Sequence
atgc intronic sequence ATGC exonic sequenceATAAAGCAAGGCCTATAGTTCCCAGGATGCGCAAATTCTATGAAGGTGGTTTTCAACCTGAAATGGCCCGAAGGGAAGCTGGTTTAATCCTGGGTGTCAGgtacatatcatataaaagcataatatgtgcaccacatttgattattatttatgttactcttagcatacagctattcatatgtatactggggatgtgtttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os01g06454.1 |
intron # | 2 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os01g06454.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G040587_T01 (Zea mays), 5'ss of exon 3
ATAAAGCAAGGCCTATAGTTCCCAGGATGCGCAAATTCTATGAAGGTGGTTTTCAACCTGAAATGGCCCGAAGGGAAGCTGGTTTAATCCTGGGTGTCAGgtacatatcatataaaag---cataatatgtgca--------ccacatttgattattatttatgttactcttagcatacagctattcatatgtatactggggatgtgtttt
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ATAAGGCAAGGCCTATAGTTCCAAGGATGCGGAAATTCTATGAAGGTGGCTTTCAACCTACAATGAACCGAAGGGAAGCTGCATTAATCCTTGGTGTCAGgtacacaatacatacaagttacataatatctgcagttcttcaccataatcgaacattgtttatgtttctgtttacataaa-------atctgcataattgatatctt----
upper sequence: LOC_Os01g06454.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv13s0019g03880.t01 (Vitis vinifera), 5'ss of exon 2
ATAAAGCAAGGCCTATAGTTCCCAGGATGCGCAAATTCTATGAAGGTGGTTTTCAACCTGAAATGGCCCGAAGGGAAGCTGGTTTAATCCTGGGTGTCAGgtac------atatcatataaaagcataatatgt-gcaccacatttgattattatttatgttactcttagcatacagctattcatatgtatactggggatgtgtttt
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TCAAGGCTCGTCCGCCAAAACCCAGGATCCGCAAATTCTATGAAGGTGGTTTCCAGCCTACAATGACAAAAAGGGAAGCAGCTCTTATTCTTGGCATTAGgtaccactaaatccttcttgaaagaaaattatattgtaagcaatcacattctagcatat-ttaattttagc---cgtctgtt-ataattaaattgctgttctctg--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|88410630|gb|CI686967.1|CI686967EST: TTTCAACCTGAAATGGCCCGAAGGGAAGCTGGTTTAATCCTGGGTGTCAG AGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGT
genomic: TTTCAACCTGAAATGGCCCGAAGGGAAGCTGGTTTAATCCTGGGTGTCAGgtacatatca ... atgcctccagAGAAAATGTCCATCCTGAGAAGGTTAAAGAGGCACACAAAAAGGTCATGGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ATAAAGCAAGGCCTATAGTTCCCAGGATGCGCAAATTCTATGAAGGTGGTTTTCAACCTGAAATGGCCCGAAGGGAAGCTGGTTTAATCCTGGGTGTCAGgtacatatcatataaaagcataatatgtgcaccacatttgattattatttatgttactcttagcatacagctattcatatgtatactggggatgtgtttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggatg