Sequence
atgc intronic sequence ATGC exonic sequence...aaacccgcccttctccgctcgttccgtttcgtttccactagccatccaataatgttgccccgccatcgatgtaccgagaagcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTACGCCGAGACGGTGAAGGCCATCCTAAGCAAGGCAACCCGCACTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G535911_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g03220.1 (Oryza sativa), 3'ss of exon 2
----------------aaacccgcccttctccgctcgttccgtttcgtttcca------ctagccatccaataa----------tgttgccccgccatcgatgtaccgaga-----agcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTACGCCGAGACGGTGAAGGCCATCCTAAGCAAGGCAACCCGCACTT
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gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgttgtgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGCGCATGTTTGGTTTTGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT-------------------
upper sequence: GRMZM2G535911_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os12g02970.1 (Oryza sativa), 3'ss of exon 2
----------------aaacccgcccttctccgctcgttccgtttcgtttcca------ctagccatccaataa----------tgttgccccgccatcgatgtaccgaga-----agcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTACGCCGAGACGGTGAAGGCCATCCTAAGCAAGGCAACCCGCACTT
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gtatcacatgttccaccatagtgcccctattgatgtgtcttgtttcaatattggagcatttcataatttaatgaatgcaatctgttttggcttgtttgtgtcatgtggggacaaccagCATGTATGGGATGGTGCAAGATGTGCGTATCCCATACCAGGAGAAGTGCATGTTTGGTTTCGTCACCTTCGCCTACCAAAAGACAGTGAAGCTAATTCTT-------------------
upper sequence: GRMZM2G535911_T03 (Zea mays), 3'ss of exon 7
lower sequence: AT3G63450.1 (Arabidopsis thaliana), 3'ss of exon 2
aaacccgcccttctccgctcgttccgt-ttcgtttccactagccatccaataatgttgccccgccatcgatgtaccgagaagcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTACGCCGAGACGGTGAAGGCCATCCTAAGCAAGGCAACCCGCACTT
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---------gtattactcttgtttggaacccattcattcttcttgttggatgttgtctacttaa-agcaatg-gtggtgcagTACGTTTGGGCCAGTTCAGGACGTGAGGATACCTTACCAGCAGAAGAGGATGTTTGGGTTCGTGACCTTCATGTACCCAGAGACTGTGAAGAGCATTCTG-------------------
upper sequence: GRMZM2G535911_T03 (Zea mays), 3'ss of exon 7
lower sequence: Vv06s0061g00150.t01 (Vitis vinifera), 3'ss of exon 2
-------aaacccgccc-ttctccgctcgttccgtttcgtttccactagccatccaataatgttgccccgcc--atcgatgtaccga-gaagcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTACGCCGAGACGGTGAAGGCCATCCTAAGCAAGGCAACCCGCACTT
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gtaattgctacgtgttggttggaaatttcttcaatttggggttcgt--gttgtgaaatttagttaacctagttggcttgtgtgcttttgaagTATTTTTGGGCCAGTTCAAGATGTGAGGATTCCATACCAGCAGAAGAGGATGTTCGGATTCGTCACTTTCGTCTACCCCGAGACTGTGAAGCTCATTTTA------------------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccaataatgttgccccgccatcgatgtaccgagaagcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTACGCCGAGACGGTGAAGGCCATCCTAAGCAAGGCAACCCGCACTT
atatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaacccgcccttctccgctcgttccgtttcgtttccactagccatccaataatgttgccccgccatcgatgtaccgagaagcatattcgggccggtgcagGACGTGCGCATCCCGTACCAGCAGAAGCGCATGTTCGGCTTCGTCACCTTCATGTACGCCGAGACGGTGAAGGCCATCCTAAGCAAGGCAACCCGCACTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - -cttctcc
- - - - - - - - - - - - - - - - - - - - gccatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaagca