Sequence
atgc intronic sequence ATGC exonic sequencegtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgcggtctggaattcacaccccaatgtttaaccctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGTCTATCTTCCACACAGAAGAAAGAAAAGG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G818643_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os09g29830.2 (Oryza sativa), 3'ss of exon 2
gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgc--ggtctggaattcacaccccaatgtttaaccctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGTCTATCTTCCACACAGAAGAAAGAAAAGG
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------------------------gtacatatttcagtgttctagtatggacagtatgctttgcaattggcatcagtacgttgaa----actgagtattttacgtttcgtgtgcagTTGAGAAGGGAGAAGATCAGTGAGAGGATGAAACTTCTTCAGGACCTAGTTCCTGGCTGCAGCAAG----------------------------------
upper sequence: GRMZM5G818643_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G13860.3 (Glycine max), 3'ss of exon 4
gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgcggtctggaattcacaccccaatgttta-accctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGT-CTATCTTCCACACAGAAGAAAGAAAAGG
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------------------------------------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAGGTGGCTTCTAAGTTTGAAACTAGAAAATTTACTA-
upper sequence: GRMZM5G818643_T02 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA02G13860.1 (Glycine max), 3'ss of exon 4
gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgcggtctggaattcacaccccaatgttta-accctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGTCTATCTTCCACACAGAAGAAAGAAAAGG
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------------------------------------gtaagattttgtgagaacttatctgtgatgaagatgaagttttttggatgaagaatttcaaattggattttcactgcagGTGAGGAGGGAAAAGATAAGTGAGAGGATGAAGTTTCTTCAAGACCTTGTACCTGGATGCAGCAAG----------------------------------
upper sequence: GRMZM5G818643_T02 (Zea mays), 3'ss of exon 2
lower sequence: PP1S145_69V6.1 (Physcomitrella patens), 3'ss of exon 2
gtacggatttgatcaacgggtggcatccccg--------tgtttaccgtctgctgtggatcgcggtctggaattcacaccccaatgtttaaccctgcttgctgcg--------tctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGTCTATCTTCCACACAGAAGAAAGAAAAGG
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gtaaaatcccagatcccaagtttccttctcgattcgattcgattcataacctcaactattagtattctgaactcgtcacacatctctgtagcactccctgacgtgagtcatcatgttgtacgctcctcagGTTCGCAGGGAGAAGATCAGCGAGCGGATGAAGTATCTTCAGGACCTAGTTCCTGGCTGCAATAAAGTGACCGGCAAGGCAGTGATGCTCGACGAGATCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tggaattcacaccccaatgtttaaccctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGTCTATCTTCCACACAGAAGAAAGAAAAGG
gtttaac putative branch site (score: 3)
ccctgcttgctgcgtc CT-rich tract
aatgtttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacggatttgatcaacgggtggcatccccgtgtttaccgtctgctgtggatcgcggtctggaattcacaccccaatgtttaaccctgcttgctgcgtctttttttctctgcagTTGAGGAGGGAGAAGATTAGCGAGAGGATGAAGCTGCTGCAGGACCTCGTTCCTGGCTGCAGCAAAGTAGGTCTATCTTCCACACAGAAGAAAGAAAAGG
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