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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgcacctccaccaaaaaaaaagggatttaaagaaaaactaaggcatggagtccgaaacggcatcctttaaatgttaatttcgtgccttacaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGAGATGTCCCTTACATGATGCAATGTTCTGGGTGCAACCTCAAGCTGGCAA

Basic information

species Oryza sativa
transcript LOC_Os02g50860.1
intron # 7
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|86258963|gb|CI004507.1|CI004507
EST:     AAGCAGAGGGAAAAGAAGTAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|88222418|gb|CI222374.1|CI222374
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|33815648|gb|CF333675.1|CF333675
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCTCGCCAAGGATGCTTTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|88199914|gb|CI199764.1|CI199764
EST:     GGAAAAGAAGAAAAAGAAATCACGACAAGGATGCCCTATGAA                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: GGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|88227817|gb|CI227297.1|CI227297
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|88264281|gb|CI368055.1|CI368055
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|89198220|gb|CI015609.1|CI015609
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|7134953|gb|AU082755.1|AU082755
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|86873773|gb|CI341206.1|CI341206
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|15852212|gb|BI805008.1|BI805008
EST:     CAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: CAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|86497574|gb|CI140207.1|CI140207
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|88837303|gb|CI078663.1|CI078663
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|88374261|gb|CI513348.1|CI513348
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|58679076|gb|CK067763.1|CK067763
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATTGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|86543716|gb|CI183922.1|CI183922
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCCCTATGAA                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|44676265|gb|CR289699.1|CR289699
EST:     AAGCAGAGGGAAAAGAAGAAAAAGGAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATTGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|87029047|gb|CI351350.1|CI351350
EST:     AGCAGAGGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AGCAGA-GGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|86495788|gb|CI138421.1|CI138421
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|89178465|gb|CI015170.1|CI015170
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|86510693|gb|CI153326.1|CI153326
EST:     AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: AAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
EST: gi|86543694|gb|CI183900.1|CI183900
EST:     GGATGCTCTATGAT                         GAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA
genomic: GGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGA

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: 71 (upstream exon), 72 (downstream exon)
Score: 34

TCAAAGGTGTGTTTGATGCTGCTATCAAGGTAGTAATCCAGCCTCCAACTAAGCAGAGGGAAAAGAAGAAAAAGAAATCACGACAAGGATGCTCTATGATgtaagtatat ... acaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGAGATGTCCCTTACATGATGCAATGTTCTGGGTGCAACCTCAAGCTGGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggagtccgaaacggcatcctttaaatgttaatttcgtgccttacaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGAGATGTCCCTTACATGATGCAATGTTCTGGGTGCAACCTCAAGCTGGCAA
                                        gccttac  putative branch site (score: 34)
                      tttaaatgttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgcacctccaccaaaaaaaaagggatttaaagaaaaactaaggcatggagtccgaaacggcatcctttaaatgttaatttcgtgccttacaactgcagGAACATGTTCCGTGGAAGGAAAATGTCATGCTTCAAATCCTGATTGATCGAGATGTCCCTTACATGATGCAATGTTCTGGGTGCAACCTCAAGCTGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - cctccac
- - - - - - -caaaaaa
- - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - gcatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcctt