Sequence
atgc intronic sequence ATGC exonic sequencegtaagtcccaaaaatgtatctgtgtactgtattcccacttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
gtaagtcccaaaaatgtatc--tgtgtactgtattcccacttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
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gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA17G07290.1 (Glycine max), 3'ss of exon 6
--------------------------gtaagtcccaaaaatgtatctgtgtactgtattcccact-tgaca-tatatctaaactatttcaatttcatttatct---agTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
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gtagggttatgcttctacatcttttagtttttctctagcatcagtgctctccctgctcctacactgtaatagcatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCTGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTTCATAAGAAGCTGAATAGTGCAGG
upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 5
--------------------------gtaagtcccaaaaatgtatctgtgtactgtattcccactt-gacat-atatctaaactatttcaatttcatttatct---agTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
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gtagggctatgcttctacatcttttagtttttctctagcatcaatactctccctgcatctacactttaataccatcttttaaattttatattttgacctttttctcagTATATAAGAAGCATTATCCACCAGCATTGACTGATGAAGTGTGGAGATTGGAGAAGATAGGCAAGGATGGGTCATTCCATAAGAAGCTGAATAATGCAGG
upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 5
gta-agtcccaaaaatgtatctgtgtactgtattc--ccacttgacatatatctaaactatttcaat------ttcatttatct--agTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
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gtatggtcttaaaagctccccttttcttctcactgtaccatctggtgtttacttcttttagtttgatgcacatttcttttatgtgcagTGTACAAGAAGCATTATCCACCTGCTCTGAATGATGATGTGTGGAGATTGGACAAGATCGGCAAGGATGGGGCATTCCATAAAAAGCTTACTGCTGAAGG
upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 5
--------gtaagtcccaaaaatgtatctgtgtactgtattccca-cttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
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gtaagttcttgctttcctttgatattagtcattgatgtatctgaatctttgtttttcttttgcctaatgtt-tttttttcctacagTGTACAAGAAACATTACCCACCTGCTTTGGATGATGAGGTCTGGAGGTTGGAAAAGATTGGAAAGGACGGGGCTTTCCATAAGAAACTCAATAAAGCAGG
upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 5
-------gtaagtcccaaaaatgtatctgtgtactgtattc-ccacttgacatatatctaaactat-------ttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
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gtatgtgttttcttttcttgttctctttttgccttgtgcttgccacttgttttct-tctaaatcaacatgttgttggattggttatgtgtagTGTACAAGAAGCATTATCCACCTGCTTTGAATGATGAGGTGTGGAGGTTAGAGAAGATTGGTAAAGATGGGGCGTTTCATAAGAGGCTAACCGCTGCAGG
upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------gtaagtcccaaaaatgtatctgtgtac-tgtattcccacttgacatatatctaaactatttcaatttcatttatct---agTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
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gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 4
------------------------gtaagtcccaaaaatgtatctgtgtactgtattcccact----tgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
| | | || | | | ||| || | | || |||||| | | || | | ||| | ||||||| ||||| |||||||||||| || | | ||||| || ||||| ||||| || || || |||||||| |||||||| |||||||| || || ||
gtaggttcaggctcatccttgtcttttatttattgaattattttattgttctttttcttatctgtgatgacatgttattgaa-tctgctgtttttccctgggtagTGTATAAGAAACACTATCCACCTGCATTAACTGATGATGTGTGGAGATTGGAGAAGATTGGCAAGGATGGTTCATTCCACAAGAGGCTAAATAATTCCCA
upper sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 5
lower sequence: PP1S336_7V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------------------gtaagtcccaaaaatgtatctgtgtactgtattcccacttgacatatatctaaactatttcaatttca---tttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAA-CAAATCTGG
| ||| |||| | || || | | | | || | ||| || || || | || || | ||||||||||||||||||||||||| | |||| || ||||| ||| | ||||| || || |||||||| || | || || ||| | || || |||| |
gtacgttgactgttttgaaccttgggtcatcttacgctataagagtttgtctgcgttcctaatttacagttagtttcgttttaggcagttaataaaagcagtttgaatatt---tatctagatggaa-gtattgaatcttttctacttgggaatttcgtgcagTGTACAAGAAGCACTATCCACCTGCCTTGAATGACGAGGTATGGCGCTTGGACAAGATTGGGAAGGACGGAGCCTTTCACAAGCGCCTCAATCAAAACCA- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtactgtattcccacttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
atctaaa putative branch site (score: 3)
tttcattt putative PPT
atatatctaaactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtcccaaaaatgtatctgtgtactgtattcccacttgacatatatctaaactatttcaatttcatttatctagTGTACAAGAAGCACTATCCACCTACACTGAAAGATGAGGTCTGGAGGTTGGAAAAAATAGGGAAGGATGGGTCATTCCATAAGAGGCTGAACAAATCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
