTCGTAAGATTAACAAAGTGAACAGGTCACTAAGGAAAATACA
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gtaatttgtttatactctcatgatctttttctgatttattcttatagaattcaattaattcctactaaattagttctgttttgtatgaaaagcactactgctaatacaaatgtagaaacaaactaatccaattgtgtcataggaagaggagcttacaggattttttttattc---cttgctgttacgttgcagTTTGTCCTACTACGCTGAAAAGGATATGCAGACAACATGGAATATCAAGGTGGCCATCTCGTAAGATAAAGAAGGTAAACCGATCCCTAAAGAAGATCCA
upper sequence: AT2G43500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: LOC_Os04g41850.1 (Oryza sativa), 3'ss of exon 5
------------------------------------------------------------------------gttagcacacaa---actatctgaccctcgacttggattttcttct----------gcagTTTGTCCAACTACATTGAAACGGATATGCAGGCAACATGGGATCATGAGGTGGCCATCTCGTAAGATTAACAAAGTGAACAGGTCACTAAGGAAAATACA
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gtgagcctctagtgtctttttgtaaaatgaacttaacaaacctttactgtgttatttgatctactttatgtaaatagggtataattaaatggttgactttctgctgatgccttcttttaatattgggtgcagTTTGTCCAACAACTTTGAAACGGATATGCCGGCATCATGGAATTTCACGATGGCCATCTCGCAAGATAAACAAGGTTAATCGTTCATTAAAGAAGATTCA
upper sequence: AT2G43500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G105004_T01 (Zea mays), 3'ss of exon 4
--------------------------------------------------------------------------------------------------------------------gttagcacacaaacta-----tctgaccctcgacttggattttcttctgcagTTTGTCCAACTACATTGAAACGGATATGCAGGCAACATGGGATCATGAGGTGGCCATCTCGTAAGATTAACAAAGTGAACAGGTCACTAAGGAAAATACA
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gtgagccctactgtattgttacgaagtctctgttaaatctagatttgctgtgacattcacagtactgattactgaagataatgccatcattgtagaagaatttcttagattaggagattatggaatgaactgcttcttctgacacttgcctataaacaccat-tgcagTTTGTCCAACGACATTGAAACGAATATGCAGACAACATGGAATTTCCCGATGGCCATCTCGAAAGATAAACAAGGTCAATCGTTCATTGAAGAAGATAGA
upper sequence: AT2G43500.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G031398_T01 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------------------------------------------------gttagcacacaaacta--tctgaccctcgacttggattttcttctgcagTTTGTCCAACTACATTGAAACGGATATGCAGGCAACATGGGATCATGAGGTGGCCATCTCGTAAGATTAACAAAGTGAACAGGTCACTAAGGAAAATACA
||| | | ||||| |||||| || | || | | | ||||||||||||||| || |||||||| |||||||| |||||||| || || ||||||||||| ||||| ||||| || ||| | ||||| | ||| || |
gtgagccctactgtactgttatgaagtcccagttaaatctaattttgctgcgacattcacagtactgaagataatgccatcaccgcagctgaatttcttaggttaggtgattatgaaatgaactacttctgacacttgcctataaacaccat-tgcagTTTGTCCAACAACTTTGAAACGAATATGCAGACAACATGGAATTTCCAGATGGCCATCTCGAAAGATAAACAAGGTCAACCGTTCACTGAAGAAGATCGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttagcacacaaactatctgaccctcgacttggattttcttctgcagTTTGTCCAACTACATTGAAACGGATATGCAGGCAACATGGGATCATGAGGTGGCCATCTCGTAAGATTAACAAAGTGAACAGGTCACTAAGGAAAATACA
atctgac putative branch site (score: 3)
ttttcttctgc putative PPT
attttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagcacacaaactatctgaccctcgacttggattttcttctgcagTTTGTCCAACTACATTGAAACGGATATGCAGGCAACATGGGATCATGAGGTGGCCATCTCGTAAGATTAACAAAGTGAACAGGTCACTAAGGAAAATACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA