Sequence
atgc intronic sequence ATGC exonic sequence...aagatgtgtggtgttgcgttgttgccaaaagtgttttcttgtcgatgcgtgtaaactactagttttagctagcttgacaagtttgtttactgccttgcagATTGGTATGAATCAATCATCTTCTGCCAGAGTTAGAAGGGATTCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGTCTCCTTACCAATGGCATAT
Basic information
species | Oryza sativa |
transcript | LOC_Os02g48370.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G421899_T03 (Zea mays), 3'ss of exon 4
-aagatgtgtggtgttgcgttgttgccaaaagtgttttcttgtcgatgcgtgtaaactactagttttagctagct-tgacaagtttgtttactgccttgcagATTGGTATGAATCAATCATCTTCTGCCAGAGTTAGAAGGGATTCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGTCTCCTTACCAATGGCATAT
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ccactcatgtggaaac-ctccggcactgggtctaccct-ttattgaaaagtgcaagttgctaattttagttcgttgtgacaagttccctgatgattctgtagGTAGTTGTAAATCAATCATCTTCTGCCAGAGTTAGAAGGGATGTTGCAGCACGTGCTATGCAGGGTTGGCATGCTCACCGCCTCCTTGCCAATGGCACTT
upper sequence: LOC_Os02g48370.2 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G110109_T01 (Zea mays), 3'ss of exon 5
aagatgtgtggtgttgcgttgttgccaaaagtgttttcttgtcgatgcgtgtaaactactagttttagctagct-tgacaagtttgtttactgccttgcagATTGGTATGAATCAATCATCTTCTGCCAGAGTTAGAAGGGATTCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGTCTCCTTACCAATGGCATAT
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-gctcgcactgttcaaggaggctgtttgctaacgcctgttgttgaaatgtgcaagttgctaattttagttcgttatgacaagttccctgatggttttgtagGTGGTTGTAAATCAATCATCTTCTGCCAGAGTTAGAAGGGATGCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGCCTTCTCACAAATGGCACTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcgtgtaaactactagttttagctagcttgacaagtttgtttactgccttgcagATTGGTATGAATCAATCATCTTCTGCCAGAGTTAGAAGGGATTCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGTCTCCTTACCAATGGCATAT
gcttgac putative branch site (score: 4)
ctgcctt putative PPT
tagtttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagatgtgtggtgttgcgttgttgccaaaagtgttttcttgtcgatgcgtgtaaactactagttttagctagcttgacaagtttgtttactgccttgcagATTGGTATGAATCAATCATCTTCTGCCAGAGTTAGAAGGGATTCTGCAGCGCGTGCTATGCAGGGTTGGCATGCTCACCGTCTCCTTACCAATGGCATAT
- - - - - gtgttgc
- - - - - - - - - -tgttgcc
- - - - - - - - - - - - - - - - - tttcttg
- - - - - - - - - - - - - - - - - - - - - - atgcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - aaactac