Sequence
atgc intronic sequence ATGC exonic sequencegtatgtttcagctaatccattagttagattaactgccattctctatttatgtgggcttattaacagagcttgttctggtccttttgggtctgctttaaggttttttctccttaaagttgcatattttaattgctctcctttctttcatttactcaatacatggattagGTTTTCGACCGGCGAACTAAGAGACTAGTTGAAGAAGTTATAGACGGAAAGATTGTGTTGTCTATGAGAGCTTTATACCAATCAAAAGTAGGGCTAACTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g72940.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G146996_T01 (Zea mays), 3'ss of exon 2
gtatgtttcagctaatccattagttagattaactgccattctctatttatgtgggcttattaacagagcttgttctggtccttttgggtctgctttaaggtttt--ttctccttaaagttgcatattttaattgctctcctttctttcatttactcaatacatgg-attagGTTTTCGACCGGCGAACTAAGAGACTAGTTGAAGAAGTTATAGACGGAAAGATTGTGTTGTCTATGAGAGCTTTATACCAATCAAAAGTAGGGCTAACTC
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-------------------------------------------------------------------gtgtgttcagttactccatatggtacattaacttaaaaattttgagtgatacaatatatggcagttgtactg-ttcccttcattaaacaatgctgtgatgtaagGTTTTCGACCGACGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCACTC
upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G133885_T01 (Zea mays), 3'ss of exon 11
gtatgtttcagctaatccattagttagattaactgccattctctatttatgtgggcttattaacagagcttgttctggtccttttgggtctgctttaaggttttttctccttaaagttgcatattttaattgctctcct--ttctttcatttactcaatacatggatt--agGTTTTCGACCGGCGAACTAAGAGACTAGTTGAAGAAGTTATAGACGGAAAGATTGTGTTGTCTATGAGAGCTTTATACCAATCAAAAGTAGGGCTAACTC
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-------------------------------------------------------------------gtgtgttcagttactccatatggtacattaa--cttaaaaattttgagtgtgcaaaatatggcagttgtactgttcccttcattaaaacaatgctgtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACGGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCACTC
upper sequence: LOC_Os01g72940.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G001814_T01 (Zea mays), 3'ss of exon 5
gtatgtttcagctaatccattagttagattaactgccattctctatttatgtgggcttattaacagagcttgttctggtccttttgggtctgctttaaggttttttctccttaaagttgcatattttaattgctctcct-ttctttcatttactcaatacatggatt--agGTTTTCGACCGGCGAACTAAGAGACTAGTTGAAGAAGTTATAGACGGAAAGATTGTGTTGTCTATGAGAGCTTTATACCAATCAAAAGTAGGGCTAACTC
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-------------------------------------------------------------------gtgtgttcagttactccatatggtacattaac-ttaaaaattttgagtgatacaagatatggcagttgtactgttcccttaattaaacaatgctgtgatgtaagGTTTTCGACCGGCGAACAAAGAGGATAGTCGAAGAAGTTATTGACAGAAAAATTGTATTGTCCATGAGGGCTTTATACCAATCAAAAGTAGGACTCGCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttgcatattttaattgctctcctttctttcatttactcaatacatggattagGTTTTCGACCGGCGAACTAAGAGACTAGTTGAAGAAGTTATAGACGGAAAGATTGTGTTGTCTATGAGAGCTTTATACCAATCAAAAGTAGGGCTAACTC
ttttaat putative branch site (score: 3)
atattttaattgct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgtttcagctaatccattagttagattaactgccattctctatttatgtgggcttattaacagagcttgttctggtccttttgggtctgctttaaggttttttctccttaaagttgcatattttaattgctctcctttctttcatttactcaatacatggattagGTTTTCGACCGGCGAACTAAGAGACTAGTTGAAGAAGTTATAGACGGAAAGATTGTGTTGTCTATGAGAGCTTTATACCAATCAAAAGTAGGGCTAACTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT