Sequence
atgc intronic sequence ATGC exonic sequencegtaagggcgccatgtattattctctgagatcattatatgaatctagtacaaatattaagcttggtagttatttgtggattaggtgaatggaaaatctatatttggttcttatcattttcccagttaataactaacatattatgttccactgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
Basic information
species | Arabidopsis thaliana |
transcript | AT3G43300.2 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GRMZM2G335287_T01 (Zea mays), 3'ss of exon 18
gtaagggcgccatgtattattctctgagatcattatatgaatctagtacaaatattaagcttggtagttatttgtggattaggtgaatggaaaatctatatttggttcttatcattttcccagttaataactaacatattatgttccactgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
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---------------------------------------------------------------gtaggtttatatgtacttatagaaaacacaaatttctttaagattttgcccccgtcaccctcagatactgatatgtt-tattt--------------gcagGTACTGTGCTGATAATCCTGAGCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCTTATGCTGTTATAATGTTGAATACTGATGCACACAATCCAATG
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA13G17610.1 (Glycine max), 3'ss of exon 20
gtaagggcgccatgtattattctctgagatcattatatgaatctagtacaaatattaagcttggtagttatttgtggattaggtgaatggaaaatctatatttggttcttatcattttcccagttaataactaacatattatgttccactgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
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------------------------------------------------------ttatactttatattt---cgtgggcatgataccttgtacctgtactgataatttatatcttttg------tactaatagaagtgtcttggtgc-ttgttgtctatggcagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: GLYMA17G04890.1 (Glycine max), 3'ss of exon 20
gtaagggcgcca-tgtatt----attctctgagatcattatatga--------atctagtacaaatattaag-cttggtagttatttg-----tggattaggtgaatggaaaatctatatttggttcttatcattttcccagttaataactaacatatta-------tgttcca----ctgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
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gtaatggcttttctgtacttgcaagtgtctcagggtgttttataaggtgtcaaatcttggttgattgtcatgtcataatgtctacttacactttatatttcgtgggcatgatacct-tgcatggttgtacctgtactgataatttatatcttttgtactaatagcagtgtctttgtgcatgttgtctatgacagATACTGTGCAGACAATCCTGGCCTTTTTAAAAATGCAGATACAGCTTATGTTCTAGCTTATGCTGTTATTATGTTAAATACTGATGCTCATAACCCAATG
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: Vv11s0016g00170.t01 (Vitis vinifera), 3'ss of exon 20
gtaagggcgccatgtattattctctgagatcattatatgaatctagtacaaatattaagcttggtagttatttgtggattaggtgaatggaaaatctatatttggttcttatcattttcccagttaataactaacatattatgttccactgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
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------------------------------------------------------ttgag--tgaaaaaaggttaccttctaggtgtcatcaagatca-----tgtcccctttcttattgctagttggtgatcta---gtcctttttgtgttttgtctctggcagTTACTGTGCAGACAATCCAGATCTTTTCAAAAATGCAGATACTGCTTATGTTCTTGCATATGCAGTTATAATGTTGAATACTGATGCACATAATCCCATG
upper sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 19
lower sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------gtaagggcgccat-gta-ttattctctgagatcatta--tatgaatctagtacaaatattaagcttggt---agttatttgtggattaggtgaatggaaaatctatatttggtt-cttatcattttcccagttaataactaacatattatgttccactgttgccttga-gtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
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gttgaacttttaatcatgttttctcatatcgtcattgcagttggcggttaatttaggtggccgagaaattatcagaacccttaaacgctatttcaagtaccttcgagataagggcagatatcagcaatgtgtcgtgacgtaacacctgcc-ggctatttctt--ctgactatgtactttggataagtgattacagGTACTGTCGAGATAATGGTAACCTTTTCAAAAATGCAGACACAGCTTATGTGCTGGCGTATGCAGTTATTATGCTCAACACAGATGCTCATAATCCTCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcattttcccagttaataactaacatattatgttccactgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
aactaac putative branch site (score: 1)
ttgcctt putative PPT
ttaataactaacatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggcgccatgtattattctctgagatcattatatgaatctagtacaaatattaagcttggtagttatttgtggattaggtgaatggaaaatctatatttggttcttatcattttcccagttaataactaacatattatgttccactgttgccttgagtagATATTGCGCAGACAATCCGGGTCTTTTCAAGAATGCAGATACAGCCTACGTTCTAGCCTATGCAGTTATCATGTTAAATACAGATGCGCATAATCCTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG