Sequence
atgc intronic sequence ATGC exonic sequencegtgagcgagcttctctttttcacctcgccagaaatggcagcagctgaactcctcatctccttcctaatcaatccgacaaaaaagattaattctattaattccgagttgctaaactctgctctcgttgctccagGAAGAACCAGCAGAAGAAGGTGGTGCGGCACGTGCCGGCGGACGGCGTGTCGGCCGACGTGTGGGCGTGGCGGAAGTACGGACAGAAGCCCATCAAGGGC
Basic information
species | Oryza sativa |
transcript | LOC_Os02g16540.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g16540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G038158_T01 (Zea mays), 3'ss of exon 1
gtgagcgagcttctctttttcacctcgccagaaatggcagcagctgaactcctcatctccttcctaatcaatccgacaaaaaagattaattctattaattccgagttgctaaactctgctctcgt-tgctccagGAAGAACCAGCAGAAGAAGGTGGTGCGGCACGTGCCGGCGGACGGCGTGTCGGCCGACGTGTGGGCGTGGCGGAAGTACGGACAGAAGCCCATCAAGGGC
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gtacgctgcgctcgctgagt-gcctcgacacggccggcggcagcgg--ttcttcgaattgtttct--------tgggggaggttgaaagctcgggtatttgcaagctgctaa-cgctgtttccgtgcactccagGAAGAACCAGGTGAAGAAGGTGGTCTGCCACGTTCCGGCGGACGGCTCGTCGCCGGACGTGTGGGCGTGGCGCAAGTACGGCCAGAAGCCCATCAAGGGC
upper sequence: LOC_Os02g16540.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G048450_T01 (Zea mays), 3'ss of exon 1
gtgagcgagcttctctttttcacctcgccagaaatggca-gcagctgaactcctcatctccttcctaatcaatccgacaaaaaagattaattctattaattccgagttgctaaactctgctctcgttgc----tccagGAAGAACCAGCAGAAGAAGGTGGTGCGGCACGTGCCGGCGGACGGCGTGTCGGCCGACGTGTGGGCGTGGCGGAAGTACGGACAGAAGCCCATCAAGGGC
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----gtactcttctctgctgagtgcctccactctccacacgccagcggttctttgaactgtttcttgaggaggctga-aagctcgggtatatgcat--actgctaagtgctaa-cgctgtttccgccgcgcactccagGAAGAACCAGGTGAAGAAGGTGGTCTGCCACGTTCCGGCGGACGGCTCGTCGTCGGACATGTGGGCGTGGCGCAAGTACGGCCAGAAGCCCATCAAGGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaagattaattctattaattccgagttgctaaactctgctctcgttgctccagGAAGAACCAGCAGAAGAAGGTGGTGCGGCACGTGCCGGCGGACGGCGTGTCGGCCGACGTGTGGGCGTGGCGGAAGTACGGACAGAAGCCCATCAAGGGC
tgctaaa putative branch site (score: 2)
ctctcgtt putative PPT
attaattctattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcgagcttctctttttcacctcgccagaaatggcagcagctgaactcctcatctccttcctaatcaatccgacaaaaaagattaattctattaattccgagttgctaaactctgctctcgttgctccagGAAGAACCAGCAGAAGAAGGTGGTGCGGCACGTGCCGGCGGACGGCGTGTCGGCCGACGTGTGGGCGTGGCGGAAGTACGGACAGAAGCCCATCAAGGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC