Sequence
atgc intronic sequence ATGC exonic sequencegtgagttacttctaaatgtccaattatagataaaaaaatcaaatgcttctctctgatctttcaaatttaataaagcacttgtaacatcgaatctacattgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g02670.3 (Oryza sativa), 3'ss of exon 5
gtgagttacttctaaatgtccaatt-atagataaaaaaatcaaatgcttctctctgatctttcaaatttaataaagcacttgtaacatcgaatctacattgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG
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gtgagtaaacttaaaattttctattcattgattaaaatat--aatatatctatctgatttttcaactgcccaatactacttttgatattgaattatcattgcagGGCAGAGCGAGAGAGGCTGGGGAGATCAACAAGAGCTTGCTGACACTTGGTCGAGTCATCAATGCTCTTGTTGAACACTCTGGACATGTCCCATACAG
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA15G04830.1 (Glycine max), 3'ss of exon 4
--gtgagttacttctaaatgtccaattatagataaaaaaatcaaatgcttctctctgatctttcaaatttaataaagcacttgtaacatcgaatctaca-ttgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG
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ttgctggcatcatct--ctgcctagttct-gtcacatttgtctggaaaaaaaatcatagctttagagcttcactaagaa---gaagaaaatacttggcacttgcagGGTAGAGCAAGGGAGGCTGGGGAGATAAATAAAAGCTTGCTTACACTTGGACGAGTGATTAATGCTCTAGTTGAGCACTCAGGTCATGTTCCATATAG
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT2G28620.1 (Arabidopsis thaliana), 3'ss of exon 4
gtgagttacttctaaatgtcc--aattatagataaaaa--aatcaaatgcttctctctgatctttcaaatttaataaagcacttgtaacatcgaatctacattgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG
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-----gtacctaaaacagtcaggaaccatgattttttattgacagaataatagtgtcttaccttgatgatttactaaacaa--tataagagtca--ctattttgcagGGTAGAGCCAGGGAAGCTGGTGAGATCAACAAAAGTTTGCTCACACTTGGACGTGTCATAAATGCTTTGGTTGAACACTCTGGTCACATTCCATATAG
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT3G45850.1 (Arabidopsis thaliana), 3'ss of exon 5
gtgagttacttctaaatgtccaattatagataaaaaaatcaaatgcttctctctgatctttcaaattta-ataaagcacttgtaacatcgaatctacattgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG
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-----gtatactttatcttattatcatcgtctctgaggtcagtgtcttccaggcagtcatggaagctagtgctaagcattt-tgacaactgtt----attgcagGGACGAGCCAGAGAAGCTGGAGAGATCAACAAGAGTTTACTTACTCTTGGCCGTGTCATTAACGCGCTTGTGGAGCACTCTGGTCATATTCCTTACAG
upper sequence: GRMZM2G024576_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv06s0004g03810.t01 (Vitis vinifera), 3'ss of exon 5
-----gtgagttacttctaaatgtccaattatagataaaaaaatcaaatgcttctctctgatctttcaaatttaataaagcacttgtaacatcgaatctacattgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG
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acaacaaaagcatatgcataatatgaagttgtgtgttaggcaatgaaaagttcatttatcttcacataaaagtttgactgca-----aaaattcaatgc---tttcagGGCAGAGCAAGGGAAGCTGGGGAGATAAATAAAAGCTTGCTTACTCTTGGGCGTGTTATTAATGCGCTGGTTGAGCACTCTGGTCATGTTCCATATAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctctctgatctttcaaatttaataaagcacttgtaacatcgaatctacattgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG
ttgtaac putative branch site (score: 2)
tgatctttcaaattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagttacttctaaatgtccaattatagataaaaaaatcaaatgcttctctctgatctttcaaatttaataaagcacttgtaacatcgaatctacattgcagGGCAGAGCGAGAGAGGCTGGAGAGATCAACAAGAGTTTGCTCACGCTTGGTCGTGTTATTAATGCTCTAGTAGAGCACTCTGGACATGTACCATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA