Sequence
atgc intronic sequence ATGC exonic sequence...gttttcttcatttaagacaaatgcgaactgcgttatgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 1
gttttcttcatttaagacaaatgcgaactgcgttatgaaatcatagatgttatctctgttcttcatagaaccttttgctt-acacttgtatgtcttt---gcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
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cttttgctcctttatttcttcttctatctcctt----gaattattttcattataaaatatttaagtgcaccattttttttgacactaatattattttctggcagATAGAGCCCATTGTTAGTGGCAACCTGCCTCCTGGATTTGATTCAAGTACATGCCGGAGTGT
upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 1
gttttcttcatttaagacaaatgcgaactgcgttatgaaa-tcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
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gtttgattagatttagttgagaggagagtggattattttgcttttagaaactctttttttcctttttttttgtttgtctttttacatctttat-tttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 1
--------gttttcttcatttaagacaaatgcgaactgcgttatgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
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cttctctcattctctgtatt---ggtagatacaatacaatttttttccctcttgatttgccctctttttccttt----ctttcctttttcacttcttcat-tttgcagATTGAACCAATTCCAAGTGGAAATCTGCCTCCTGGTTTTGATCCAAGTACTTGCCGCAGTGT
upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA17G05530.4 (Glycine max), 3'ss of exon 2
-------gttttcttcatttaagacaaatgcgaactgcgtt-atgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
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gaaatgcgatttgtttgattagattagttgagaggagggtggataattttacttttaggaactcttttttttt-----ctgtcttcttacatttttat---tttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCACCTGGCTTTGATTCGAGTTCATGCCGCAGTGT
upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 1
---gttttcttcatttaagacaaatgcgaactgcgttatgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
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gtgtctttatatatctatgaaatgctctcagtgagtgttgatattttatttctaggatttttttttcttctttctattttttcacatttttat---tttgcagATAGAGCCTATCTTGAGTGGAAATCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGTGT
upper sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 1
gttttcttcatttaagacaaatgcgaact-gcgttatgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
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-cttgatgtgggtagatgatttaggggcttgtctttttatattatttttgttctttttctttcttttattttcttttcttttttacatttttattttgcagATAGAGCCAATACCAAGTGGAAATCTGCCTCCTGGTTTTGATTCAAGTACATGCCGCAGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
tgcttac putative branch site (score: 2)
tgtcttt putative PPT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttttcttcatttaagacaaatgcgaactgcgttatgaaatcatagatgttatctctgttcttcatagaaccttttgcttacacttgtatgtctttgcagATAGAGCCCATAGTCAGTGGAAACCTGCCTCCTGGGTTTGATTCAAGTACATGCCGCAGCGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA