Sequence
atgc intronic sequence ATGC exonic sequenceTGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTACTGCTGGAAGGCATTTGGAGGCACTTGCTGTACTCCAGCATATCAAGGATAGCgtacgttctttctccagaaatgagagaagaaaagtgttttttttaatgtttcttttttgggttccatgatttaacttagtttgagcaatttctacctattgttgatttcattttttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os06g49670.2 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g49670.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G028108_T03 (Zea mays), 5'ss of exon 2
TGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTACTGCTGGAAGGCATTTGGAGGCACTTGCTGTACTCCAGCATATCAAGGATAGCgtacgttctttctccagaaatgagagaagaaaagtgttttttttaatgtttcttttttgggttccatgatttaacttagtttgagcaatttctacctattgttgatttcattttttcag
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TGAGCCAAACCTTGTTATGCTGAATTCGTTAATCAATGCTTTTGGCACTGCTGGAAGGCATTTGGAGGCACTAGCTGTATTTCAGCATATCAAGGATAGTgtatgtaccacatctagaaacgagatgaaaa-----ttgtttttaaaaatcttgttttgaa-------gttttgctttctttgcactcctatgattaactgtt--cttttttcttatag
upper sequence: LOC_Os06g49670.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G127360_T01 (Zea mays), 5'ss of exon 1
TGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTACTGCTGGAAGGCATTTGGAGGCACTTGCTGTACTCCAGCATATCAAGGATAGCgtacgttctttctccagaaatgagagaagaaaagtgttttttttaatgtttcttttttgggttccatgatttaacttagtttgagcaatttctacctattgttgatttcattttttcag
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TGAGCCAAGCCTTGTTATGCTGAATTCGTTAATCAATGCTTTTGGCACTGCTGGAAGGCATTTGGAGGCACTAGCTGTATTTCAGCATATCAAGGATAGTgtatgcaccacatctagaaacgagatgaaaa-----ttgtttttaaaaatcttgttttgaagttt-tgctttctttgcactc---ctatgattacctgttctttttcttatag------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|27547470|gb|CA765633.2|CA765633EST: CTGGAAGGCATTTGGAGGCACTTGCTGTACTCCAGCATATCAAGGATAGC GGTATGAGCCCAGATGTTGTGACTTACACAACACTTATGAAGGCTTTCATG
genomic: CTGGAAGGCATTTGGAGGCACTTGCTGTACTCCAGCATATCAAGGATAGCgtacgttctt ... attttttcagGGTATGAGCCCAGATGTTGTGACTTACACAACACTTATGAAGGCTTTCATG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAGCCAAATCTTGTTATGCTGAATTTGCTAATAAATGCTTTTGGTACTGCTGGAAGGCATTTGGAGGCACTTGCTGTACTCCAGCATATCAAGGATAGCgtacgttctttctccagaaatgagagaagaaaagtgttttttttaatgtttcttttttgggttccatgatttaacttagtttgagcaatttctacctattgttgatttcattttttcag
- - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG