Sequence
atgc intronic sequence ATGC exonic sequenceACCCACATCTGTAAAGATTGAACTGATACACAAATTGGTGGCTTCTGGTCTATCAGTAGTTGAAGCCACAAGTTTTGTGTCCCCAAAATGGGTGCCACAGgtaattacttagattaggtgaaggcgtgtactagtatcatacattaatttaaatcacagacatttgagagattgtcacgatagctcttgatttgtttttt...
Basic information
species | Oryza sativa |
transcript | LOC_Os12g04020.2 |
intron # | 5 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g04020.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv06s0009g02640.t01 (Vitis vinifera), 5'ss of exon 3
ACCCACATCTGTAAAGATTGAACTGATACACAAATTGGTGGCTTCTGGTCTATCAGTAGTTGAAGCCACAAGTTTTGTGTCCCCAAAATGGGTGCCACAGgtaattacttagattaggtgaaggcgtgtactagtatcatacattaatttaaatcacagacatttgagagattgtcacgatagctcttgatttgtttttt-------
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ACCTACAGCTGTAAAAGTGGAACTAATCCATAGGCTAGTTTCTTGTGGATTGCCTGTTGTTGAGGCTACAAGTTTTGTGTCGCCAAAATGGGTACCTCAGgtaatt---cagat--gccatttcttttttgttctttaaggcaccagttttactgattataaattcagt-attgt-gcgttttatgttgacttcttaaatttacatg
upper sequence: LOC_Os12g04020.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv08s0040g01170.t01 (Vitis vinifera), 5'ss of exon 4
ACCCACATCTGTAAAGATTGAACTGATACACAAATTGGTGGCTTCTGGTCTATCAGTAGTTGAAGCCACAAGTTTTGTGTCCCCAAAATGGGTGCCACAGgtaa-------ttacttagattaggtgaaggcgtgtactagtatcatacattaatttaaatcacagacatttgagagattgtcacgatagctcttgatttgtttttt
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GCCTACTGTTGTAAAGGTTGAGCTGATTAAGATGCTAGTTTCTTCAGGATTGCCTATTGTAGAGGCTACAAGTTTTGTCTCACCAAAATGGGTGCCACAGgtaaagtaggctttggtagtttttgggagatagtcaacct-tcttgtaaagtcatttgctttgcatgcctattctgtatgttcatttttgca-tagatttgt-----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|86848655|gb|CI293960.1|CI293960EST: TATCAGTAGTTGAAGCCACAAGTTTTGTGTCCCCAAAATGGGTGCCACAG CTAGCAGATGCAAAGGATGTGGTTGAAGGGATTAAGCATGTGCCAGATGTG
genomic: TATCAGTAGTTGAAGCCACAAGTTTTGTGTCCCCAAAATGGGTGCCACAGgtaattactt ... ggagttgcagCTAGCAGATGCAAAGGATGTGGTTGAAGGGATTAAGCATGTGCCAGATGTG
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ACCCACATCTGTAAAGATTGAACTGATACACAAATTGGTGGCTTCTGGTCTATCAGTAGTTGAAGCCACAAGTTTTGTGTCCCCAAAATGGGTGCCACAGgtaattacttagattaggtgaaggcgtgtactagtatcatacattaatttaaatcacagacatttgagagattgtcacgatagctcttgatttgtttttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC