Sequence
atgc intronic sequence ATGC exonic sequenceTGGCAGAGCCAAAAGATTTTGTATATCTACTTGATAACTGCCCCCATGACTGGCTCTTCCTGCAGTGTAAAGCAGTGgtaagcattttgcttgtcatgcttggcatgaagtagatatctttaagtttaactttcagagattagtagttattacttcttaatagtttttagtactgat...
Basic information
species | Oryza sativa |
transcript | LOC_Os04g04254.1 |
intron # | 11 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os04g04254.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G021849_T02 (Zea mays), 5'ss of exon 6
TGGCAGAGCCAAAAGATTTTGTATATCTACTTGATAACTGCCCCCATGACTGGCTCTTCCTGCAGTGTAAAGCAGTGgtaagcattttgcttgtcatgcttggcatgaagtagatatctttaagtttaactttcagagattagtagttattacttcttaatagtttttagtactgat---------------------------------------------------------------------------------
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TGGCAGAACCAAAAGATTTTGTATATCTACTAGACAACTGCCCTCATGACTGGCTTTTTCTGCAATGCAAAGCAGTGgtaagccattc-cttgaaacgtctctcttttagcatattatctgacctttacaatgtgtgcgtgcgtgcgcacctgcgtggagagagagtggctacaagtttacatgaaatacttatgggtgaatttatgctgcttgttaagacagttgtgcttacactttcattttttctgcctccatag
upper sequence: LOC_Os04g04254.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G007721_T01 (Zea mays), 5'ss of exon 9
TGGCAGAGCCAAAAGATTTTGTATATCTACTTGATAACTGCCCCCATGACTGGCTCTTCCTGCAGTGTAAAGCAGTGgtaagcattttgcttgtcatgcttggcatgaagtagatatctttaagtttaactttcagagattagtagttattacttct-taatagtttttagtactgat-----------------------
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TGTCAGAACCAAAAGATTTTGTGTATCTACTAGACAACTGCCCTCATGACTGGCTTTTTCTGCACTGCAAAGCAGTGgtaatcgact-gcttcaagcttttggaacatctcgtttagcatgttatctgacctttacatactacttattaagacaggagttaaggttttatgctttactctttcattttcctgcatccatagMapped 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|218504178|gb|FG958866.1|FG958866EST: TACTTGATAACTGCCCCCATGACTGGCTCTTCCTGCAGTGTAAAGCAGTG GTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
genomic: TACTTGATAACTGCCCCCATGACTGGCTCTTCCTGCAGTGTAAAGCAGTGgtaagcattt ... acttctgtagGTACATCATGGCGGTGCTGGAACAACAGCTGCTGGCCTCAAAGCAGCG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGGCAGAGCCAAAAGATTTTGTATATCTACTTGATAACTGCCCCCATGACTGGCTCTTCCTGCAGTGTAAAGCAGTGgtaagcattttgcttgtcatgcttggcatgaagtagatatctttaagtttaactttcagagattagtagttattacttcttaatagtttttagtactgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG