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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGACGCTGGTCAACCTCCAGGACATCTCGCTCGAGATGATCCTGGATGACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccaccgtgtccctgcctcgcgacaatcggtgacgcatccatcagagtactaccagaccatgagcaatgttcctgatcaagcctgtttggggtctgtctatcttctttcag

Basic information

species Oryza sativa
transcript LOC_Os12g41860.1
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g41860.1 (Oryza sativa), 5'ss of exon 17
lower sequence: AT1G30490.1 (Arabidopsis thaliana), 5'ss of exon 17
GACGACGCTGGTCAACCTCCAGGACATCTCGCTCGAGATGATCCTGGATGACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccaccgtgtccctgcctcgcgacaatcggtgacgcatccatcagagtactaccagaccatgagcaatgttcctgatcaagcctgtttggggtctgtctatcttctttcag
 || || || ||    || ||||| ||   |||||| |  |  || ||||||   || || |  || || ||||| |||||| ||||||||||||||||||| ||||     | | |  ||        | ||  | | |  |    | |   | ||| |      ||   |   | ||  |||                                
AACTACACTTGTGGCACTTCAGGATATAATGCTCGACAAAACACTTGATGACTCTGGTCGTAGAGCTCTTTGCTCCGAGTTCGCCAAGATCATGCAGCAGgttaaac----attttctagct-------agtcttttaagtctttccctggaaaatactaagtttggattgaatcttct--tcag-------------------------------
















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|86597684|gb|CI274675.1|CI274675
EST:     ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAG                         GGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
genomic: ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
EST: gi|86827198|gb|CI270885.1|CI270885
EST:     ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAG                         GGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
genomic: ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
EST: gi|88246775|gb|CI246624.1|CI246624
EST:     ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAG                         GGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
genomic: ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
EST: gi|88835093|gb|CI370396.1|CI370396
EST:     ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAG                         GGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
genomic: ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
EST: gi|88903995|gb|CI006228.1|CI006228
EST:     ACGAGGGCCGGAAGACGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAG                         GGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
genomic: ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
EST: gi|58668065|gb|CK056751.1|CK056751
EST:     ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAG                         GGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
genomic: ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
EST: gi|88268442|gb|CI378377.1|CI378377
EST:     GCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAG                         GGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
genomic: GCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
EST: gi|87036350|gb|CI190972.1|CI190972
EST:     ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAG                         GGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
genomic: ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG
EST: gi|66924702|gb|CX111550.1|CX111550
EST:     ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAG                         GGTTTCACCTATCTCCCTGGAAGCGTCTGCAAGTCGAGCATGGGGCGGCAG
genomic: ACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAG

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: 70 (upstream exon), 62 (downstream exon)
Score: 10

GACGACGCTGGTCAACCTCCAGGACATCTCGCTCGAGATGATCCTGGATGACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccac ... cttctttcagGGTTTCACCTATCTCCCTGGAGGCGTCTGCAAGTCGAGCATGGGGCGGCAGGCATCGTATGAGCAGGCGGTGGCGTGGAAGGTTCTTAGCGACGACGACG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGACGCTGGTCAACCTCCAGGACATCTCGCTCGAGATGATCCTGGATGACGAGGGCCGGAAGGCGCTGTGCTCGGAGTTCCCCAAGATCATGCAGCAGgtaaaaccaccgtgtccctgcctcgcgacaatcggtgacgcatccatcagagtactaccagaccatgagcaatgttcctgatcaagcctgtttggggtctgtctatcttctttcag

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