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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCAGAGAGGATCCTGTCTTCCGTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactctttctgtttggtttccctgtttgatgctgttatgattatatatgacttaggtctttacatatacattttatgtaaactacacctcttttaggaaaaaggaaaatcatgtagcgcatgatgaccaattctgctgtctatgcagatattccttttatgattaatagttctaaaactgcttgattttcag

Basic information

species Oryza sativa
transcript LOC_Os12g07060.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g07060.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G118316_T01 (Zea mays), 5'ss of exon 14
ATCAGAGAGGATCCTGTCTTCCGTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactctttctgtttggtttccctgtttgatgctgttatgattatatatgacttaggtctttacatatacattttatgtaaactaca--cctcttttaggaaaaaggaaaatcatgtagcgcatgatgaccaattctgctgtctatgcagatattccttttatgattaatagttctaaaactgcttgattttcag
 |||||||||| |||   || || |||||||||| |||||||||||||||  || || |||||||||| |||||||    ||||| |      |       | |  |       |   |    ||| ||  |   ||| ||| | | |||    |||||| ||  |     ||                                                                                                  
GTCAGAGAGGACCCTACTTTTCGAAGAGAAGGCATCCATGTGCATGTTGATTCTGTTTTAAGCATTGCTCAGgtcagtcttcttttttccgtttcggttcatcttctatcaaagtacatgcccatg-ctatgccattttcatcttcgtttcccttaaactgcaaacacacatt--------------------------------------------------------------------------------------------------
















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|218480866|gb|FG958004.1|FG958004
EST:     GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAG                         GCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
genomic: GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactc ... tgattttcagGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
EST: gi|218491432|gb|FG970302.1|FG970302
EST:     AAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAG                         GCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
genomic: AAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactc ... tgattttcagGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
EST: gi|218496597|gb|FG964017.1|FG964017
EST:     GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAG                         GCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
genomic: GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactc ... tgattttcagGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
EST: gi|89175720|gb|CI042741.1|CI042741
EST:     GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAG                         GCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
genomic: GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactc ... tgattttcagGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
EST: gi|88228631|gb|CI228111.1|CI228111
EST:     GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCGCAG                         GCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
genomic: GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactc ... tgattttcagGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
EST: gi|58680289|gb|CK068976.1|CK068976
EST:     GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAG                         GCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
genomic: GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactc ... tgattttcagGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
EST: gi|86501480|gb|CI144113.1|CI144113
EST:     GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAG                         GCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
genomic: GTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactc ... tgattttcagGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
EST: gi|58657698|gb|CK046378.1|CK046378
EST:     CCATGTGCATGTTGACGCTATTATAAGCATTGCCCAG                         GCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA
genomic: CCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactc ... tgattttcagGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCA

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: 66 (upstream exon), 57 (downstream exon)
Score: 13

ATCAGAGAGGATCCTGTCTTCCGTAGAGAAGGCAACCATGTGCATGTTGACGCTATTATAAGCATTGCCCAGgtcaccactc ... tgattttcagGCTGTACTAGGTGGAACTGTCACAGTACCAACCCTTACGGGCAACGTTTCAGTCAAG




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