Sequence
atgc intronic sequence ATGC exonic sequenceCAGAGTGCTCAAGACCATCAGCTTACGTGATGAAGAGCGATGTCTACAGCTTCGGAGTCATCATGCTGGAGCTACTAACCGGCCGAAAGCCTTATGATAGgtgaattaagggggcaaaaagataaaaccttgaaattcactactgatatccataatgtgatgcatcatctaatgtctgcactctgcacattatgcttactttctctatgtggctgtctgatggttctacag
Basic information
species | Oryza sativa |
transcript | LOC_Os09g38700.1 |
intron # | 13 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g38700.1 (Oryza sativa), 5'ss of exon 13
lower sequence: EFJ07060 (Selaginella moellendorffii), 5'ss of exon 4
CAGAGTGCTCAAGACCATCAGCTTACGTGATGAAGAGCGATGTCTACAGCTTCGGAGTCATCATGCTGGAGCTACTAACCGGCCGAAAGCCTTATGATAGgtgaattaagggggcaaaaagataaaaccttgaaattcactactgatatccataatgtgatgcatcatctaatgtctgcactctgcacattatgcttactttctctatgtggctgtctgatggttctacag
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CGGAGTTTGCCATGTCTGGCGTGTACACTGTCAAGAGCGATGTTTACAGCTTTGGAGTGGTGATGCTGGAGCTTCTAACCGGAAGAAAATCGCTAGACAGgtaaaatcttgaagttcttccatccaagagttttatgta--agtaagctcca-aacttgaaacttccag--------------------------------------------------------------
upper sequence: LOC_Os09g38700.1 (Oryza sativa), 5'ss of exon 13
lower sequence: EFJ18843 (Selaginella moellendorffii), 5'ss of exon 4
CAGAGTGCTCAAGACCATCAGCTTACGTGATGAAGAGCGATGTCTACAGCTTCGGAGTCATCATGCTGGAGCTACTAACCGGCCGAAAGCCTTATGATAGgtgaattaagggggcaaaaagataaaaccttgaaattcactactgatatccataatgtgatgcatcatctaatgtctgcactctgcacattatgcttactttctctatgtggctgtctgatggttctacag
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CGGAGTTTGCCATGTCTGGCGTGTACACTGTCAAGAGCGATGTTTACAGCTTTGGAGTGGTGATGCTGGAGCTTCTAACCGGAAGAAAATCGCTAGACAGgtaaa-------agcttgaaga---agttcttccatccaagagttttatgta-agtaagctccaa-acttgaaacttccag--------------------------------------------------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|86481507|gb|CI124140.1|CI124140EST: TTCGGAGTCATCATGCTGGAGCTACTAACCGGCCGAAAGCCTTATGATAG CTCCAAGCCAAGAACAGAGCAGTGCTTGGTCAAGTATGTGGCTCCACAGCT
genomic: TTCGGAGTCATCATGCTGGAGCTACTAACCGGCCGAAAGCCTTATGATAGgtgaattaag ... ggttctacagCTCCAAGCCAAGAACAGAGCAGTGCTTGGTCAAGTATGTGGCTCCACAGCT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CAGAGTGCTCAAGACCATCAGCTTACGTGATGAAGAGCGATGTCTACAGCTTCGGAGTCATCATGCTGGAGCTACTAACCGGCCGAAAGCCTTATGATAGgtgaattaagggggcaaaaagataaaaccttgaaattcactactgatatccataatgtgatgcatcatctaatgtctgcactctgcacattatgcttactttctctatgtggctgtctgatggttctacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT