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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttggtaatataattgtaagatctgaaatttacctttggttgctgccaaaacctgatgattccctctcttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGATCGTTGCAGTTTTGCTGGCAGTTTTTATGGCAATCATTACTTTAGTTCG

Basic information

species Oryza sativa
transcript LOC_Os02g04020.1
intron # 12
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|38481030|gb|CF965119.1|CF965119
EST:     TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAG                         ACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
genomic: TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAGgtttgttggt ... ttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
EST: gi|58591675|gb|CF989983.1|CF989983
EST:     TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAG                         ACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
genomic: TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAGgtttgttggt ... ttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
EST: gi|88458341|gb|CI695727.1|CI695727
EST:     ATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAG                         ACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
genomic: ATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAGgtttgttggt ... ttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
EST: gi|58587946|gb|CF986254.1|CF986254
EST:     TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAG                         ACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
genomic: TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAGgtttgttggt ... ttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
EST: gi|29640360|gb|CB645369.1|CB645369
EST:     TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAG                         ACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
genomic: TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAGgtttgttggt ... ttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
EST: gi|58663368|gb|CK052054.1|CK052054
EST:     TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAG                         ACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
genomic: TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAGgtttgttggt ... ttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
EST: gi|29625319|gb|CB630330.1|CB630330
EST:     TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAG                         ACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
genomic: TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAGgtttgttggt ... ttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
EST: gi|58677461|gb|CK066148.1|CK066148
EST:     TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAG                         ACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA
genomic: TGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAGgtttgttggt ... ttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGA

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), 72 (downstream exon)
Score: 70

TCTACTCGCATGCCTGAATACGATGTTCCTGTCGTCGATAAGGCTGTAGATGCAACATGGAAGAGAGAAGTGACTCGAAAGACTGCCTTCTCATCCAAAGgtttgttggt ... ttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGATCGTTGCAGTTTTGCTGGCAGTTTTTATGGCAATCATTACTTTAGTTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaatttacctttggttgctgccaaaacctgatgattccctctcttcaatatagACTCTTCTTTGACAAGCACAGAAAGTTCATCCAATGGCTCTTTGGACCGGATCGTTGCAGTTTTGCTGGCAGTTTTTATGGCAATCATTACTTTAGTTCG
                           acctgat  putative branch site (score: 70)
                                 tgattccctctcttc  CT-rich tract
                                             ttcaatata  TA-rich tract