Sequence
atgc intronic sequence ATGC exonic sequencegtaaggttctatggtgtgcttgattcttcacctaatacatcagaaaaagattaagattgcacctactgtaatttttaactccctgtgtgaactatgctctagcttttattacttgtacagaaaattctcactctgctgtttcattctttgtgataaagATGGAATTTTGCTCCTTGAGATCAATAGAATGCTGCGCGCTGGAGGATATTTTGCTTGGGCTGCACAGCCTGTTTATAAGCATGAACCCGCTTTGGAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT2G39750.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g62800.1 (Oryza sativa), 3'ss of exon 3
gtaaggttctatggtgtgcttgattcttcacctaatacat-cagaaaaagattaagattgcacctactgtaatttttaactccctgtgtgaactatgctctagcttttattacttgtacagaaaattctcactctgctgtttcattctttgtgataaagATGGAATTTTGCTCCTTGAGATCAATAGAATGCTGCGCGCTGGAGGATATTTTGCTTGGGCTGCACAGCCTGTTTATAAGCATGAACCCGCTTTGGAAGA
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---------------------------------attgttttcaacaaaatatcaacacaaagataactgttttttgtagcaccctg-----act----tccaatttgcttaactt----------ttgttgccatgatttgccacttt-------aaagATGGAATCCTGCTTCTGGAGGTTAATAGAATGCTCAGAGCCGGCGGTTATTTTGCTTGGGCAGCACAGCCTGTTTATAAGCATGAAGAGGCTCAGCAAGA
upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G042295_T01 (Zea mays), 3'ss of exon 3
gtaaggttctatggtgtgcttgattcttcacctaatacatcagaaaaagattaagattgcacctactgtaatttttaactccctgtgtgaactatgctctagcttttattacttgtacagaaaattctcactctgctgtttcattctttgtgataaagATGGAATTTTGCTCCTTGAGATCAATAGAATGCTGCGCGCTGGAGGATATTTTGCTTGGGCTGCACAGCCTGTTTATAAGCATGAACCCGCTTTGGAAGA
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--------------------------------------------------------atatctttacatttaaacttgatcgcaaatatga--tgtgccactcatctatgtactttccaagtttgcctaagttttgttatcatatttgtttatttggagATGGTATCCTGCTCCTGGAGGTTAATAGATTACTTAGAGCTGGAGGCTACTTTGCTTGGGCAGCACAACCTGTTTATAAGCATGAACAGGCCCAACAAGA
upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G092120_T02 (Zea mays), 3'ss of exon 3
gtaaggttctatggtgtgcttgattcttcacctaatacatcagaaaaagattaagattgcacctactgtaatttttaactccctgtgtgaactatgctctagcttttattacttgtacagaaaattctcactctgctgtttcattctttgtgataaagATGGAATTTTGCTCCTTGAGATCAATAGAATGCTGCGCGCTGGAGGATATTTTGCTTGGGCTGCACAGCCTGTTTATAAGCATGAACCCGCTTTGGAAGA
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--------------------------------------------------------tttcatttaaacttgatctcaaagg--tatgtgcacttatctatgtactttccaaatttgcctaagttttgtacttttgttatcatatttgtttatttgaagATGGTATCCTGCTCCTGGAGGTTAATAGATTGCTTAGAGCTGGAGGCTACTTTGCTTGGGCAGCCCAACCTGTTTATAAGCATGAAGAGGCCCAACAAGA
upper sequence: AT2G39750.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv13s0019g02250.t01 (Vitis vinifera), 3'ss of exon 3
gtaaggttctatggtgtgcttgattcttcacctaatacatcagaaaaagattaagattgcacctactgtaatttttaactccctgtgtgaactatgctctagcttttattacttgtacagaaaattctcactctgctgtttcattct-ttgtgataaagATGGAATTTTGCTCCTTGAGATCAATAGAATGCTGCGCGCTGGAGGATATTTTGCTTGGGCTGCACAGCCTGTTTATAAGCATGAACCCGCTTTGGAAGA
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----------------------------------------------aagagaaagagaaagctcacttaagatttt---tttttgt-ttaattgt----taaatt----tactaggggacact-ttctgatcatgctttttcctttcattttgatgaagATGGAATCTTGCTGCTTGAGGTAAATAGAATGCTTCGGGCAGGAGGATACTTTGCTTGGGCAGCACAGCCAGTTTATAAGCATGAAGAAAACCTAGAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttattacttgtacagaaaattctcactctgctgtttcattctttgtgataaagATGGAATTTTGCTCCTTGAGATCAATAGAATGCTGCGCGCTGGAGGATATTTTGCTTGGGCTGCACAGCCTGTTTATAAGCATGAACCCGCTTTGGAAGA
ttctcac putative branch site (score: 2)
ctgtttcattcttt putative PPT
agaaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaggttctatggtgtgcttgattcttcacctaatacatcagaaaaagattaagattgcacctactgtaatttttaactccctgtgtgaactatgctctagcttttattacttgtacagaaaattctcactctgctgtttcattctttgtgataaagATGGAATTTTGCTCCTTGAGATCAATAGAATGCTGCGCGCTGGAGGATATTTTGCTTGGGCTGCACAGCCTGTTTATAAGCATGAACCCGCTTTGGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA