Sequence
atgc intronic sequence ATGC exonic sequencegttagccttgctaatctgttagtttactactggtctgctgtttcctttatttgttgtataatgattgacatatttaagtagagaaatttatatttctcctctgctgttgtggaagtccaattgtcaccattaactgtgaaatattgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g22940.1 (Oryza sativa), 3'ss of exon 5
gttagccttgctaatctgttagtttactactggtctgctgtttcctttatttgttgtataatgattgacatatttaagt---agagaaatttatatttctcctctgctgttgtggaagtccaattgtcaccattaactgtgaaatattgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
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----------------------------gttagttcagctcatccctcaac-acaacattttcgtt--tctatttaagttagggaaaaatctctacgaccctccaatt--tctgaacatccaattttcaccatcaactgcaa----tcacagATAGCAGAGAGAACAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCATCTGAGAATCCTGAACTTCCAGATGCGCTGACTGCAAAAGGAATTGTTT
upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G11120.1 (Glycine max), 3'ss of exon 1
gttagccttgctaatctgttagtttactactggtctgctgtttcctttatttgttgtataatgattgacatatttaagtagagaaatttatatttctcctctgctgttgtggaagtccaattgtcaccattaactgtgaaatattgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
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-----------------------------------------ttgttcttgtcattgta----gattttagtgcttatgtagtaatgattct-tttgacctatataacttatataatctgcttactggcatgcaatgt---actgcccagATGGCTGAGATAACTCATGTTGATGCGGTGTGGCCTGGTTGGGGTCATGCATCAGAAAATCCTGAGCTTCCAGATGCATTAAAAGCAAAAGGAATTGTAT
upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G11550.1 (Glycine max), 3'ss of exon 1
gttagccttgctaatctgttagtttactactggtctgctgtttcctttatttgttgtataat-gattgacatatttaagtagagaaatttatatttctcctctgctgttgtggaagtccaattgtcaccattaactgtgaaatattgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
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----------------------------------------------ttattcttgtcattatagattttagtgcttatgtaataatgattct-ttttacctatataacttatatattctgcttactggcatgcaatgt---acttcccagATGGCTGAGATAACTCATGTTGATGCGGTGTGGCCTGGTTGGGGTCATGCATCAGAAAATCCTGAGCTCCCAGATGCATTAAAAGCAAAAGGAATTGTAT
upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G36160.2 (Arabidopsis thaliana), 3'ss of exon 2
gttagccttgctaatctgttagtttactactggtctgctgtttcctttatttgttgtata----atgattgacatatttaagtagagaaatttatatttctcctctgctgttgtggaa-gtccaattgt-caccattaactgtgaaatat-tgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
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gtgaatccaact--tttgggaact-actatta-tctga-attatcgtgttttactgtacagaacacatgtattaagctcaatttcagcaatgaagttttggtctttggagttatttttcattcatctgaacatctttgtctacaacctgtgtgcagATGGCTGAAGTAACACGCGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAAAACCCCGAATTACCTGATGCCCTAGATGCAAAAGGAATCATAT
upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT1G36180.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagccttgctaatctgttagtttactactggtctgctgtttcctttatttgttgtataatgattgacatatttaagtagagaaatttatatttctcctctgctgttgtggaagtccaattgtcaccattaactgtgaaatattgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
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------------------------------------------------------------gtgattagtgcaactttttggaaaa-----tacttatgttttgttatt--cgtcattcatatatgtatataaa---tgatatgt-gcagATGGCTGAGGTCACGCGTGTGGATGCAGTTTGGCCTGGTTGGGGTCATGCATCTGAGAACCCTGAATTACCTGATGCTTTAAAGGAGAAAGGAATTATAT
upper sequence: GRMZM5G858094_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv18s0001g04980.t01 (Vitis vinifera), 3'ss of exon 2
gttagccttgctaatctgttagtttactactggtctgctgtttcctttatttgttgtataatgattgacatatttaagtagagaaat-ttatatttctcctctgctgttgtggaagtccaattgtcaccattaactgtga-aatattgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
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---------------------------------------------------aagtaaatccggaatgaaatttcattcttgctagctgttgtttttgcctgttggctatgtttgattatacctaaatctggttggtttgacaatgctacagATGGCAGAGATAACACATGTTGATGCAGTTTGGCCTGGTTGGGGCCATGCATCTGAGAACCCTGAGCTGCCAGATGCTCTGAATGCTAAGGGGATTGTAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcctctgctgttgtggaagtccaattgtcaccattaactgtgaaatattgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
cattaac putative branch site (score: 2)
tgaaatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagccttgctaatctgttagtttactactggtctgctgtttcctttatttgttgtataatgattgacatatttaagtagagaaatttatatttctcctctgctgttgtggaagtccaattgtcaccattaactgtgaaatattgcagATGGCACAAAAACTAGGTGTTTCTGCTGTTTGGCCTGGTTGGGGTCATGCTTCTGAGAATCCTGAACTGCCAGATGTATTGACCGCAAAAGGGATCGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG