Sequence
atgc intronic sequence ATGC exonic sequence...taggcagtgaagagtgtattcatatatttatgtgggagctcagaagagtatattccttttgaaactaaatctcttatgtaaaatttgttgcttccttcagGTTCAGCTGATAAAACTGTCAAGTTCTGGGATTTGGAGACATTTGAGTTGATTGGATCTACAGGACCTGAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os04g58130.1 (Oryza sativa), 3'ss of exon 5
taggcagtgaagagtgtat-tcatatatt-tatgtgggagctcagaagagtatattccttttgaaactaaa--tctcttatgtaaaatttgtt-gcttccttcagGTTCAGCTGATAAAACTGTCAAGTTCTGGGATTTGGAGACATTTGAGTTGATTGGATCTACAGGACCTGAG
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-----atataactgtttatgtcagaagttgtgcttgcctcttttttgtttcctgtacgctttgctactaaagattcattgtatgactcctgtttgcctcattcagGTTCATCCGATAAAACTGTCAAGTTTTGGGATTTGGAGACCTTTGAATTGATTGGGTCTACTGGACCTGAG
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 5
lower sequence: AT5G23430.2 (Arabidopsis thaliana), 3'ss of exon 6
--taggcagtgaaga-gtgtattcatatatttatgtgggagctcagaagagtatattccttttgaaactaaatctcttatgtaaaatttgttgcttccttcagGTTCAGCTGATAAAACTGTCAAGTTCTGGGATTTGGAGACATTTGAGTTGATTGGATCTACAGGACCTGAG
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ctcactctctgttaacgttcacctaaatatttacatggaatatgtaaaattagtgtgattacaaatatttgaagcattctgt---ttttgcctgtgctaacagGTTCAGCTGATAGAACTGTAAAATTCTGGGATCTGGAAACATTCGAGCTGATTGGTTCTGGTGGACCTGAG
upper sequence: GRMZM2G406553_T04 (Zea mays), 3'ss of exon 5
lower sequence: Vv10s0071g01150.t01 (Vitis vinifera), 3'ss of exon 5
-taggcagtgaagagtgtattcatatatttatgtgggagctcagaagagtatattccttttgaaactaaatctcttatgtaaaatttgttgcttccttcagGTTCAGCTGATAAAACTGTCAAGTTCTGGGATTTGGAGACATTTGAGTTGATTGGATCTACAGGACCTGAG
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ttatgttttatgctctgacttatcacacttttgttctgtcatctaaaattgtgttttatatggtttattttactttaactttggtcttgtcctttca-cagGTTCAGCTGATAGAACTGTTAAATTCTGGGACCTTGAAACTTTTGAGTTGATTGGTTCAGCTGGACCTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gagtatattccttttgaaactaaatctcttatgtaaaatttgttgcttccttcagGTTCAGCTGATAAAACTGTCAAGTTCTGGGATTTGGAGACATTTGAGTTGATTGGATCTACAGGACCTGAG
aactaaa putative branch site (score: 2)
tttgttgcttccttc putative PPT
taaatctcttatgtaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taggcagtgaagagtgtattcatatatttatgtgggagctcagaagagtatattccttttgaaactaaatctcttatgtaaaatttgttgcttccttcagGTTCAGCTGATAAAACTGTCAAGTTCTGGGATTTGGAGACATTTGAGTTGATTGGATCTACAGGACCTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA