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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaacagttgctccaatttttatgctatatcttgctgcaaaattgtgatttcttaggagcctgctttatgtttgtaatgttctatacttgatcaggtgagatcataagTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAGTTATTCAGGAGAAAAAGGTGCTTGAGGTTCATATTGAGAAGGGAATGCAACATGGCCAAAAA

Basic information

species Oryza sativa
transcript LOC_Os04g46390.3
intron # 5
splice site 3'
intron type U2

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|29644137|gb|CB649144.1|CB649144
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGGTGAGATCATAAG             
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGC--A-G---A---G-GATC---AGgtatgcaaca ..
EST: gi|29639999|gb|CB645008.1|CB645008
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29639999|gb|CB645008.1|CB645008
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29643236|gb|CB648243.1|CB648243
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29643236|gb|CB648243.1|CB648243
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29643291|gb|CB648298.1|CB648298
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29643291|gb|CB648298.1|CB648298
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29678521|gb|CB674796.1|CB674796
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29678521|gb|CB674796.1|CB674796
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|25798325|gb|CA754286.1|CA754286
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGGTGAGATCATAAG             
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGC--A-G---A---G-GATC---AGgtatgcaaca ..
EST: gi|29668764|gb|CB665039.1|CB665039
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29668764|gb|CB665039.1|CB665039
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29637040|gb|CB642049.1|CB642049
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29637040|gb|CB642049.1|CB642049
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29645124|gb|CB650131.1|CB650131
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         TGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAGTTATTCAGGAGAA
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataagTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAGTTATTCAGGAGAA
EST: gi|29685950|gb|CB682225.1|CB682225
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGGTGAGATCATAAG             
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGC--A-G---A---G-GATC---AGgtatgcaaca ..
EST: gi|29614042|gb|CB619055.1|CB619055
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29614042|gb|CB619055.1|CB619055
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29683515|gb|CB679790.1|CB679790
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGGTGAGATCATAAG             
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGC--A-G---A---G-GATC---AGgtatgcaaca ..
EST: gi|29680639|gb|CB676914.1|CB676914
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29680639|gb|CB676914.1|CB676914
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAG                         G
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataag-
EST: gi|29670817|gb|CB667092.1|CB667092
EST:     AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGGTGAGATCATAAG             
genomic: AGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGC--A-G---A---G-GATC---AGgtatgcaaca ..

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: 75 (upstream exon), 50 (downstream exon)
Score: 26

TATGGTTGTCATGGTGTAGGAATGAGGAATATAATGCGACAGATAGGACTAGGCATGATTCAACATATGCAGACTGTCTGTCCTGAATGCAGAGGATCAGgtatgcaaca ... agatcataagTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAGTTATTCAGGAGAAAAAGGTGCTTGAGGTTCATATTGAGAAGGGAATGCAACATGGCCAAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggagcctgctttatgtttgtaatgttctatacttgatcaggtgagatcataagTGACAGGGATAAATGCACAAACTGCAGAGCTAGCAAAGTTATTCAGGAGAAAAAGGTGCTTGAGGTTCATATTGAGAAGGGAATGCAACATGGCCAAAAA
                                acttgat  putative branch site (score: 26)
           tttatgtttgtaat  TA-rich tract