Sequence
atgc intronic sequence ATGC exonic sequence...aatccacaacattttaagcttctcctattattgtattgcctaaaatttgaaatgtatctctgttgacggatatttctaatagtaaaacttgtttttttagCGGAATGTTTCAAGGATCGGACAGATGTGCAATGCTTGCACAGGTGGCAGAAGGTCTTGAATCCAGAACTTGTCAAAGGTCCATGGTCAAAAGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g13570.1 (Oryza sativa), 3'ss of exon 3
aatccacaacattttaa-gcttctcctattattgtattgcctaaaatttgaaatgtatctctgttgacggatatttctaatagtaaaacttgt--ttttttagCGGAATGTTTCAAGGATCGGACAGATGTGCAATGCTTGCACAGGTGGCAGAAGGTCTTGAATCCAGAACTTGTCAAAGGTCCATGGTCAAAAGAG
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aagtcatgctcttctggcattgtttttcctactttgttgatgagattcttg--tatatcgttaaaaatccaagctt-tgacagagatccttctaattttccagCGGAATGTTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTGGTCAAAGGGCCATGGTCCAAAGAA
upper sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g12860.1 (Oryza sativa), 3'ss of exon 3
aatccacaacattttaagcttctcctattattgtattgcc--taaaatttgaaatgtatctctgttgacggatatttcta-atagtaaaacttgtttttttagCGGAATGTTTCAAGGATCGGACAGATGTGCAATGCTTGCACAGGTGGCAGAAGGTCTTGAATCCAGAACTTGTCAAAGGTCCATGGTCAAAAGAG
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---tttcattaactcacaccctagacatgcttaccctgttgatgagatttccagtatattgttaaaaatccaagttttgacagagaacattctaattttccagCGGAATGCTTTCCGGATAGAACCGATGTACAATGCTTGCACAGGTGGCAAAAGGTTCTAAACCCTGAATTAGTCAAAGGGCCATGGTCCAAAGAA
upper sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S120_159V6.1 (Physcomitrella patens), 3'ss of exon 3
-----------------------aatccaca-acattttaagc--ttctcctattattgtattgcctaaaatttgaaatgtatctctgttgacggat--atttctaatagtaaaacttgttttttt--agCGGAATGTTTCAAGGATCGGACAGATGTGCAATGCTTGCACAGGTGGCAGAAGGTCTTGAATCCAGAACTTGTCAAAGGTCCATGGTCAAAAGAG-----
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gtgagttgtctgctgtaaatctcaattgtcatacactctgcacaactttcgtgtgatttcgatgtttcccagtccaacgccctcctaacctgggaaagaaccaccaaccttgaatttcctcattttgcagCGGAATTCTTCACGGATCGAACAGATGTGCAATGCCTGCATCGATGGCAGAAGGTTCTTAATCCGGATTTGGTTAAGGGCGCCTGGACTAAAGAGGAAGA
upper sequence: Vv04s0008g03780.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S36_43V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------aatccacaacattttaagcttctcctattattgtattgcctaaaatttgaaatgtatctctgttgacgg-atatttctaatagtaaaacttgtt-----tttttagCGGAATGTTTCAAGGATCGGACAGATGTGCAATGCTTGCACAGGTGGCAGAAGGTCTTGAATCCAGAACTTGTCAAAGGTCCATGGTCAAAAGAG-----
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gtgagtgaattcaagcaaattccagtactttgaatctactcttttgagaaattgc---gagtccaagttaattctctactcgtgtcacagatcacatatctggattttttacaattttgcagCGGAGTTCTTCACGGATCGAACAGATGTGCAATGCTTGCACAGATGGCAAAAGGTTCTCAACCCAGATCTGGTCAAGGGTGCATGGACCAAAGAGGAAGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgaaatgtatctctgttgacggatatttctaatagtaaaacttgtttttttagCGGAATGTTTCAAGGATCGGACAGATGTGCAATGCTTGCACAGGTGGCAGAAGGTCTTGAATCCAGAACTTGTCAAAGGTCCATGGTCAAAAGAG
ttctaat putative branch site (score: 2)
cttgttttttt putative PPT
atatttctaatagtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatccacaacattttaagcttctcctattattgtattgcctaaaatttgaaatgtatctctgttgacggatatttctaatagtaaaacttgtttttttagCGGAATGTTTCAAGGATCGGACAGATGTGCAATGCTTGCACAGGTGGCAGAAGGTCTTGAATCCAGAACTTGTCAAAGGTCCATGGTCAAAAGAG
- -ccacaac
- - - - - - - - - cttctcc
- - - - - - - - - - - - - - - - - - - cctaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaac