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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcataacgtttaccaccaattatagtatttgcacttgtggtacctggcaaaatctaggatcacatgtggtcttacagagttacacctctacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCAGGATTTGTACTTTGATGCATCATGCATCCACTGAATGTCATTCAGTCCC

Basic information

species Oryza sativa
transcript LOC_Os06g12220.1
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|86853054|gb|CI324756.1|CI324756
EST:     AAATTATCGATGCTAGAACAATCTTTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATGTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|9886252|gb|AU102145.1|AU102145
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|88443978|gb|CI552523.1|CI552523
EST:     AAATTATCGATGGTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|88452189|gb|CI552897.1|CI552897
EST:     AAATTATCGATGGTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|86852803|gb|CI323112.1|CI323112
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|88428269|gb|CI562535.1|CI562535
EST:     ATCGATGGTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATTTATCTGACTTCA
genomic: ATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|88366357|gb|CI553755.1|CI553755
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|88447454|gb|CI544328.1|CI544328
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|109711581|gb|CI013186.1|CI013186
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|396941186|gb|HO188395.1|HO188395
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|88445836|gb|CI549559.1|CI549559
EST:     CTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: CTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|117221019|gb|CT852619.1|CT852619
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAA                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|88474000|gb|CI411271.1|CI411271
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|88969824|gb|CI383326.1|CI383326
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|33662702|gb|CF293669.1|CF293669
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATTTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|89191141|gb|CI392994.1|CI392994
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|88452285|gb|CI555362.1|CI555362
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
EST: gi|3766944|gb|AU031054.1|AU031054
EST:     AAATTATCGATGCTAGAACAATCTGTTGTTCNCGACCACATACTCATCAG                         GTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA
genomic: AAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCA

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: 27 (upstream exon), 75 (downstream exon)
Score: 27

ATGGCCAGGGCTGAAAGAGAATCATGGGGCGAAAATCCATTCTATGATAAAAATTATCGATGCTAGAACAATCTGTTGTTCACGACCACATACTCATCAGgttagcataa ... tacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCAGGATTTGTACTTTGATGCATCATGCATCCACTGAATGTCATTCAGTCCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggcaaaatctaggatcacatgtggtcttacagagttacacctctacttcccagGTTGCCGGCTTATCTGGGTTGAGGATAAAGCTTTCCATGTATCTGACTTCAGGATTTGTACTTTGATGCATCATGCATCCACTGAATGTCATTCAGTCCC
                         gtcttac  putative branch site (score: 27)
                                       cacctctacttccc  putative PPT
     aaaatcta  TA-rich tract