Sequence
atgc intronic sequence ATGC exonic sequencegtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgattttattttgctatccggaatccctacagAACTTTGCAGAAGCTGATTCTTTCTTCTGCTTCATGGAGTTACTTAGTGGGTTTAGAGACAACTTCTGCCAGAAACTAGACAACAGTGCTGTTGGCATTC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g68010.3 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G068392_T03 (Zea mays), 3'ss of exon 6
gtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgattttattttgctatccggaatccctacagAACTTTGCAGAAGCTGATTCTTTCTTCTGCTTCATGGAGTTACTTAGTGGGTTTAGAGACAACTTCTGCCAGAAACTAGACAACAGTGCTGTTGGCATTC
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gtaagagattgttttttttaccaagttcttagtgccctgcat--tgtacttctga---tagccgaa-gct-ttcatgtttgctttagtcattactatatcttctg----tatcgtgatcttgctattcggaacccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTC
upper sequence: LOC_Os01g68010.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G068392_T01 (Zea mays), 3'ss of exon 6
-------gtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgattttattttgctatccggaatccctacagAACTTTGCAGAAGCTGATTCTTTCTTCTGCTTCATGGAGTTACTTAGTGGGTTTAGAGACAACTTCTGCCAGAAACTAGACAACAGTGCTGTTGGCATTC
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gtatggagtaagagattgttttttttaccaagttcttagtgccctgcat--tgtacttctga---tagccgaa-gct-ttcatgtttgctttagtcattactatatcttctg----tatcgtgatcttgctattcggaacccttgtagGAATTCGCGGAAGCGGATTCATTCTTTTGCTTCGTCGAGTTGCTTAGTGGGTTCAGAGACAACTTCTGCCAGAAACTGGACAACAGTGCTGTTGGCATTCMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|58604226|gb|CK014754.1|CK014754EST: TCTCTTCTTTGTGTTTCGGAATGATCCAGATGATAAAAATGCTGTATGGA AACTTTGCAGAAGCTGATTCTTTCTTCTGCTTCATGGAGTTACTTAGTGGG
genomic: TCTCTTCTTTGTGTTTCGGAATGATCCAGATGATAAAAATGCTGTATGGAgtaagcaatt ... atccctacagAACTTTGCAGAAGCTGATTCTTTCTTCTGCTTCATGGAGTTACTTAGTGGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttctgtgggactatctaaccatgattttattttgctatccggaatccctacagAACTTTGCAGAAGCTGATTCTTTCTTCTGCTTCATGGAGTTACTTAGTGGGTTTAGAGACAACTTCTGCCAGAAACTAGACAACAGTGCTGTTGGCATTC
atctaac putative branch site (score: 2)
tccctac putative PPT
attttattttgctat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcaattgttttaccatatatatgcttaatgccctgtatgatttagagcagactgtagtcagttgctgttcgttatagcaatagtttctgtgggactatctaaccatgattttattttgctatccggaatccctacagAACTTTGCAGAAGCTGATTCTTTCTTCTGCTTCATGGAGTTACTTAGTGGGTTTAGAGACAACTTCTGCCAGAAACTAGACAACAGTGCTGTTGGCATTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT