Sequence
atgc intronic sequence ATGC exonic sequence...ttttggtacaagtattgttgatttctttggaatcagaaccaattaggttttagttcattagttaggcactgattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTGTCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 3'ss of exon 4
ttttggtacaagtattgttgatttctttggaatcagaaccaattaggtttt---agttcatta--gttaggcactgattctgtaaa-ttctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTGTCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG
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-----cttaagacactaa-actttttttgcgatcagttctatcgtatcttcaaaagtatattattgtgagatattaaaattttgaccttttttttattcatttcagATGTCACCCAGCCCCTGCTTGTGGAGGTTGACCAAATCTATCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACCCTGTCAAG
upper sequence: GRMZM2G177373_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA11G15010.1 (Glycine max), 3'ss of exon 4
ttttggtacaagtattgttgatttctttggaatcagaaccaattagg--ttttagttcattagttaggcactgattctgtaaattctttctatttgttt---tagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTGTCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG
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----aacataa-catgaatgattctatcaggtgcagagtttctctgcgtttttagatgtgttttaatttaattaaaatgcatgtacttttcttttccctgaacagATGTCACAGAGCAATTGTTGATTGAGGTTGATCAAATCTATCATCTTGCATGCCCTGCTTCTCCAATCTTCTACAAATACAACCCTGTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggttttagttcattagttaggcactgattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTGTCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG
cactgat putative branch site (score: 3)
ttctttctatttgttt putative PPT
taaattctttctattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttttggtacaagtattgttgatttctttggaatcagaaccaattaggttttagttcattagttaggcactgattctgtaaattctttctatttgttttagATGTCACCGAGCCGCTTCTTGTGGAAGTTGACCAAATCTGTCACCTTGCTTGCCCTGCTTCACCAATCTTCTACAAGCACAACTCTGTTAAG
ttttggt
- - - - - - - -tgttgat
- - - - - - - - - - - - - - - - -cagaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gattctg