Sequence
atgc intronic sequence ATGC exonic sequence...ttacagttaatttacagtagtagcagtgtccattaagtctaatttggtactacatttatatattcagtttgatttaaatttgtgttcttaatttggacagGTTTCATGTGCTTGCTGAGTTTGATGAGGCGAAGAGGAGCTGCCGGAAGAGGCTCACCGAGCACAACCGCCGCCGCCGGAAGCCCACCGCCGGCGGCCAA
Basic information
species | Oryza sativa |
transcript | LOC_Os02g08070.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g08070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G111136_T01 (Zea mays), 3'ss of exon 1
ttacagttaatttacagtagtagcagtgtccattaa-gtctaatttggtactacatttatatattcagtttgatttaaatttgtgttcttaatttggacagGTTTCATGTGCTTGCTGAGTTTGATGAGGCGAAGAGGAGCTGCCGGAAGAGGCTCACCGAGCACAACCGCCGCCGCCGGAAGCCCACCGCCGGCGGCCAA
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-cactgcacccgcacacttttatcaaccatcattattgcaaaaggtcgtatttagagctgatatgaaactatactatactattcatttctttggctagtagGTTTCATGTGCTTGCTGAGTTTGATGAGGCCAAGAGGAGCTGCCGGAAGCGGCTCACCGAGCACAACCGCCGCCGCCGGAAGCCGAGCAGCGCACAGGAC
upper sequence: LOC_Os02g08070.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G168229_T02 (Zea mays), 3'ss of exon 1
-ttacagttaatttacagt---agtagcagtgtccattaagtctaatttggtactacatttatatattcagtttgatttaaatttgtgttcttaatttggacagGTTTCATGTGCTTGCTGAGTTTGATGAGGCGAAGAGGAGCTGCCGGAAGAGGCTCACCGAGCACAACCGCCGCCGCCGGAAGCCCACCGCCG-GCGGCCAA
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agtagaattcgtttcagattaaagtggaaggaacatcttgtttcacttcaccactag--ctatagcatcgtatttatcctggtccat-ttcttggct-agctagGTTTCATGTGCTTGCGGAGTTTGACGAGGCCAAGAGGAGCTGCCGGAAGCGGCTCACCGAGCACAACCGACGCCGCCGGAAGCCGATCAGCGCACAGGGC- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtactacatttatatattcagtttgatttaaatttgtgttcttaatttggacagGTTTCATGTGCTTGCTGAGTTTGATGAGGCGAAGAGGAGCTGCCGGAAGAGGCTCACCGAGCACAACCGCCGCCGCCGGAAGCCCACCGCCGGCGGCCAA
tcttaat putative branch site (score: 3)
tacatttatatattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttacagttaatttacagtagtagcagtgtccattaagtctaatttggtactacatttatatattcagtttgatttaaatttgtgttcttaatttggacagGTTTCATGTGCTTGCTGAGTTTGATGAGGCGAAGAGGAGCTGCCGGAAGAGGCTCACCGAGCACAACCGCCGCCGCCGGAAGCCCACCGCCGGCGGCCAA
- - - - - - - - - -gtagcag
- - - - - - - - - - - - - - - - - - - - - - tggtact