Sequence
atgc intronic sequence ATGC exonic sequence...tcagagctctcttctgacaaactacaacataactttatgatcactgttgcaaatttctaaaaccctgcttgacgggcaatattttcctgttaatttgcagGTTCTGATATGAACAAGATCCTAATGGCAACTGCTATTTCTAAAATGTTCCTCTCTGAGCCGATGAAATCTTCCCTTGGAGAAGATGGTGCAGTTGAGCC
Basic information
species | Oryza sativa |
transcript | LOC_Os01g72000.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g72000.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G037422_T01 (Zea mays), 3'ss of exon 2
---tcagagctctcttctgacaaactacaacataactttatgatcactgttgcaaatttctaaaaccctgcttgacgggcaat-attttcctgtta-atttgcagGTTCTGATATGAACAAGATCCTAATGGCAACTGCTATTTCTAAAATGTTCCTCTCTGAGCCGATGAAATCTTCCCTTGGAGAAGATGGTGCAGTTGAGCC
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ctataaaaaaattgggaattcaatgtagaatgcaattttct--ccactctatctaa---ccataccatcacctaataagcttccgccctcctgtttcgtttgcagGTTCAGACATGAACAAGGTCCTCATGGCAACGGCCATCTCGAAAATGTTCCTATCTGAACATATGAAATCTTCCCTCGGCGAGGATGGAGCTATTGAACCMapped 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|29632235|gb|CB637244.1|CB637244EST: GATGGCCGAGGCTGGTTATTTTCCACCATTGATACATTACCTGAAAGAAG GTTCTGATATGAACAAGATCCTAATGGCAACTGCTATTTCTAAAATG
genomic: GATGGCCGAGGCTGGTTATTTTCGACCATTGATACATTACCTGAAAGAAGgtagtttaat ... taatttgcagGTTCTGATATGAACAAGATCCTAATGGCAACTGCTATTTCTAAAATG
EST:
gi|29628748|gb|CB633759.1|CB633759EST: GATGGCCGAGGCTGGTTATTTTCGACCATTGATACATTACCTGAAAGAAG GTTCTGATATGAACAAGATCCTAATGGCAACTGCTATTTCTATAATGTTCC
genomic: GATGGCCGAGGCTGGTTATTTTCGACCATTGATACATTACCTGAAAGAAGgtagtttaat ... taatttgcagGTTCTGATATGAACAAGATCCTAATGGCAACTGCTATTTCTAAAATGTTCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttgcaaatttctaaaaccctgcttgacgggcaatattttcctgttaatttgcagGTTCTGATATGAACAAGATCCTAATGGCAACTGCTATTTCTAAAATGTTCCTCTCTGAGCCGATGAAATCTTCCCTTGGAGAAGATGGTGCAGTTGAGCC
ttttcctgtt CT-rich tract
aaatttctaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tcagagctctcttctgacaaactacaacataactttatgatcactgttgcaaatttctaaaaccctgcttgacgggcaatattttcctgttaatttgcagGTTCTGATATGAACAAGATCCTAATGGCAACTGCTATTTCTAAAATGTTCCTCTCTGAGCCGATGAAATCTTCCCTTGGAGAAGATGGTGCAGTTGAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - -tcttctg
- - - - - - - - acaaact
- - - - - - - - - - - - caacata
- - - - - - - - - - - - - - - - - ttatgat
- - - - - - - - - - - - - - - - - - - - - -ctgttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ctaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctgctt