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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagttgttaacacaatatattttgatttcttagtgcatgaaaatctttaacgcatgcctcttactctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAAGAACATTCGGCATTGATTACGGATGTTCGATTTAGTCCAAGCATGTCAC

Basic information

species Oryza sativa
transcript LOC_Os01g42260.1
intron # 13
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|33794564|gb|CF323169.1|CF323169
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|58665681|gb|CK054367.1|CK054367
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|58608277|gb|CK036310.1|CK036310
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         G-TCTGGTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|33794705|gb|CF323235.1|CF323235
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|66923385|gb|CX110233.1|CX110233
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|58604540|gb|CK015068.1|CK015068
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|32948512|gb|BP185084.1|BP185084
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|58598175|gb|CK008703.1|CK008703
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|218488081|gb|FG946110.1|FG946110
EST:     CGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: CGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
EST: gi|3107649|gb|D43389.1|D43389
EST:     ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAG                         GTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA
genomic: ACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAA

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: 69 (upstream exon), 72 (downstream exon)
Score: 27

TGCTGAAGTTGCGAAGGCACGTGCAAGTGCAACCAAAGTTACCTGTTGTCACTTCTCCTCTGATGGCAAACTGCTCGCTACTGGTGGACATGATAAAAAGgtgcagttgt ... ctctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAAGAACATTCGGCATTGATTACGGATGTTCGATTTAGTCCAAGCATGTCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttgatttcttagtgcatgaaaatctttaacgcatgcctcttactctgcgcagGTTCTTTTATGGTGTACAGAGCCTGCTCTAAAGCCTACATCTTCATTAGAAGAACATTCGGCATTGATTACGGATGTTCGATTTAGTCCAAGCATGTCAC
                                       ctcttac  putative branch site (score: 27)
                                      cctcttactct  CT-rich tract
                  atgaaaatctttaa  TA-rich tract