Sequence
atgc intronic sequence ATGC exonic sequenceTTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAGgtaatgaatatacttttgtttttttccttattatcatatattcctctgcttgcaatccatgtttcttggggtttcttctctgggcaatgtcagttacgcatctttggttag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g49730.3 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g49730.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G457881_T04 (Zea mays), 5'ss of exon 6
TTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAGgtaatgaatata--cttttgtttttttccttattatcat-atattcctc----tgcttgcaatccatgtttctt---ggggtttcttctctgggcaatgtcagttacgcatct--ttggttag-------------
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-----------------TTTTGATATTTGATGGTAGGACAGCATATGTTCGTGCATTGCAACCGATAAATAAAGATGAAGAGgtaaggaatatataccttgcatcctgatcatataatccttaaattgcatgtcacgctttcattctttctccttttccattgttatctttctggttaatattgtttgtgtatctgactgtctgttgtcacttgtcag
upper sequence: LOC_Os03g49730.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G457881_T03 (Zea mays), 5'ss of exon 7
TTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAGgtaatgaatata--cttttgtttttttccttattatcat-atattcctc----tgcttgcaatccatgtttctt---ggggtttcttctctgggcaatgtcagttacgcatct--ttggttag-------------
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TTGTGTACCAAATGCAGTTTTGATATTTGATGGTAGGACAGCATATGTTCGTGCATTGCAACCGATAAATAAAGATGAAGAGgtaaggaatatataccttgcatcctgatcatataatccttaaattgcatgtcacgctttcattctttctccttttccattgttatctttctggttaatattgtttgtgtatctgactgtctgttgtcacttgtcag
upper sequence: LOC_Os03g49730.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G399311_T01 (Zea mays), 5'ss of exon 6
TTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAGgtaatgaat--atacttttgtttttttccttattatcatatattcctctg-----cttgcaatccatgtttctt-------ggggtttcttctctgggcaatgtcagttacgcatct--ttggttag-------------
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TTGTGTACCAAATGCAGTTTTGATATTTGATGGTAGGACAACATATGTTCGTGCATTGCAACCGATAGACAAAGATGAAGAGgtaaggaatctataccttgcatcctgatcatataatccttcaattgcatgtcacactttcattatatctttctccttttccattgttatctttctggttaatattgttcgtgtatctgattgtctgttgtcacttgtcagMapped 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|58682029|gb|CK070716.1|CK070716EST: GTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAG GTATCAATAAGTTACATTGAAACTGCGGCAACCACTATGAAGAGACAGGAC
genomic: GTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAGgtaatgaata ... ctttggttagGTATCAATAAGTTACATTGAAACTGCGGCAACCACTATGAAGAGACAGGAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTGTGTACCAAATGCAGTTTTGATATTTGAAGGTCGGACAGCATATGTTCGTGCATTGCAACCTATAAGTAAAAATGAGGAGgtaatgaatatacttttgtttttttccttattatcatatattcctctgcttgcaatccatgtttcttggggtttcttctctgggcaatgtcagttacgcatctttggttag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG