Sequence
atgc intronic sequence ATGC exonic sequence...agcccatatcatacagacttggatggccttcaggaattaaaagtactgttttcttagtgagaataatgtatcactgatacgttttgcctatgaatttcagCTCAAGGAACTTGAGAAGTTGGGTCCCAAGAAGGGTGTTATCAGCCAGTCTGTGAAAGATGTTGTCCAAAGTCTAGTCGACGATGACCTTGTTGCAAAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv11s0016g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g10850.1 (Oryza sativa), 3'ss of exon 2
agcccatatcatacagacttg--------gatggccttcaggaattaaaagta--ctgttttcttagtgagaataatgtatcactgatacgttttgcctatgaatttcagCTCAAGGAACTTGAGAAGTTGGGTCCCAAGAAGGGTGTTATCAGCCAGTCTGTGAAAGATGTTGTCCAAAGTCTAGTCGACGATGACCTTGTTGCAAAAG
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--cccatgccatacattgctattctaagcgctgttctgctaggtttctgagtagactatattttcatatgtcctaagtcccaatccatac-ttctgc-------tttcagCTTAAAGAGCTTGAGAAGTTGGGTCCCAAAAAGGGTGTCATCAGTCAGTCAGTGAAGGATGTTGTGCAAAGCCTGGTGGATGATGATCTTGTCTTGAAAG
upper sequence: Vv11s0016g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA01G00780.1 (Glycine max), 3'ss of exon 2
-----------------------agcccatatcatac-agacttggatggccttc-----aggaattaaaagtactgttttcttagtgagaataatgtatcactgatacgttttgcctatgaatttcagCTCAAGGAACTTGAGAAGTTGGGTCCCAAGAAGGGTGTTATCAGCCAGTCTGTGAAAGATGTTGTCCAAAGTCTAGTCGACGATGACCTTGTTGCAAAAG
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gtaatcaccattactatttcgttattacatagaagatgatgttttcttttccttctttttaattatgtaatttattgactgatttatgtgctttttgtttt-tggtttttttttttcggttttttgtagCTTAAGGAGCTCGAGAAGATGGGTCCCAGGAAGGGTGTCATTTCTCAGTCTGTGAAAGATGTGGTCCAAAGTTTAGTGGATGATGACCTTGTTTCCAAAG
upper sequence: Vv11s0016g02770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G29170.1 (Arabidopsis thaliana), 3'ss of exon 2
------------------------------------------------------------------------agcccatatcatacagacttggatggccttcaggaattaaaagtactgttttc-----ttagtgagaataatgtat-cactgatacgt-------tttgcctatgaatttcagCTCAAGGAACTTGAGAAGTTGGGTCCCAAGAAGGGTGTTATCAGCCAGTCTGTGAAAGATGTTGTCCAAAGTCTAGTCGACGATGACCTTGTTGCAAAAG
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gtgagcactttctttagtttttacaacttgctaatttttggacgcctttgaactagctttatctaccaagtgatctgatatc-tagagtcgtgaagtgcatatactgcctaaatttgttgctattgaacttttgggtttgtgatacaagcacttatgggtctctacttttgtaaaaaaatttcagCTAAAGGAACTTGAGAAGATGGGGCCGAAGAAGGGTGTAATTAGTCAGTCTGTGAAAGATGTTATCCAGAGTTTAGTCGATGATGATCTTGTTGCGAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgttttcttagtgagaataatgtatcactgatacgttttgcctatgaatttcagCTCAAGGAACTTGAGAAGTTGGGTCCCAAGAAGGGTGTTATCAGCCAGTCTGTGAAAGATGTTGTCCAAAGTCTAGTCGACGATGACCTTGTTGCAAAAG
cactgat putative branch site (score: 3)
aataatgtat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agcccatatcatacagacttggatggccttcaggaattaaaagtactgttttcttagtgagaataatgtatcactgatacgttttgcctatgaatttcagCTCAAGGAACTTGAGAAGTTGGGTCCCAAGAAGGGTGTTATCAGCCAGTCTGTGAAAGATGTTGTCCAAAGTCTAGTCGACGATGACCTTGTTGCAAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
agcccat
- - - - - atacaga
- - - - - - - - - - - - -gccttca
- - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgatac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgcc