Sequence
atgc intronic sequence ATGC exonic sequence...cgattgttgatccatctgcatccgatctgtgtagcattgattattttagtctccacatatcctcttccaaatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCCGCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os07g48450.2 (Oryza sativa), 3'ss of exon 1
--cgattgt-tgatccatctgcatccgatctgtgtagcatt-gattattttagtctccacatatcctcttcca--aatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCCGCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG
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catgcatgtgtggttattatcgatttaaagtatgtagcttttgacaatgataggcatgacatttttgtgctcatcgatccatctgcttaat-tacg-----tgcagCTGGACGACTGGGTGCTCTGCCGGATCTACAAGAAGTCCGGCCAGGCGTCGCCGATGATGCCGCCGCTCGCCGCCGACTACGACCACGACGAGCCGTCCG
upper sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ36823 (Selaginella moellendorffii), 3'ss of exon 1
-cgattgttgatccatctgcatccgatctgtgta-gcattgattattttagtctcca-catatcctcttccaaatctatcatctcaatct-gcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCCGCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG
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gtaagtttcaattcctccaagt---agttgcataagtcctgcatattggggaaaaaaacaaaaaaaaaaaaaaaaaagagagctcgagctcatgagtggtattaaaaaccgatggcttactttggcaag-ctgttcttctttc-gttgcagCTGGACGACTG-GGTGCTGTGCCGGATCTAC-AGAAAGAAGACA---------
upper sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ07271 (Selaginella moellendorffii), 3'ss of exon 1
--cgattgttgatccatctgcatcc------gatctgtgtagcattgattattttagtctccacatatc---ctcttccaaatcta---tcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCCGCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG------
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gtaagtgatagagccttgtgtgttcttgagcgttctatgttatattatatggatctgtgttcttggatcaatctctcgcgagggagagttcttttcggcaatcgcgggatgggttttgatgggt--ttttcttcctctttcttttggtcagCTGGACGACTGGGTTCTCTGCCGGATCTACAAGAAGCAATCGAGCGATTGGAAGAGCCCCGCGGCCTCA
upper sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ07841 (Selaginella moellendorffii), 3'ss of exon 1
------------------------------------------cgat-tgttgatccatctgcat---ccgatct---gtgtagcattgattattttagtctccacatatcctcttccaaatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCCGCCGATGGCGGTGCCGCCGCTCTCCGACCAC-GAGCAGGACGAGCCCTGCG-
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gtaagtgatagagccttgtgttttcttgagcgttctatgttatattatatggatctgtgttcttggatcaatctctcgcgagggagaggttttttcggcaatcgcgggatgggttttgatgggtttttcttcctctttcttttggtcagCTGGACGACTGGGTTCTCTGCCGGATCTACAAGAAG--CAATCGAGCGATTGGAAGAGCCCCGCGGCCTCACAAGAAGCGCCAAGCCGCGAGAACGTGAAAA
upper sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ27849 (Selaginella moellendorffii), 3'ss of exon 1
cgattgttgatccatctgcatccgatctgtgtagcattgattattttagtctccacatatcctcttccaaatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAA--GAAGGCCAGCCACGTGCCGCCGATGGCGGT--GCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG-----------
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-------------gtaagt-ttcaattcctcca--agtagttgcatccagtcctgcatattggggaaaaaaacaaaaaaaacaaaaaaaaaaaaaaaagaaagagcgag-agctcgtgagtggtattaaaaaccgatggcttactttggcaagctgttcttctttcgttgcagCTGGACGACTGGGTGCTGTGCCGGATCTACAGAAAGAAGACA
upper sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ20531 (Selaginella moellendorffii), 3'ss of exon 1
cgattgttgatccatctgcatccgatctgtgtagcattgattatttt-agtctccacatatcct-----cttccaaatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCCGCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG
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----cgtt--tcctctagagttttcatggtgaatcatcgattctttcgagagatcgtgtcttgtgaggtcatttcttccagtttttctcatcgattttttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAG----------------------------------------------------------------
upper sequence: GRMZM2G042494_T01 (Zea mays), 3'ss of exon 3
lower sequence: EFJ28600 (Selaginella moellendorffii), 3'ss of exon 1
cgattgttgatccatctgcatc-cgatctgtgtagcatt--gattattttagtctccacatatcctct-tccaaatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCC---GCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG
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cgtttcttctagagttttcatggtgaatcatcgattctttcgagagatcgtgtcttgtgaggtcatttcttccagtttttctcatcgatttt----ttttccagCTCGACGACTGGGTACTGTGCCGGATTTACAAGAAGAGCAGTGGAGCATTCAAGCCGATG-CTATCCGGCAGCACCACGCCCAGGAGCAGCATGAAATCCG-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttagtctccacatatcctcttccaaatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCCGCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG
aaatctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cgattgttgatccatctgcatccgatctgtgtagcattgattattttagtctccacatatcctcttccaaatctatcatctcaatctgcgcatggtgcagCTGGACGACTGGGTTCTGTGCCGGATCTACAAGAAGGCCAGCCACGTGCCGCCGATGGCGGTGCCGCCGCTCTCCGACCACGAGCAGGACGAGCCCTGCG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - tgttgat
- - - - - - - - tgcatcc
- - - - - - - - - - - - - - -tgtagca
- - - - - - - - - - - - - - - - - - - - - - - - - ctccaca