Sequence
atgc intronic sequence ATGC exonic sequence...nnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtgtaatcaatccagctacaggcactaaccctccggtccctcacctttgcatcttgataatattatatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G020544_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g01480.1 (Oryza sativa), 3'ss of exon 1
--nnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtgtaatcaatccagctacaggcactaaccctccggtccctcacctttgcatcttgataatattatatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG
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gttactgaacactagttctctctattgaatgtaaacaaatgcattagcgttggaaaaattgaaactgatccatttgcatgaaatctt--tgacttgatgtagGTGGAGGGCAAGATAATCAAGGCGCAGATCTGGGACACCGCAGGTCAAGAGCGATACAGAGCTATCACCAGCGCTTACTACCGTGGAGCTCTAGGAGCAG
upper sequence: GRMZM2G020544_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv12s0035g01140.t01 (Vitis vinifera), 3'ss of exon 1
-nnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtgtaatcaatccagctacaggcactaaccctccggtccctcacctttgcatcttgataatatt--atatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG
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tgttgtagatttatggttatttttatatagtat-taattgttacaggta--actgtgaaagctcagatatggtattaattgttttttactgtatttggttcagGTCGAGGGACGAACTGTGAAAGCTCAGATATGGGACACAGCAGGGCAGGAGCGGTACAGAGCAATTACCAGTGCCTACTATAGGGGTGCCCTTGGAGCTC
upper sequence: GRMZM2G020544_T01 (Zea mays), 3'ss of exon 1
lower sequence: EDP04353 (Chlamydomonas reinhardtii), 3'ss of exon 2
nnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtgtaatcaatccagctacaggcactaaccctccggtccctcacctttgcatcttgataatattatatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG
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gcaaggctatctgcaagagaggatttgactg-------------gtcatggccattgacaaaatg------cgctgttgc--tctga---------gcagGTCGACGGCAAGACCATCAAGGCGCAAATTTGGGACACTGCAGGCCAGGAGCGCTACCGCGCCATTACGAGCGCATACTACCGTGGCGCTGTCGGAGCCC
upper sequence: GRMZM2G020544_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ30172 (Selaginella moellendorffii), 3'ss of exon 1
nnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtgtaatcaatccagctacaggcactaaccctccggtccctcacctttgcatcttgataatattatatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG
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--gtaacaaagaattctctctttccctcttttctcatc--tcaaattcc---ttctttctatggtggttgtgttcttcccggacggatggaactct--agGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC
upper sequence: GRMZM2G020544_T01 (Zea mays), 3'ss of exon 1
lower sequence: EFJ06060 (Selaginella moellendorffii), 3'ss of exon 1
nnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtgtaatcaatccagctacaggcactaaccctccggtccctcacctttgcatcttgataatattatatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG
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--gtaacaaagaattctctctttccctcttttctcatc--tcaaattcc---ttctttctatggtggtggtgttcttcccggacggatggaactct--agGTGGATGGCAAGACGATCAAAGCCCAAATCTGGGACACGGCCGGGCAAGAGCGCTACCGCGCCATCACCAGCGCCTACTACCGGGGCGCGGTGGGGGCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctacaggcactaaccctccggtccctcacctttgcatcttgataatattatatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG
atcttgataatattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
nnnnnnnnnnnnnnnnnnnnnnnnnnnnntgtgtaatcaatccagctacaggcactaaccctccggtccctcacctttgcatcttgataatattatatagGTTGAGGGCAAGATCATCAAGGCGCAGATCTGGGACACGGCAGGCCAGGAGCGGTACCGGGCGATCACCAGCGCCTACTATCGCGGGGCGCTGGGCGCGG
- - - - - - - - - - - - - - - - - - - - - - gctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttgca