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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacctatagactgtggcgctcttgttattcttatttgaactataataccttcgtggtagatataagattatcttgtggaaattgtattatagaaatattgaaacattgaattgctgtcttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAGCTTGGGATGGCACCAGTCTATATGGCCTTTCTCCGTTTCATGGGTGATG

Basic information

species Oryza sativa
transcript LOC_Os01g13370.1
intron # 2
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|36355241|gb|CF589206.1|CF589206
EST:     ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACG                         GTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
genomic: ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACGgtaagtacct ... ttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
EST: gi|58662050|gb|CK050730.1|CK050730
EST:     ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACG                         GTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
genomic: ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACGgtaagtacct ... ttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
EST: gi|218487864|gb|FG958478.1|FG958478
EST:     AAAATGCCACCT-GATGCTGACG                         GTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
genomic: AAAATGCCACCTGGATGCTGACGgtaagtacct ... ttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
EST: gi|58598903|gb|CK009431.1|CK009431
EST:     ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACG                         GTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
genomic: ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACGgtaagtacct ... ttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
EST: gi|218492826|gb|FG967876.1|FG967876
EST:     ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACG                         GTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
genomic: ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACGgtaagtacct ... ttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
EST: gi|7274049|gb|C99378.2|C99378
EST:     ATGTCAAGTCCAACCCACGAGAAGTCGAAAATNCCACCTGGATGCTGACG                         GTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
genomic: ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACGgtaagtacct ... ttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
EST: gi|218486724|gb|FG964628.1|FG964628
EST:     ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACG                         GTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
genomic: ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACGgtaagtacct ... ttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
EST: gi|29639877|gb|CB644886.1|CB644886
EST:     ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACG                         GTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG
genomic: ATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACGgtaagtacct ... ttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAG

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), 58 (downstream exon)
Score: 14

GGATGATCACAAAGTTGATATGCATAGTGGTTGCACATTCAACCATAGATATGTCAAGTCCAACCCACGAGAAGTCGAAAATGCCACCTGGATGCTGACGgtaagtacct ... ttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAGCTTGGGATGGCACCAGTCTATATGGCCTTTCTCCGTTTCATGGGTGATG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggaaattgtattatagaaatattgaaacattgaattgctgtcttgtgagtagGTCTTCCACTGTTTCGGGCAATACTTCTGCCTGCACTTTGAGGCCTTCCAGCTTGGGATGGCACCAGTCTATATGGCCTTTCTCCGTTTCATGGGTGATG
                                        ctgtctt  CT-rich tract
     aaattgtattatagaa  TA-rich tract