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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cactagaaactatctgaggactactgttctgcttaccattgttttctgcagtaaagtgatttatatgttttttgatataatctctttttgcgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCTTCTGGTGGAAATGGGGGAGTAAAAGGCTACTGTACGAAGTGCTATTTGA

Basic information

species Oryza sativa
transcript LOC_Os07g06980.2
intron # 15
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|88836451|gb|CI078348.1|CI078348
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88908189|gb|CI090784.1|CI090784
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88464129|gb|CI509613.1|CI509613
EST:     GGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: GGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88379281|gb|CI508799.1|CI508799
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88374012|gb|CI510830.1|CI510830
EST:     TTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATNCAGGAGGGGCAGGACCCT
genomic: TTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|58689470|gb|CK078157.1|CK078157
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88253934|gb|CI352560.1|CI352560
EST:     ATCCTTTGCATCAGTTCTGGCACTACAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88318764|gb|CI508360.1|CI508360
EST:     TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88563232|gb|CI493949.1|CI493949
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88849201|gb|CI087723.1|CI087723
EST:     ATCCTTTGCATCAGTTCGGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGGAAAAGGAAGCATGCAGGAGGGGCAGGACCC
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGAT-GAAAAGGAAGCATGCAGGAGGGGCAGGACCC
EST: gi|88562711|gb|CI493428.1|CI493428
EST:     GCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: GCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88564989|gb|CI495706.1|CI495706
EST:     CTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: CTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|89183692|gb|CI046257.1|CI046257
EST:     TCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: TCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|58681037|gb|CK069724.1|CK069724
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|86868864|gb|CI334236.1|CI334236
EST:     GGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAGGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: GGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|86426424|gb|CI071521.1|CI071521
EST:     TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGNNNNNNNCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGG-TTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88565171|gb|CI495888.1|CI495888
EST:     CACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: CACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|86874298|gb|CI335910.1|CI335910
EST:     TGGCAGTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGTCAGGACCCT
genomic: TGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88294040|gb|CI510348.1|CI510348
EST:     TTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: TTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88561850|gb|CI492567.1|CI492567
EST:     TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88265021|gb|CI368795.1|CI368795
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88523857|gb|CI451719.1|CI451719
EST:     CAGTTCTGGCACTGCAGCGGTCGGNNNNNNNCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: CAGTTCTGGCACTGCAGCGGTCGG-TTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88318994|gb|CI510789.1|CI510789
EST:     GTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: GTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88262774|gb|CI366548.1|CI366548
EST:     TTTTCCAGATATA                         CCACTGAA-TAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCA-GACCCT
genomic: TTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|86415170|gb|CI069573.1|CI069573
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|86881379|gb|CI322516.1|CI322516
EST:     ATCCTTTGCATCAGTTCTGGCACTGCACCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88845329|gb|CI084254.1|CI084254
EST:     TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGNNNNNNNCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGG-TTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88539932|gb|CI469930.1|CI469930
EST:     AGTTCTGGCACTGCAGCGGTCGGNNNNNNNCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: AGTTCTGGCACTGCAGCGGTCGG-TTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|89194187|gb|CI116624.1|CI116624
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88272674|gb|CI386529.1|CI386529
EST:     TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGNNNNNNNCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: TCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGG-TTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|22306323|gb|BQ907545.1|BQ907545
EST:     ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         GCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88562524|gb|CI493241.1|CI493241
EST:     TGGCACTGCAGCGGTCGGTTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: TGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|88546533|gb|CI476181.1|CI476181
EST:     TTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: TTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
EST: gi|86877970|gb|CI320774.1|CI320774
EST:     ATCCTGGGCATCAGTTCTGGCACTGCAGC-GTCGGGTTTTTCCAGATATA                         CCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT
genomic: ATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCT

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), 66 (downstream exon)
Score: 9

GTCTTACAAGTCCTGAGTATCCAGCAGCAATTTTGGCCAGTTTTAGTTCCATCCTTTGCATCAGTTCTGGCACTGCAGCGGTCGGTTTTTTCCAGATATAgtgagtgaca ... cgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCTTCTGGTGGAAATGGGGGAGTAAAAGGCTACTGTACGAAGTGCTATTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcagtaaagtgatttatatgttttttgatataatctctttttgcgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCTTCTGGTGGAAATGGGGGAGTAAAAGGCTACTGTACGAAGTGCTATTTGA
                        ttttgat  putative branch site (score: 9)
                                   tctctttttgc  putative PPT
             atttatatgttttttg  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cactagaaactatctgaggactactgttctgcttaccattgttttctgcagtaaagtgatttatatgttttttgatataatctctttttgcgatgtgtagCCACTGAAGTAAACAAGATGAAAAGGAAGCATGCAGGAGGGGCAGGACCCTTCTGGTGGAAATGGGGGAGTAAAAGGCTACTGTACGAAGTGCTATTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - -gaaacta
- - - - - - - - - -actactg
- - - - - - - - - - - - - ttctgct
- - - - - - - - - - - - - - - - - - - - - tttctgc