Sequence
atgc intronic sequence ATGC exonic sequence...ggccaatgctaacataccaatgttgatttggcaagagaaaaatattatatggatttctgatttttttaatatgtgctgactttttgtgcgtttgtctcagGACATATTACGGTTTCATGCAGTTTATTGGCCAGCCATGTTAATGTCAGCAGGTTTAAGTGTTCCTGATACAGTTTTTGGTCATGGATTCTTGACTAAG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G029055_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g11120.1 (Oryza sativa), 3'ss of exon 6
ggccaatgctaacataccaatgttgatttggcaagagaaaaatattatatggatttctgattttttta--atatg-----tgctgactttttgtgcgtttgtctcagGACATATTACGGTTTCATGCAGTTTATTGGCCAGCCATGTTAATGTCAGCAGGTTTAAGTGTTCCTGATACAGTTTTTGGTCATGGATTCTTGACTAAG
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-----gtgtacaggcaagaatgttggatgaacttcttgag--ttttatttctattttttattttgttataatatggtttatgatgattctttgtacatctacctcagGACATATTGCGGTTTCATGCAGTATATTGGCCAGCAATGTTAATGTCAGCAGGAATAAGTGTTCCTGATGCAGTTTTTGGTCATGGATTTTTGACAAAG
upper sequence: GRMZM2G029055_T02 (Zea mays), 3'ss of exon 6
lower sequence: Vv13s0019g00810.t01 (Vitis vinifera), 3'ss of exon 6
ggccaatgctaacatacc----aatgttgatttggcaagagaaaaatattatatggatttctgatttttttaatatgtgctgactttttgtgcgtttgtctcagGACATATTACGGTTTCATGCAGTTTATTGGCCAGCCATGTTAATGTCAGCAGGTTTAAGTGTTCCTGATACAGTTTTTGGTCATGGATTCTTGACTAAG
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-tctgttgtcaaaattcttttggaagtttcctttatactgtgccactgtcatttgaatatcagtaccatgatgcttctcttatatttttgttgttttg---cagGATATTTTACGTTTTCATGCAGTTTACTGGCCGGCTATGTTATTGTCAGCCGGATTAAGCCTTCCTAAGATGGTTTTTGGCCATGGATTCTTGACAAAA
upper sequence: GRMZM2G029055_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ16264 (Selaginella moellendorffii), 3'ss of exon 6
ggccaatgctaacataccaatgttgatttggcaagagaaaaatattatatggatttctgatttttttaatatg--tgctgactttttgtgcgtttgtctcagGACATATTACGGTTTCATGCAGTTTATTGGCCAGCCATGTTAATGTCAGCAGGTTTAAGTGTTCCTGATACAGTTTTTGGTCATGGATTCTTGACTAAG
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--------------------------------------gttcgttcgagtaaccggtttattctcctaaagttatttctttctttttttccaactttgacagGACATATTACGCTTTCATGCCGTTTATTGGCCTGCAATGCTTTGGTCAGCGGGGTTTGCAATACCAGAAACAGTGTTCGGCCATGGATTTCTTACAAAG
upper sequence: GRMZM2G029055_T02 (Zea mays), 3'ss of exon 6
lower sequence: EFJ17733 (Selaginella moellendorffii), 3'ss of exon 6
ggccaatgctaacataccaatgttgatttggcaagagaaaaatattatatggatttctgatttttttaatatgtgctgactttttgtgcgtttgtctcagGACATATTACGGTTTCATGCAGTTTATTGGCCAGCCATGTTAATGTCAGCAGGTTTAAGTGTTCCTGATACAGTTTTTGGTCATGGATTCTTGACTAAG
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--------------------------------------gttcgttcgagtagccggtttatttctcctaaagttttttctttttcttccaactttgacagGACATATTACGCTTTCATGCCGTTTATTGGCCTGCAATGCTTTGGTCAGCGGGGTTTGCAATACCAGAAACAGTGTTCGGCCATGGATTTCTCACAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatatggatttctgatttttttaatatgtgctgactttttgtgcgtttgtctcagGACATATTACGGTTTCATGCAGTTTATTGGCCAGCCATGTTAATGTCAGCAGGTTTAAGTGTTCCTGATACAGTTTTTGGTCATGGATTCTTGACTAAG
tgctgac putative branch site (score: 2)
tttgtctc putative PPT
atttctgattttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggccaatgctaacataccaatgttgatttggcaagagaaaaatattatatggatttctgatttttttaatatgtgctgactttttgtgcgtttgtctcagGACATATTACGGTTTCATGCAGTTTATTGGCCAGCCATGTTAATGTCAGCAGGTTTAAGTGTTCCTGATACAGTTTTTGGTCATGGATTCTTGACTAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA