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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGCGGATGCGCGTGGCCTTCACCTGCAATGTGTGCGGGCAGCGAACCACGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgtatagccatataaacggcatggctaccgaatggaaatctgttcactaaattatatccaagttgagctgatcctgattctctcaacattgtt...

Basic information

species Oryza sativa
transcript LOC_Os06g50870.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50870.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G152056_T02 (Zea mays), 5'ss of exon 2
GCGGCGGATGCGCGTGGCCTTCACCTGCAATGTGTGCGGGCAGCGAACCACGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgca-tgtatagcca-tataaacggcatggctaccgaatggaaatctgttcactaaattatatccaagttgagctgatcctgattctctcaacattgtt
|||||| ||||| ||||||||||||||||| |||||||||||||| || ||  | |||||||| || || ||||||||||| || ||||| |||||||||||||| | | | |    | | ||  |     |   |    |   || |        ||   |    |    || || |   | |  |     |  | |   |
GCGGCGCATGCGGGTGGCCTTCACCTGCAACGTGTGCGGGCAGCGTACGACCAGGGCCATCAATCCTCATGCCTACACTGATGGAACTGTGTTTGTTCAGgtatggactatgtgattagtgtatccaatgcgttaataagagtcaagttaagctgata--cttgccctgcctttagttatgcgtattgactgctgcttctgt
















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|218488200|gb|FG957706.1|FG957706
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|89171275|gb|CI040552.1|CI040552
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|87014426|gb|CI283938.1|CI283938
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|87017335|gb|CI301371.1|CI301371
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTG
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTG
EST: gi|89162620|gb|CI099312.1|CI099312
EST:     CACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|88211922|gb|CI211562.1|CI211562
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|88993664|gb|CI112568.1|CI112568
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCGATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|86823325|gb|CI256326.1|CI256326
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|88506378|gb|CI433884.1|CI433884
EST:     AACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: AACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|86528443|gb|CI168649.1|CI168649
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCGTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|88511832|gb|CI439338.1|CI439338
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|86862735|gb|CI331633.1|CI331633
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGGCTGCGGGTGCAACATATTCCATAAGGCTGGTGGACAACCTGAACCTGT
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagT-GCTGCGGGTGCAACATATTCCATAA-GCTGGTGGACAACCTGAACCTGT
EST: gi|88958197|gb|CI095716.1|CI095716
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|86254564|gb|CI059291.1|CI059291
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|88210783|gb|CI210632.1|CI210632
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|88242849|gb|CI240700.1|CI240700
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|88383305|gb|CI540718.1|CI540718
EST:     TCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: TCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|86498184|gb|CI140817.1|CI140817
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
EST: gi|87028314|gb|CI263656.1|CI263656
EST:     CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAG                         TGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC
genomic: CGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTC

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: 72 (upstream exon), 38 (downstream exon)
Score: 6

GCGGCGGATGCGCGTGGCCTTCACCTGCAATGTGTGCGGGCAGCGAACCACGCGCGCCATCAACCCGCACGCCTACACTGACGGCACTGTCTTTGTTCAGgtatgcatgt ... gtcgtaccagTGCTGCGGGTGCAACATATTCCATAAGCTGGTGGACAACCTGAACCTGTTCCATGAGATGAAATGCTATGTTGGTCCAGACTTCCGCTACGAAGGAGATG




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