Sequence
atgc intronic sequence ATGC exonic sequence...tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGTTGTATGCCAAGAAGGACTACAACCTGGCGAAGCATCCGCAGATCGATGTGCCCAACCTCCAGGACTCCAGGTGATCAAGCTCATGCAGAGC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G459828_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g35090.1 (Oryza sativa), 3'ss of exon 2
tccaaatttatttgccccttaaactatggattccttgttat-acattcatctgcgttatgttcatacg-atttctgttagtttgatgtat-ttgctgctgcagAGGGCGTGTTGTATGCCAAGAAGGACTACAACCTGGCGAAGCATCCGCAGATCGATGTGCCCAACCTCCAGGACTCCAGGTGATCAAGCTCATGCAGAGC--------
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---cgctgttggtgtatgtcagtacagcgttcgcatgccaagaggctcaaactgaaagtgattgtaggtgctggttttaacttggtgtatgctgttgttgcagAGGGAGTGCTGTATGCCAAGAAGGACTACAACCTGGCGAAGCACCCGCAGATCGATGTGCCGAACCTGCAGG--------TGATCAAGCTCATGCAGAGCTTCAAGTC
upper sequence: GRMZM2G459828_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g34460.1 (Oryza sativa), 3'ss of exon 2
--tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttg-atgtatt-tgctgc--tgcagAGGGCGTGTTGTATGCCAAGAAGGACTACAACCTGGCGAAGCATCCGCAGATCGATGTGCCCAACCTCCAGGACTCCAGGTGATCAAGCTCATGCAGAGC--------
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ataataagaccatatgtct-tcatcctat----ttcgactgatgaact-agaaggatattgtttctcatttcttcatttgtttgtgtgcattgtggtgcatcatagAGGGGGTTTTGTACGCCAAGAAGGACTACAATTTGGCAAAACACCCACAGATTGATGTGCCAAACCTTCAGGTC--------ATCAAGCTCATGCAGAGCTTCAAGTC
upper sequence: GRMZM2G459828_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ29946 (Selaginella moellendorffii), 3'ss of exon 1
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGTTGTATGCCAAGAAGGACTACAACCTGGCGAAGCATCCGCAGATCGATGTGCCCAACCTCCAGGACTCCAGGTGATCAAGCTCATGCAGAGC--------
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-------------gtgaggggatcta-gcttctcctggcgcgctcgcgctcacgcatttctaatccgagatttctc--cccaat-tgttcggc---gcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCT--------CCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC
upper sequence: GRMZM2G459828_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ29946 (Selaginella moellendorffii), 3'ss of exon 1
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGTTGTATGCCAAGAAGGACTACAACCTGGCGAAGCATCCGCAGATCGATGTGCCCAACCTCCAGGACTCCAGGTGATCAAGCTCATGCAGAGC--------
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-------------gtgaggggatcta-gcttctcctggcgcgctcgcgctcacgcatttctaatccgagatttctc--cccaat-tgttcggc---gcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCT--------CCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC
upper sequence: GRMZM2G459828_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25099 (Selaginella moellendorffii), 3'ss of exon 1
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGTTGTATGCCAAGAAGGACTACAACCTGGCGAAGCATCCGCAGATCGATGTGCCCAACCTCCAGGACTCCAGGTGATCAAGCTCATGCAGAGC--------
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----------------------gtgaggggatctagctcgcgcatttctcc-cttttttctaatccgagatttctc--cccaat-tgttcggc---gcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCT--------CCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC
upper sequence: GRMZM2G459828_T01 (Zea mays), 3'ss of exon 2
lower sequence: EFJ25099 (Selaginella moellendorffii), 3'ss of exon 1
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGTTGTATGCCAAGAAGGACTACAACCTGGCGAAGCATCCGCAGATCGATGTGCCCAACCTCCAGGACTCCAGGTGATCAAGCTCATGCAGAGC--------
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----------------------gtgaggggatctagctcgcgcatttctcc-cttttttctaatccgagatttctc--cccaat-tgttcggc---gcagAGGGCGTCCTCTACGCCAAGAAGGACTACAATCTCCCCAAGCACCCGGAGATCGATGTCCCCAATCT--------CCAGGTGATCAAGCTCATGCAGAGCTTCAAGTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGTTGTATGCCAAGAAGGACTACAACCTGGCGAAGCATCCGCAGATCGATGTGCCCAACCTCCAGGACTCCAGGTGATCAAGCTCATGCAGAGC
gtttgat putative branch site (score: 5)
atgtattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tccaaatttatttgccccttaaactatggattccttgttatacattcatctgcgttatgttcatacgatttctgttagtttgatgtatttgctgctgcagAGGGCGTGTTGTATGCCAAGAAGGACTACAACCTGGCGAAGCATCCGCAGATCGATGTGCCCAACCTCCAGGACTCCAGGTGATCAAGCTCATGCAGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - catctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgatg