Sequence
atgc intronic sequence ATGC exonic sequencegtgaatatatttgatataaacttatctatgaacttcagctgggatctgcagacgggactatggttcactgaaactgagctgtatgactgacatttatttccagGTGCCGCAATGTTCGACGTCGACTACGCCCGGTGGCTGGAGGAAGACAGCCAGCGCATGGCTGAACTGCACGGAGGGCTGCACGCACATCTGCCGGACAG
Basic information
species | Oryza sativa |
transcript | LOC_Os11g05480.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os11g05480.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G030877_T01 (Zea mays), 3'ss of exon 9
gtgaatatatttgat-ataaacttatctatgaact--tcagctggg-----atctgcag--acgggactatggttcactgaaactgagctgt-atgactgacatttatttccagGTGCCGCAATGTTCGACGTCGACTACGCCCGGTGGCTGGAGGAAGACAGCCAGCGCATGGCTGAACTGCACGGAGGGCTGCACGCACATCTGCCGGACAG
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gtgcct-catctgatgatacatttctcggcgttctcttcagctgtgtacataccaactgccacggtatgccatttctctctgactgacgagtgacgagtggtgtacgtgtccagGTGCCGCCATGTTTGACGTGGAGTACGCCCGGTGGCTGGACAACCACAGCCGGCGCCTGGCCGAGCTGAACGGAGCCCTACACGCGCACCTGGCAGACGGMapped 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|10423526|gb|AU108122.1|AU108122EST: GGCTTACTGCTTGGAGCTCCAGGTGGAAACACCAGCTCAG GTGCCGCAATGTTCGACGTCGACTACGCCCGGTGGCTGGAGGAAGACAGCC
genomic: GGCTTACTGCTTGGAGCTCCAGGTGGAAACACCAGCTCAGgtgaatatat ... ttatttccagGTGCCGCAATGTTCGACGTCGACTACGCCCGGTGGCTGGAGGAAGACAGCC
EST:
gi|58652975|gb|CK041655.1|CK041655EST: GGCTTACTGCTTGGAGCTCCAGGTGGAAACACCAGCTCAG GTGCCGCAATGTTCGACGTCGACTACGCCCGG
genomic: GGCTTACTGCTTGGAGCTCCAGGTGGAAACACCAGCTCAGgtgaatatat ... ttatttccagGTGCCGCAATGTTCGACGTCGACTACGCCCGG
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:
60 (upstream exon),
72 (downstream exon)
Score:
9GGCTTACTGCTTGGAGCTCCAGGTGGAAACACCAGCTCAGgtgaatatat ... ttatttccagGTGCCGCAATGTTCGACGTCGACTACGCCCGGTGGCTGGAGGAAGACAGCCAGCGCATGGCTGAACTGCACGGAGGGCTGCACGCACATCTGCCGGACAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagacgggactatggttcactgaaactgagctgtatgactgacatttatttccagGTGCCGCAATGTTCGACGTCGACTACGCCCGGTGGCTGGAGGAAGACAGCCAGCGCATGGCTGAACTGCACGGAGGGCTGCACGCACATCTGCCGGACAG
gactgac putative branch site (score: 9)
tttatttcc CT-rich tract
acatttattt TA-rich tract