Sequence
atgc intronic sequence ATGC exonic sequence...aacaagtttacaagtcaaagttagtaaatcaaacatttatatctatgctgtttgttatgtttgtaagtatccagctgctgattttcttttaaccattcagGCTATAGAAGTTGTAGATCTGGATCAGCAGACTAAAATGGTCATGGAGCTAGATGGTAATGTCATGCGTTGTGTACGTGATCAAAATGGGAACCATGTTA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv13s0019g02000.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os05g01910.1 (Oryza sativa), 3'ss of exon 4
aacaagtttacaagtcaaagttagtaaatcaaacatttatatctatgc-tgtttgttatgtttgtaagtatccagctgctgattttct----tttaaccattcagGCTATAGAAGTTGTAGATCTGGATCAGCAGACTAAAATGGTCATGGAGCTAGATGGTAATGTCATGCGTTGTGTACGTGATCAAAATGGGAACCATGTTA
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-----ctatacaaagtacagaccctttgttaagtgtatgaatgcataaatgattgaaggatatcaaggaaggcaaaatctgatgtcatggatgatatatatgcagGCTATAGAGGTTGTTGGTTTAGATCAGCAGACTAAAATGGTTGCTGAGCTGGATGGACACGTCATGCGCTGTGTACGTGATCAAAATGGGAACCATGTAA
upper sequence: Vv13s0019g02000.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g74030.1 (Oryza sativa), 3'ss of exon 4
--aacaagtttacaagtcaaagttagtaaatcaaacatttatatctatgctgtttgttatgtttgtaagtatccagctgctgattttcttt-taaccattcagGCTATAGAAGTTGTAGATCTGGATCAGCAGACTAAAATGGTCATGGAGCTAGATGGTAATGTCATGCGTTGTGTACGTGATCAAAATGGGAACCATGTTA
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tatttgtgtccatgcacatatacccttatatattgcatgaagggctcaaaggtgcagcaaata---agatgtttaactgatgttatggacaatattcatgcagGCCATAGAAGTTGTTGATTTAGATCAGCAGACTAAAATGGTTGCTGAGCTTGATGGACAAGTGATGCGCTGTGTACGTGATCAAAATGGAAATCACGTTA
upper sequence: Vv13s0019g02000.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G012964_T01 (Zea mays), 3'ss of exon 4
aacaagtttacaagtcaaagttagtaaatcaaacatttatatctatg-ctgtttg-ttatgtttgtaagtatccagctgctgat----tttcttttaaccattcagGCTATAGAAGTTGTAGATCTGGATCAGCAGACTAAAATGGTCATGGAGCTAGATGGTAATGTCATGCGTTGTGTACGTGATCAAAATGGGAACCATGTTA
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------atgagaagtatacacttgcatctctagaatttacataattggctggaagattgtatcaagcaacatgttgtttctgacaatattgatgatatatgtgcagGCTATAGAAGTTGTTGATTTGGATCTGCAGACTAAAATGGTTGCGGAGCTGGAGGGTCATGTCATGCGCTGTGTACGTGATCAAAATGGGAACCATGTTA
upper sequence: Vv13s0019g02000.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G042623_T02 (Zea mays), 3'ss of exon 5
aacaagtttacaagtcaaagttagtaaatcaaacatttatatctatgct--gtttgttatgtttgtaagtatccagctgctgattttcttt----taaccattcagGCTATAGAAGTTGTAGATCTGGATCAGCAGACTAAAATGGTCATGGAGCTAGATGGTAATGTCATGCGTTGTGTACGTGATCAAAATGGGAACCATGTTA
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------tagccttgtacaagttgtcatctctagaatttacataattggctaaaaggttgtagcaagtaacatgttgttcctcatgctattgatgatatatgtgcagGCTATAGAAGTTGTTGATTTGGAGCTGCAGACTAAAATGGTTGCGGAGCTGGAGGGCCATGTCATGCGCTGTGTGCGTGATCAAAATGGGAACCATGTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgctgtttgttatgtttgtaagtatccagctgctgattttcttttaaccattcagGCTATAGAAGTTGTAGATCTGGATCAGCAGACTAAAATGGTCATGGAGCTAGATGGTAATGTCATGCGTTGTGTACGTGATCAAAATGGGAACCATGTTA
ttttaac putative branch site (score: 2)
ttttctttta CT-rich tract
tgattttcttttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacaagtttacaagtcaaagttagtaaatcaaacatttatatctatgctgtttgttatgtttgtaagtatccagctgctgattttcttttaaccattcagGCTATAGAAGTTGTAGATCTGGATCAGCAGACTAAAATGGTCATGGAGCTAGATGGTAATGTCATGCGTTGTGTACGTGATCAAAATGGGAACCATGTTA
- - - - - - - - - - - - -aaatcaa
- - - - - - - - - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgctg