Sequence
atgc intronic sequence ATGC exonic sequence...agatctacatctttgatcacacaatccattgagtgctttagcttatatgtcatgctgtgcaagtattgaagctgaaaattactgatcttttttcctgtagTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 3
-agatctacatctttgatcacacaatccattgagtgctttagcttatatgtcatgctgtgcaagtattgaagctgaa-aattactgatcttttttcctgtagTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
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tgtttctagagttgacattatgcaattta--gagtggtgtagtttttttattaagttggacaggtgttgaaatgaaataatttctcaaaattttctgttcagTATTATCTGAAGACTGGAACATGCAAGTTTGGGCCTACATGCAAATTCCATCATCCCAGAGAAAAAGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
upper sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 3
---agatctacatctttgatcacacaatccattg-agtgctttagcttatatgt---catgc------tgtgcaagtattgaa-gctgaaaattactgatcttttttcc--------tgtagTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
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gcacgtactagtttctcaaccttgtactgcagtgcagagcattaatttgtatcttggcatgcattctttatttaaacattcaccaatcatcataacagagttttttccccctgtttttctagTACTATCTGAAGACAGGAACGTGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGGATTGCTGGAAGAGTTGCCTTAAATATTT
upper sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA10G31370.3 (Glycine max), 3'ss of exon 3
----------------------agatctacatctttgatcacacaatcc--attgagtgctttagcttatatgtcatgctgtgcaagtattgaagctgaaaattactgatcttttttcctgt--------agTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
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gcatgtactagtttctcaaccttttactgcagtgcagagcactaatttgtaattttgtatcttggcatgcatctttatttaaacattcaccaatcgtcataacaaagtgttttttttcccctgtctttccagTACTATCTGAAGACAGGAACATGCAAATTTGGAGCCACATGCAAATTTCATCATCCTAAAGATCAGGCTGGAATTGCTGGAAGAGTTGCCTTAAATATTT
upper sequence: GRMZM2G087032_T04 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 3
----agatctacatctt-tgatcacacaatccattgagtgctttagcttatatgtcatgctgtgcaagtattgaagctgaaaattactgatcttttttcctgtagTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
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tttaatgtcctcatatcatgtgtaagatctctattttctcatttttttaatatgttctgagttggaagagttgac----aaatttgctt-tgaatggttctccagTACTACTTGAAGACAGGAACTTGCAAGTTTGGAGCCACATGCAAGTTTCATCATCCTAGAGACAAGGCTGGAATTGCTGGAAGAGTTTCTTTAAATATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatgtcatgctgtgcaagtattgaagctgaaaattactgatcttttttcctgtagTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
tactgat putative branch site (score: 2)
ctgatcttttttcct CT-rich tract
tgaaaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agatctacatctttgatcacacaatccattgagtgctttagcttatatgtcatgctgtgcaagtattgaagctgaaaattactgatcttttttcctgtagTATTATCTGAAGACTGGAACATGCAAGTTTGGCCCTACATGCAAATTTCACCATCCCAGGGAAAAGGCTGGAATTGCAGGGAGGGTGCAGCTAAACACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT