Sequence
atgc intronic sequence ATGC exonic sequenceGACAAGGAGCTCGAGCTCTACCGCATCTTCCAGGCCATCGACGTCGAGCACAACGGCTGCATCCTCCCCGAGGAGCTCTGGGACGCGCTCGTCAAGGCTGgtatgtatgcgctcgcctcaccttcaccctcaccttccgcagccattgatcgcctccttcccgtgctgtcacacgtcgctccgctgtccgtattctgacg...
Basic information
species | Oryza sativa |
transcript | LOC_Os06g40200.1 |
intron # | 1 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g40200.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G041831_T03 (Zea mays), 5'ss of exon 1
GACAAGGAGCTCGAGCTCTACCGCATCTTCCAGGCCATCGACGTCGAGCACAACGGCTGCATCCTCCCCGAGGAGCTCTGGGACGCGCTCGTCAAGGCTGgtatgtatgcgctcgcctcaccttcaccctcaccttccgcagccattgatcgcctccttcccgtgctgtcacacgtcgctccgctgtccgtattctgacg
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GACAAAGAGCTCGAGCTCTACCGCATCTTCCAGGCCATAGACGTCGAGCACAACGGATGCATCCTCCCCGAGGAGCTCTGGGACGCGCTCATCAAGGCTGgtatgtgtttcctaggccgaaccacgcttctcgcctccctgatccccagtatctgtgcagccgcgcccgtgattctggccaccttggtgctgtgctgacg
upper sequence: LOC_Os06g40200.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA19G28020.1 (Glycine max), 5'ss of exon 2
GACAAGGAGCTCGAGCTCTACCGCATCTTCCAGGCCATCGACGTCGAGCACAACGGCTGCATCCTCCCCGAGGAGCTCTGGGACGCGCTCGTCAAGGCTGgtatgtat---gcgctcgcctcaccttcaccctcaccttccgcagccattga---tcgcctccttcccgtgctgtcacacgtcgctccgctgtccgtattctgacg
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----AGGAACTGGAGCTTTACCGCATTTTTCAGGCCATCGATGTCGCGCACAATGGCTGCATTTTGCCCGAGGAGCTCTGGGAGGCGCTTGTTAGAGCAGGCATgtgtcttgtacctcttgtgttttaacggaaattgttcgtattcttgcaaattcagttgatgtttatgttgt-gtgtttcgcttttctttaggtagattagt-Mapped 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|29620619|gb|CB625630.1|CB625630EST: CAACGGCTGCATCCTCCCCGAGGAGCTCTGGGACGCGCTCGTCAAGGCTG GTATAGAGATTGATGATGAGGAGCTTGCACGGTTTGTCGAGCATGTGGACA
genomic: CAACGGCTGCATCCTCCCCGAGGAGCTCTGGGACGCGCTCGTCAAGGCTGgtatgtatgc ... ttgtttgcagGTATAGAGATTGATGATGAGGAGCTTGCACGGTTTGTCGAGCATGTGGACA
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GACAAGGAGCTCGAGCTCTACCGCATCTTCCAGGCCATCGACGTCGAGCACAACGGCTGCATCCTCCCCGAGGAGCTCTGGGACGCGCTCGTCAAGGCTGgtatgtatgcgctcgcctcaccttcaccctcaccttccgcagccattgatcgcctccttcccgtgctgtcacacgtcgctccgctgtccgtattctgacg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT