Sequence
atgc intronic sequence ATGC exonic sequencegtaagccccaagcccatctcatctatcatgttgtttgtttttgggcttcggcctgctcgttctaaaagcccaccatgatcactttatgcttttactgggccgttataatatcagtatctttgtactgatggtgaatgggtgattaacggtgatgattttctgttgccagGCGGTGGCCGGAAAGTTACAAGGGTAGAGGTGACCCTGGACGGCGGCGAGACGTGGCAGGTGTGCAACCTTGACCACCCGGAGAGGCCGACCAAGTACGG
Basic information
species | Oryza sativa |
transcript | LOC_Os02g53130.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G428027_T01 (Zea mays), 3'ss of exon 2
gtaagccccaagcccatctcatctatcatgttgtttgtttttgggcttcggcctgctcgttctaaaagcccaccatgatcactttatgcttttactgggccgttataatatcagtatctttgtactgatggtgaatgggtgattaacg-gtgatgattttctgttgccagGCGGTGGCCGGAAAGTTACAAGGGTAGAGGTGACCCTGGACGGCGGCGAGACGTGGCAGGTGTGCAACCTTGACCACCCGGAGAGGCCGACCAAGTACGG
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--------------------------------------------------------------------aatgttgtgggcttttgttgggctatccaaggctccctcttctc-gtttccttacttttttttttctcgtgggataaacgcatggcgatga-ctgttgccagGTGGCGGCCGGAAAGTAACACGGGTGGAGGTGACACTGGACGGCGGCGAGACGTGGCAGGTGTGCTCGCTCGACCACCCGGAGCGCCCAACCAAGTACGG
upper sequence: LOC_Os02g53130.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM5G878558_T01 (Zea mays), 3'ss of exon 2
gtaagccccaagcccatctcatctatcatgttgtttgtttttgggcttcggcctgctcgttctaaaagcccaccatgatcactttatgcttttactgggccgttataatatcagtatctttgta--ctgatgg--tgaatgggtgattaacggtgatgat-tttctgttgccagGCGGTGGCCGGAAAGTTACAAGGGTAGAGGTGACCCTGGACGGCGGCGAGACGTGGCAGGTGTGCAACCTTGACCACCCGGAGAGGCCGACCAAGTACGG
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-------------------------------------------------------------------------aaacaacgtttgaggcttctattgggct-ttccaagcctattttcctagtttccttgtgggctaaaaccgaaactcacggtggtggtgcctctgttgccagGTGGCGGCCGGAAAGTAACCCGGGTGGAGGTGACGCTGGACGGCGGCGAGACGTGGCATGTGTGCTCGCTCGACCACCCGGAGCGTCCAACCAAGTACGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctttgtactgatggtgaatgggtgattaacggtgatgattttctgttgccagGCGGTGGCCGGAAAGTTACAAGGGTAGAGGTGACCCTGGACGGCGGCGAGACGTGGCAGGTGTGCAACCTTGACCACCCGGAGAGGCCGACCAAGTACGG
gattaac putative branch site (score: 2)
ttttctgtt putative PPT
atgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagccccaagcccatctcatctatcatgttgtttgtttttgggcttcggcctgctcgttctaaaagcccaccatgatcactttatgcttttactgggccgttataatatcagtatctttgtactgatggtgaatgggtgattaacggtgatgattttctgttgccagGCGGTGGCCGGAAAGTTACAAGGGTAGAGGTGACCCTGGACGGCGGCGAGACGTGGCAGGTGTGCAACCTTGACCACCCGGAGAGGCCGACCAAGTACGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG