Sequence
atgc intronic sequence ATGC exonic sequence...cttgtattaatgtaactgtgctaattagactgttctcaaacttctttgtgggttatgcatctagttcttttggacttaccatcttttggtggtactgcagGTTGTAGCCCTTGTTTGTAATTTTGCCGGTTCACGCAGTTCATCTTCTGCAAAGCTGAACCATTGGGAAGTAGAAACTCTTTTTCATGAGTTTGGACATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv16s0022g01280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g47210.1 (Oryza sativa), 3'ss of exon 12
cttgtattaatgtaactgtgctaatta-gactgttctcaaact-tctttgtgggttatgcatctagttcttttg-----gacttaccatcttttggtggtactgcagGTTGTAGCCCTTGTTTGTAATTTTGCCGGTTCACGCAGTTCATCTTCTGCAAAGCTGAACCATTGGGAAGTAGAAACTCTTTTTCATGAGTTTGGACATG---
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------tcaacatagatgaagaacttttgacagcatttaaatgatccttacaaggataatatctaagattcacgccaccaattcacttcattctgatgctttt-cagATCGTTGCTCTAGTTTGCAATTTTTCAAGTTCGAGCAAAATAATG---GCAAGGCTTAACCATTGGGATGTTGAAACTCTGTTTCATGAGTTTGGCCATGCCC
upper sequence: Vv16s0022g01280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G450659_T02 (Zea mays), 3'ss of exon 5
cttgtattaatgtaactgtgcta-attagactgttctcaaacttctttgtgg-gttatgcatctagttcttttggacttaccatcttttggt-ggtactgcagGTTGTAGCCCTTGTTTGTAATTTTGCCGGTTCACGCAGTTCATCTTCTGCAAAGCTGAACCATTGGGAAGTAGAAACTCTTTTTCATGAGTTTGGACATG---
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---taaataaagtaaaaaaatcataatagattgctgttgtacaatttcacaaagttgtttcgtttgggcttttaacctatggactccatgctcgctttttcagATCATTGCCTTAATATGCAACTTCTCAGGTGCTTGTAGAAAAACT---GCAAGGCTTAACCATGGGGATGTTGAAACTCTTTTTCATGAGTTTGGGCATGCCC
upper sequence: Vv16s0022g01280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G13080.1 (Glycine max), 3'ss of exon 9
cttgtattaatgtaactgtgctaattagactgttct---caaacttctttgtgggttatgca---tctagttcttttggacttaccatcttttggtggtactgcagGTTGTAGCCCTTGTTTGTAATTTTGCCGGTTCACGCAGTTCATCTTCTGCAAAGCTGAACCATTGGGAAGTAGAAACTCTTTTTCATGAGTTTGGACATG
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------tgcacaatgctcatttaagcacatttttctgaccaagttactgtataggtggcagactgtttattcttcttattgatgcttgattgtgataattttgcagATTGTAGCTCTTGTTTGTAACTTTTCGGGTTCTCGGAATCCATCAGCTGTAAGGCTCAATCATTGGGAAGTAGAAACTCTATTTCATGAGTTTGGACATG
upper sequence: Vv16s0022g01280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G06470.1 (Glycine max), 3'ss of exon 9
cttgtattaatgtaactgtgctaattagactgttctcaaacttctttgtgggttatgcatctagttcttttggact-taccatcttttggtggtactgcagGTTGTAGCCCTTGTTTGTAATTTTGCCGGTTCACGCAGTTCATCTTCTGCAAAGCTGAACCATTGGGAAGTAGAAACTCTTTTTCATGAGTTTGGACATG
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ctcatttaagcacattttt-ctgactaaatcacagtattcgccataaagatggcagactgcttattcttctgattcatgcctgattctgataattttgcagATTGTAGTTCTTGTTTTTAACCTTTCGGGTGCATGGAATTCGTCTGCTGTAAGTCTCAGTCATTGGGAAGTAGAAACTCTATTTCATGAGTTTGGACATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgtgggttatgcatctagttcttttggacttaccatcttttggtggtactgcagGTTGTAGCCCTTGTTTGTAATTTTGCCGGTTCACGCAGTTCATCTTCTGCAAAGCTGAACCATTGGGAAGTAGAAACTCTTTTTCATGAGTTTGGACATG
gacttac putative branch site (score: 2)
ttctttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttgtattaatgtaactgtgctaattagactgttctcaaacttctttgtgggttatgcatctagttcttttggacttaccatcttttggtggtactgcagGTTGTAGCCCTTGTTTGTAATTTTGCCGGTTCACGCAGTTCATCTTCTGCAAAGCTGAACCATTGGGAAGTAGAAACTCTTTTTCATGAGTTTGGACATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - actgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccatctt