Sequence
atgc intronic sequence ATGC exonic sequenceGGATATGTTGGAGAAACTGGCCATAAAATTAGCATTTACTCTACCAGCATCATCTTATGCTACAATGGCTATTAGGGAGTTGATGAAGACTTCAACTTCGgtatttctccaattctctgatcatttctttgatttttccaaactaaaacttagttatgagcaaatttcatctgttttctgtgtcgttaatatatttttatctttttggctgcacacag
Basic information
species | Oryza sativa |
transcript | LOC_Os01g56620.1 |
intron # | 18 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g56620.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G459702_T01 (Zea mays), 5'ss of exon 17
GGATAT-GTTGGAGAAACTGGCCATAAAATTAGCATTTACTCTACCAGCATCATCTTATGCTACAATGGCTATTAGGGAGTTGATGAAGACTTCAACTTCGgtatttctccaattctctgatcatttctttgatttttccaa-actaaaacttagttatgagcaaatttcatctgttttctgtgtcgttaatatatttttatctttttggctgcacacag
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-TCTGTCACCAGAGAAACTGGCTGTGAAATTAGAATTTACTCTACCAGCATCATCTTATGCTACAATGGCCATAAGGGAGTTGACGAAAACTTCAACTTCGgtgacttcc---tgttcaattcttttttttggttttgtaaatacttaaattatctttgctactcttttttttcatcttttg-gtcattgaa-----ccgaaccatttga----------
upper sequence: LOC_Os01g56620.1 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA03G40600.1 (Glycine max), 5'ss of exon 21
-GGATATGTTGGAGAAACTGGCCATAAAATTAGCATTTACTCTACCAGCATCATCTTATGCTACAATGGCTATTAGGGAGTTGATGAAGACTTCAACTTCGgta--tttctccaattctctgatcatttctttgatttttccaaactaaaacttagttatgagcaaatttcatctgttttctgtgtcgttaatatatttttatctttttggctgcacacag
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CTCTCAAGATTCCCAAATCG-CTCTAAAATTGAGCTTTACTCTTCCTGCTTCATGTTATGCAACAATGGCCATAAGGGAGCTGCTGAAGACTTCAACATCTgtaagcacccccaatt---tgaaaagtcttgtgtctgttactacaggtgctctaattaatcatgattgggaaaaacttttagcattgggaatatgcacataaa-----------------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|66922868|gb|CX109716.1|CX109716EST: CATCTTATGCTACAATGGCTATTAGGGAGTTGATGAAGACTTCAACTTCG GTTGCTCATCAGAAAACATTAAACATCTGAACCTTCGGCCATTTGCATTAT
genomic: CATCTTATGCTACAATGGCTATTAGGGAGTTGATGAAGACTTCAACTTCGgtatttctcc ... ctgcacacagGTTGCTCATCAGAAAACATTAAACATCTGAACCTTCGGCCATTTGCATTAT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGATATGTTGGAGAAACTGGCCATAAAATTAGCATTTACTCTACCAGCATCATCTTATGCTACAATGGCTATTAGGGAGTTGATGAAGACTTCAACTTCGgtatttctccaattctctgatcatttctttgatttttccaaactaaaacttagttatgagcaaatttcatctgttttctgtgtcgttaatatatttttatctttttggctgcacacag
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