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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttttgtgccaactatggtagatatattaatgtcgaaaactcatccactcggtggagttttttttaaagaacttttttaagtttactttccagtgtaatagaagctaactgtggtgttagcaccttttttttttttgcagaaggcattcttaattgatttcctgtttatgatttgcatttgttctgcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGGGAGTTGCCTGTGAGTATCAAAATCAGCATTATATTATCAATTTCTAGAC

Basic information

species Oryza sativa
transcript LOC_Os03g01750.7
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g01750.6 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G052546_T04 (Zea mays), 3'ss of exon 9
gtatgcttttgtgccaactatggtagatatattaatgtcgaaaactcatccactcggtggagttttttttaaagaacttttttaagtttactttccagtgtaatagaagctaactgtggt-gttagcaccttttttttttttgcagaaggcattcttaattgatttcctgtttatgatttgcatttgttctgcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGGGAGTTGCCTGTGAGTATCAAAATCAGCATTATATTATCAATTTCTAGAC
                                                                                                 | |  ||    | | |    |    |   |   ||   | |||||     |   | ||            || |   ||||||  |||| | ||      ||||| |||||||||||||||  |  |||||||| ||||||||| ||||||||  |||||||||                                        
------------------------------------------------------------------------------------------------ggggctatgatggttgaacaagcccatctacctgttacatgtttttattagatataatcccgtgcataagtctctaactgatttctatttatcct-----ttcagAGAATTCCTTTGACATATGATGAGGAGAAAGGAGCTTGGTTTCTTGAGAAAGAGTTGCCT----------------------------------------
















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|58656051|gb|CK044731.1|CK044731
EST:     ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAG                         ATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG
genomic: ATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGG




















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: 45 (upstream exon), 50 (downstream exon)
Score: 5

CTGACAGGCTTATCAAAGAATTCCATCACTTTGAAGTGGGAAAGTGATAGTTGTTCTTCTGTTGAAATTTCTGGGCTTGATGTCGGGTGGGGACAGgtatgctttt ... gcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGGGAGTTGCCTGTGAGTATCAAAATCAGCATTATATTATCAATTTCTAGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggcattcttaattgatttcctgtttatgatttgcatttgttctgcttactcagATAATTCCTTTGACATACAACAAGGAGAAAAGAGCTTGGTATCTTGAGAGGGAGTTGCCTGTGAGTATCAAAATCAGCATTATATTATCAATTTCTAGAC
                                            tgcttac  putative branch site (score: 5)
                                         ttctgctt  CT-rich tract
     attcttaattgattt  TA-rich tract