Sequence
atgc intronic sequence ATGC exonic sequence...gataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G816636_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g05860.1 (Oryza sativa), 3'ss of exon 4
gataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttct-ttcgttctttgtaacctctggttgt-cttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
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---------------gtata-taacattgtattcatatactaacacaaataagttggaaaaaaactattctttttttctcacttcatattattcctggtcagGTGTTTTTTGAATCGGATGAGGTCCATGCATGCATTGTCACATGTGGAGGACTGTGCCCTGGACTGAACACTGTCATTAGGGAAATTGTATGTGGCTTAT
upper sequence: GRMZM5G816636_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G09180.1 (Glycine max), 3'ss of exon 4
----------------gataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtct--tggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
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gtcatttcccttgtttgtctgtgcatatatattata-tattattaagaactaagaatattaaaaaatgtataattaattttgtttccactcaccaacacctaatcatatgctgttcagGTATACTTTAAATCGGATGAAGTGCATGCATGCATTGTCACGTGTGGTGGACTCTGCCCTGGCCTCAACACTGTCATAAGGGAAATTGTCTGTGGTCTTT
upper sequence: GRMZM5G816636_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G09320.1 (Glycine max), 3'ss of exon 3
----------------gataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtct--tggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
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gtcatttcccttgtttgtctgtgcgtatattatatattattaagaat----taagaatattaaaaatgtataattaattttgtatcaactcaccaacacctaatcatatgctgttcagGTATACTTTAAATCGGATGAAGTGCATGCATGCATTGTCACGTGTGGTGGACTCTGCCCTGGCCTCAACACTGTCATAAGGGAAATTGTCTGTGGTCTTT
upper sequence: GRMZM5G816636_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv11s0016g02850.t01 (Vitis vinifera), 3'ss of exon 4
gataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
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-------gtaagtctttgtt-tgtta-tattcatggaatttgaaatgataaaagacaataggttttctcttaacatattcttttgggttttttt--ccagGTGTATTTTGAGTCTGATGAAGTTCATGCATGTATTGTGACATGTGGTGGTTTATGCCCTGGCCTCAACACAGTGATTAGGGAAATAGTATGTGGCTTGA
upper sequence: GRMZM5G816636_T01 (Zea mays), 3'ss of exon 3
lower sequence: PP1S81_165V6.4 (Physcomitrella patens), 3'ss of exon 5
------------------------gataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaa----ccttgtaagtttctttcgttctttgtaacctctggttgtcttggtt-------agGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
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gttcttaatatccattactcttctcttgatttttaggtaatttga-atacataccaagctaatttactgtcaagaagtgcctttttaagtgacttccacttttgacatttcgtgacactctttccttgtccgcagATATACTTCCAGTCGGAGGATGTGAAGGCATGCATTGTAACTTGTGGAGGATTATGCCCCGGAATCAATACTGTGATTCGTGAGATTGTCTGTGGTCTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
ttgtaac putative branch site (score: 2)
ttgtctt putative PPT
taagttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gataagggggagacaatataatatcactaaccttgtaagtttctttcaaaaaccttgtaagtttctttcgttctttgtaacctctggttgtcttggttagGTATATTTTGAACCGGATGAGGTCCATGCATGCATTGTCACTTGTGGAGGATTGTGCCCGGGACTTAATACTGTGATTAGGGAAATTGTATGTGGATTAT
- - - - - - - - - - - - - - - - - - - - - - - caaaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggttg