Sequence
atgc intronic sequence ATGC exonic sequence...ctctgtctgttagggccaaacagttcagactgtttgaaccgcgactgttttatactgaatgatggagggttttgtttgtgttggattggattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g12950.1 (Oryza sativa), 3'ss of exon 2
ctctgtctgttagggccaaacagttcagactgtttgaaccgcgactg-----ttttatactgaatgatggagggttttgtttgtgttggattggattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
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-tgtattgatgaggcacctactcttttgtttttgagcaaatcatttgaccctttttatattgaatgacgaagg--tttgtgtgtgtttgatt-----cactggagcagGCACAGGTGGACTGGAAGATATGAAGCCCACCTCTGGGATAACAGTTGCAAAAAGGATGGACAGACAAGGAAGGGAAGGCAAG
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA17G17010.1 (Glycine max), 3'ss of exon 3
ctctgtctgttagggccaaacagttcagactgtttgaaccgcgactgttttatactgaatgatg-gagggttttgtttgtgttggattggattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
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--gcaatgagcatcctccaacacatttaactgttc--atcaccctttttgtgttttgtgttttatgatttttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G40380.1 (Glycine max), 3'ss of exon 1
ctctgtctgttagggccaaacagttcagactgtttgaaccgcgactgttttatactgaatgatggagggttttgtttgtgttggattggat-tcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
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-tccttgctcaagaagttaagggttca---tgtaagattaatgtcaacaacatatttgactgtttattttttgctttgatttccaaagaatatttgttcaacagGCATAGGTGGACTGGTAGATATGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA11G04910.1 (Glycine max), 3'ss of exon 3
ctctgtctgttagggccaaa-cagttcagactgtttgaaccgcgactgttttatactgaatgatggagggttttgtttgtgttggattggat-tcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
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--ttaagtgttcatgtaagagcaattccaacaacata---tttgactgtttacttttattttttttatgttttgctttaatttctaaggaatgtttgttcatcagGCATAGGTGGACTGGTAGATACGAAGCTCATCTATGGGACAACAGCTGCAAGAAAGAGGGCCAAGGAAGGAAAGGAAGGCAAG
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA05G22970.1 (Glycine max), 3'ss of exon 4
ctctgtctgttagggccaaacagttcagactgtttgaaccg-----cgactgttttatactgaatgatggagggttt-tgtttgtgttggattggattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
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---------tgagcaatgagcattctcaactcatttaactgttcatcttcctttttgtgttttgtgttttatgatttctctttatttctaaagggtgtttgtgtatcagGCATAGGTGGACTGGGAGATATGAAGCTCATCTTTGGGACAACAGCTGCAAGAAAGAGGGGCAAAGCAGGAAAGGAAGACAAG
upper sequence: GRMZM2G021573_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv18s0001g08610.t01 (Vitis vinifera), 3'ss of exon 2
-------------------------------------------------------------------------------------ctctgtctgt-tagggccaaacagttcagactgtt---tgaaccgcgactgttttatactgaatgatggagggtt--ttgtttgtgttgg-attg--gattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
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gttagttcatattcttttccttcatctttggtcttatctataatgttttttgaattgagtttgttttctagtttatttgaggtctccctgcaggtgtattgtatcactgttttctctattatattgtcctcgccttttctgctggaaatattgtaggtttggttttccaagtaaacattgtcaatttatttccccagGCATAGATGGACTGGTAGATATGAAGCCCATCTTTGGGATAATAGTTGCAAGAAGGAGGGGCAGACTAGGAAAGGAAGACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttttatactgaatgatggagggttttgtttgtgttggattggattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
ttttgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctctgtctgttagggccaaacagttcagactgtttgaaccgcgactgttttatactgaatgatggagggttttgtttgtgttggattggattcactggagCAGGCACAGGTGGACTGGGAGATACGAAGCCCACCTCTGGGACAACAGCTGCAGGAAGGATGGGCAGACTAGAAAAGGCAGACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- ctgtctg
- - - - - - - -ccaaaca
- - - - - - - - - - - - - - actgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatg