Sequence
atgc intronic sequence ATGC exonic sequence...gcataccaatttatacttattgtggtggcctcagagatcattgacatttgttctgctgataattttctgatctgatatgtatttacctacaatcttacagATTTGTGTTTGGTGCTGGCACCATATAATGGACATGGCAGAGAAAGATCAATCAGAAGGGCGCTGTCCAGCTTGCCGCACTCCATATGACAAAGAAAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT3G45630.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G45630.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os12g01190.3 (Oryza sativa), 3'ss of exon 2
gcataccaatttatacttattgtggtggcctcagagatcattgacatttgttctgctgataattttctgatctgatatgtatttacctacaatcttacagATTTGTGTTTGGTGCTGGCACCATATAATGGACATGGCAGAGAAAGATCAATCAGAAGGGCGCTGTCCAGCTTGCCGCACTCCATATGACAAAGAAAAGA
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-------------------gtttcttcccttccctccccaccac--tctactctccacaccccccttccattcacctcccttttgcatctcac--tgcagATTTGTGTCTGGTGCTGGCACCACATCATTGATATGGCTGAGAAAGAGGACACTGAGGGCCGCTGCCCCGCATGCCGCACTCGCTATGACAAAGATAGGA
upper sequence: AT3G45630.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g01190.1 (Oryza sativa), 3'ss of exon 2
gcataccaatttatacttattgtggtggcctcagagatcattgacatttgttctgctgataattttctgatctgatatgtatttacctacaatcttacagATTTGTGTTTGGTGCTGGCACCATATAATGGACATGGCAGAGAAAGATCAATCAGAAGGGCGCTGTCCAGCTTGCCGCACTCCATATGACAAAGAAAAGA
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--------gtttcttcccttccc--ttccctcccctccccaccac-tctactctccacacccccttccattc--acctcccttttgcatctccactgcagATTTGTGTCTGGTGCTGGCACCACATCATTGATATGGCTGAGAAAGAGGACACTGAGGGCCGCTGCCCCGCATGCCGCACTCGCTATGACAAAGATAGGA
upper sequence: AT3G45630.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G146267_T02 (Zea mays), 3'ss of exon 2
gcataccaatttatact--tattgtggtg-gcctcagagatcattgac-atttgttctgctgataattttctgatctgatatgtatttacctacaatcttacagATTTGTGTTTGGTGCTGGCACCATATAATGGACATGGCAGAGAAAGATCAATCAGAAGGGCGCTGTCCAGCTTGCCGCACTCCATATGACAAAGAAAAGA
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gtatgtctactgattctcctatcctattgtaccaatcagattgcagcccaccttgtctgcactttgtttcatcatataacaagaactgtcacttaactctgcagATTTGTGTTTGGTGCTGGCACCACATCATAGACATGGCTGAGAAGGAGGAAACAGTGGGCCGCTGCCCTGCATGCCGCACATGCTATGACAAGGACAGGA
upper sequence: AT3G45630.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G400238_T02 (Zea mays), 3'ss of exon 1
gcataccaatttatacttattgtggtggcctcagagatcattgacatttgttctgctgataattt----tctgatctgatatgtatttacctacaatcttacagATTTGTGTTTGGTGCTGGCACCATATAATGGACATGGCAGAGAAAGATCAATCAGAAGGGCGCTGTCCAGCTTGCCGCACTCCATATGACAAAGAAAAGA
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gtatgtctactgat-cttcttcctatcctatcaatcat-attgcagcctgccttgcatgcactttgtgccatcatctaaca-ataactgcc-ataactctgcagATTTGTGTTTGGTGCTGGCACCACATCATAGACATGGCTGAGAAGGAGGAAACAGTGGGCCGCTGCCCTGCATGCCGCACATGCTATGACAAGGACAGGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttgttctgctgataattttctgatctgatatgtatttacctacaatcttacagATTTGTGTTTGGTGCTGGCACCATATAATGGACATGGCAGAGAAAGATCAATCAGAAGGGCGCTGTCCAGCTTGCCGCACTCCATATGACAAAGAAAAGA
atatgtattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcataccaatttatacttattgtggtggcctcagagatcattgacatttgttctgctgataattttctgatctgatatgtatttacctacaatcttacagATTTGTGTTTGGTGCTGGCACCATATAATGGACATGGCAGAGAAAGATCAATCAGAAGGGCGCTGTCCAGCTTGCCGCACTCCATATGACAAAGAAAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- ataccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgatct