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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCCCTTGTTGCTTCTAACAGGATAGGAAGGGAAACCGTTGAGACTGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcagcatcttgttcttttactgctggatgtgtaacaaactaaaatcattagcatatggttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g33080.2
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g33080.2 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G073950_T01 (Zea mays), 5'ss of exon 8
GTTCCCCTTGTTGCTTCTAACAGGATAGGAAGGGAAACCGTTGAGACTGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag-catct-tgttcttttactgctggatgt---gtaacaaactaaaatca-----ttagcatatggttgtgcag
|| || ||||||||||| ||| |||| || || ||||| ||||| |||||||||||  | ||| | ||||| ||||  |||||||| ||||| ||||||||| |    | | | | |  || ||||  | |||     || | |    | || ||     | |    |    | |||||
GTCCCTCTTGTTGCTTCCAACCGGATTGGCAGAGAAACTGTTGACACTGAGCATGGCAAGAGCTCGATAACCTTCTATGGGAATTCCTTCATTGCAGgtaatctagctcgtgtatatctttatacttgtagatagaaggttaaatgtcagaaacacgacttcaattgaattctctgcag
















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|88201190|gb|CI201545.1|CI201545
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|88902349|gb|CI374957.1|CI374957
EST:     GGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: GGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|86256202|gb|CI007918.1|CI007918
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|109713088|gb|CI105696.1|CI105696
EST:     AATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: AATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|226698500|gb|GO497078.1|GO497078
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|58600835|gb|CK011363.1|CK011363
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|88830953|gb|CI080377.1|CI080377
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|88201556|gb|CI201911.1|CI201911
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|86499502|gb|CI142135.1|CI142135
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|88220016|gb|CI219576.1|CI219576
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGATAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|29667322|gb|CB663597.1|CB663597
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|66923772|gb|CX110620.1|CX110620
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|29639686|gb|CB644695.1|CB644695
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|4715119|gb|AU056236.1|AU056236
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|86850816|gb|CI338792.1|CI338792
EST:     AAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: AAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|55410603|gb|CV722979.1|CV722979
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|88840913|gb|CI080367.1|CI080367
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|29671593|gb|CB667868.1|CB667868
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|86503748|gb|CI146381.1|CI146381
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTC
EST: gi|88440825|gb|CI693394.1|CI693394
EST:     TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAG                         GGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGT
genomic: TGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGT

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: 73 (upstream exon), 73 (downstream exon)
Score: 103

GTTCCCCTTGTTGCTTCTAACAGGATAGGAAGGGAAACCGTTGAGACTGAGCATGGTGAAAGCACTATAACATTCTTCGGGAATTCATTCATAGCAGgtaatttcag ... ggttgtgcagGGCCAACCGGTGAAATTGTGAAGCTTGCAAATGACAAAGATGAAGACGTTCTTGTAGCAGAGTTCGACTTGGACGAGATCAAGTCTACCAGGCATGGTTG




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