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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaatttcggctactccaccatgtcgtcttttgctatgatggtgttgatgttgttactgatttctctgttgcatatgctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g55730.1
intron # 4
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|88302743|gb|CI668589.1|CI668589
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
EST: gi|88739397|gb|CI762905.1|CI762905
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTG
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTG
EST: gi|33381195|gb|CF196538.1|CF196538
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
EST: gi|38470771|gb|CF954902.1|CF954902
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
EST: gi|3767261|gb|AU031371.1|AU031371
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
EST: gi|428826|gb|D24982.1|D24982
EST:     GAAGTNTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTTGCTCCAAGGACCTTGGGATTTGCGCGA-GTGCTTGCACTTGTGTTAA
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTT-GCTCCAAGGACCTTGGGATTTGCGCGAAGTGCT-GCACTTGTGTTAA
EST: gi|88718954|gb|CI742464.1|CI742464
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCA
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCA
EST: gi|88727187|gb|CI750842.1|CI750842
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
EST: gi|88420754|gb|CI564590.1|CI564590
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCACGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
EST: gi|88296284|gb|CI667674.1|CI667674
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCAAGGACCTTGGGATCTGCGCGAAGTGCTGCACTTGTGTTAAAG
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
EST: gi|66932185|gb|CX119033.1|CX119033
EST:     GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGG                         CTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG
genomic: GAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAG

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: 64 (upstream exon), 53 (downstream exon)
Score: 21

TCAGAAGTGTGGGAAACGGAACGTCCGACAGGCGTATCACAACGTCTGCACGGgtgaatttcg ... ctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatgatggtgttgatgttgttactgatttctctgttgcatatgctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG
                      tactgat  putative branch site (score: 21)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatttcggctactccaccatgtcgtcttttgctatgatggtgttgatgttgttactgatttctctgttgcatatgctcaatgcagCTTGCTCCAAGGACCTTGGGATTTGCGCGAAGTGCTGCACTTGTGTTAAAGCGCTTGTCGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC