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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcagtatcacctactcccatcccatccatggtggcgcgcggtggctgctctctctctctctcagactcactcagatcgatctgtggatggatggattgaattgaatggcagGGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCCTCCAACTCCAACCACGACGACGACCTCGCCGGCGCCGACTCCTAGCTAG

Basic information

species Oryza sativa
transcript LOC_Os01g74350.1
intron # 1
splice site 3'
intron type U2

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|88469980|gb|CI407251.1|CI407251
EST:     TCCTCCTCGTCTGGGCTGCCGCGCTCCAG                         GGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
genomic: TCCTCCTCGTCTGGGCTGCCGCGCTCCAGgtatcagtat ... tgaatggcagGGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
EST: gi|163925462|gb|EG713351.1|EG713351
EST:     AGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAG                         GGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
genomic: AGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAGgtatcagtat ... tgaatggcagGGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
EST: gi|66917643|gb|CX104491.1|CX104491
EST:     AGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAG                         TGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
genomic: AGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAGgtatcagtat ... tgaatggcagGGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
EST: gi|88477957|gb|CI415228.1|CI415228
EST:     AGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAG                         GGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
genomic: AGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAGgtatcagtat ... tgaatggcagGGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
EST: gi|58592900|gb|CF991208.1|CF991208
EST:     AGAGGTGCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAG                         GGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
genomic: AGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAGgtatcagtat ... tgaatggcagGGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
EST: gi|3763347|gb|AU030099.1|AU030099
EST:     AGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTG-C-CGCTCCAG                         GGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC
genomic: AGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAGgtatcagtat ... tgaatggcagGGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCC

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: 75 (upstream exon), 50 (downstream exon)
Score: 8

AGGGGTGGAATTGAAGAAGATGGGGACGATGAGGAGGGTGGTGAAGGAGAAGAGGTTCTGGGTCGCCTCCTTCCTCCTCGTCTGGGCTGCCGCGCTCCAGgtatcagtat ... tgaatggcagGGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCCTCCAACTCCAACCACGACGACGACCTCGCCGGCGCCGACTCCTAGCTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctctcagactcactcagatcgatctgtggatggatggattgaattgaatggcagGGGCACATGATGTGGATGCAGCGCCAGGACGCCTTCAAGCAAAAGTTCCCCTCCAACTCCAACCACGACGACGACCTCGCCGGCGCCGACTCCTAGCTAG
       gactcac  putative branch site (score: 8)
                                      attgaatt  TA-rich tract