Sequence
atgc intronic sequence ATGC exonic sequencegtgtccaaagcacttagattcacgtggaaagagaactcctggcaatcagaatgatgctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 5
gtgtccaaagcacttagattcacgtggaaagagaac---tcctggcaatcagaatgatgctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
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gtactcatc-tgcttatgttcacatgaaatgaaaatctgtcatagaggttgaattgatgctaacttgtatct-gatcttaatttcagTGCGGTCAGCAAAATTTATTTCACGGAAACAATGGGTTGTAGCTGGTGCAGACGATATGTTCATTCGTGTCTACAACTACAACACGATGGACAAAGTTAA
upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------gtgtccaaagcacttagattcacgtggaaagagaact-cctggca-atcagaatgatgctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
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gtataacaagtttatgagcatcttctgatttcattgttatagatttttcacttgctgtatattgccttgtatagtctgtcgctgttactgaaatttatatatgactttgcagTTAGGTCGGCCAAGTTTATTCCGCGCAAGCAATGGGTTGTGGCTGGAGCGGATGATATGTACATCCGTGTATACAATTACAATACAATGGACAAGGTCAA
upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgtccaaagcacttagattcacgtggaaagagaac-tcctggcaatcagaatgatgctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
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----gtatgatatatagcatctcattgttccttcttattctttcgcacatcatttgttgaatctctgtcctggtgttgt--gcagTTCGGTCAGCAAAGTTCATTGCACGGAAGCAGTGGGTTGTAGCTGGAGCTGATGACATGTTTATTCGTGTCTACAACTACAACACTATGGATAAGATCAA
upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 5
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------gtgtccaaagcacttagattcacgtggaaagagaactcctggcaatca--gaatgatg-----ctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
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gttgcatttttactttcttccagctttgtttc-catttcaaagttattgatgaaattcactgaatgaagttcttctcattcactccttccgttt-cttgcagTTCGATCAGCAAAATTTATTCCTCGCAAGCAGTGGATAGTAGCGGGCTCTGACGACATGTTCATTCGAGTCTACAACTATAACACGATGGATAAAGTGAA
upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ09529 (Selaginella moellendorffii), 3'ss of exon 2
------------------gtgtccaaagcactt-agattcacgtggaaagagaactcctggcaatcagaatgatgctaatgtatattttaaac--------------ttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
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gtaacttttggagtggatttctctaagtccctcgagagtatttttccaagtctgtgttgctccatctcgatttttctaagtttctctctaaaccattgtgtgatctcttgcttgtagTCCGCTCGGCCAAGTTCATATCGCGAAAGCAGTGGATAGTCGCTGGTGCCGACGACATGTACATTCGAGTCTACAACTACAATACCATGGACAAGGTCAA
upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 5
lower sequence: EFJ36319 (Selaginella moellendorffii), 3'ss of exon 2
------------------gtgtccaaagcactt-agattcacgtggaaagagaactcctggcaatcagaatgatgctaatgtatattttaaa--------------cttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
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gtaacttttggagtaaatttctctaagtcccttgagagtatttttccaagtctgtgttgctccatctcgatttttctaagtttctctctaaaaaattgtgtgatctcttgcttgtagTCCGCTCGGCCAAGTTCATATCGCGAAAGCAGTGGATAGTCGCTGGTGCCGACGACATGTACATTCGAGTCTACAACTACAATACCATGGACAAGGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agagaactcctggcaatcagaatgatgctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
tgctaat putative branch site (score: 2)
cttattttc putative PPT
atgctaatgtatattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtccaaagcacttagattcacgtggaaagagaactcctggcaatcagaatgatgctaatgtatattttaaacttattttcagTGAGGTCGGCAAAGTTTATTTCAAGGAAACAATGGGTTGTAGCTGGTGCAGACGACATGTTCATTCGTGTCTACAACTACAATACCATGGACAAAGTTAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA