Sequence
atgc intronic sequence ATGC exonic sequence...tgccacatttgcagtggcatggatccaattaacccttatttttaacctaatgctatgcgaaatgtttgatgttagaattgatgctcttgttctgtaacagGAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAAACTTCCATGTAGCTTTAATGATTTCTCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os09g29404.1 |
intron # | 17 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G150796_T02 (Zea mays), 3'ss of exon 17
tgccacatttgcagtggcatggatccaattaacccttatttttaacctaatgctatgcgaaatgtttgatg---ttagaattgatgctcttgttctgtaacagGAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAAACTTCCATGTAGCTTTAATGATTTCTCAG
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-gtattacctaccttttca--aactaaagtatggtatttttttcatttaattttacgttgcatatttagtgctattaaaatttgtgctcttgccatattacagGAGAAACAAATGATTTGAATGTGCTAAGTCTTCGTTCAAGGCAAATGAAGAACTTCCATGTGGCATTAATGATTTCCCAG
upper sequence: LOC_Os09g29404.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G076508_T01 (Zea mays), 3'ss of exon 5
--tgccacatttgcagtggcatggatccaattaacccttatttttaacctaatgctatgcgaaatgtt-tgatgttagaattgatgctcttgttctgtaacagGAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAAACTTCCATGTAGCTTTAATGATTTCTCAG
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gtaactatacgtgta-tgactt--ttcaaactaaagcatggagatgtttttccatttaattttacgtagtgttactaaaatttctgttgttgccatattacagGAGGAACAAATGATTTGAATGTGTTAAGTCTTCGTTCTAGGCAAATGAAGAACTTCCATGTGGCATTAATGATTTCCCAGMapped 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|218500325|gb|FG953825.1|FG953825EST: TGGCTGTGATGGATGCAATGACAACTTTAGCTGGAACTGTGGTGTTGAAG GAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAA
genomic: TGGCTGTGATGGATGCAATGACAACTTTAGCTGGAACTGTGGTGTTGAAGgtacctgctt ... tctgtaacagGAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAA
EST:
gi|66947191|gb|AU312035.1|AU312035EST: TGGCTGTGATGGATGCAATGACAACTTTAGCTGGAACTGTGGTGTTGAAG GAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAA
genomic: TGGCTGTGATGGATGCAATGACAACTTTAGCTGGAACTGTGGTGTTGAAGgtacctgctt ... tctgtaacagGAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAA
EST:
gi|33797263|gb|CF324494.1|CF324494EST: TGGCTGTGATGGATGCAATGACAACTTTAGCTGGAACTGTGGTGTTGAAG GAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAA
genomic: TGGCTGTGATGGATGCAATGACAACTTTAGCTGGAACTGTGGTGTTGAAGgtacctgctt ... tctgtaacagGAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAA
RNA-Seq data
ATGC Supported by RNA-Seq exonic block that spans over the splice site
atgs Truncated intron sequence
Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.
Found data for 1 RNA-Seqlibrary.
Block sizes:
56 (upstream exon),
42 (downstream exon)
Score:
3CACAATGATGCTAATGGAGAAGGTGGCTGTGATGGATGCAATGACAACTTTAGCTGGAACTGTGGTGTTGAAGgtacctgctt ... tctgtaacagGAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAAACTTCCATGTAGCTTTAATGATTTCTCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctaatgctatgcgaaatgtttgatgttagaattgatgctcttgttctgtaacagGAGAAACAAATGATCTGAATGTGTTAAGTCTGCGTTCAAGACAAATGAAAAACTTCCATGTAGCTTTAATGATTTCTCAG
aattgat putative branch site (score: 3)
ctcttgttct CT-rich tract
aaatgttt TA-rich tract