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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcttacctcatctcccctgatcgctccgatttatggattgcaaggccgtcgtgcgaatttttgagattttcggggtcggatttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCTGACGGAGTCGGATCTGAAGGGGAAGAAGGTGTTCCTCCGCGCCGATCTG

Basic information

species Oryza sativa
transcript LOC_Os06g45710.1
intron # 1
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|58589338|gb|CF987646.1|CF987646
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCC-TTGTGGTGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|33658427|gb|CF281040.1|CF281040
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|58677408|gb|CK066095.1|CK066095
EST:     GGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: GGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|58668078|gb|CK056764.1|CK056764
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|88313529|gb|CI671652.1|CI671652
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|88327337|gb|CI645117.1|CI645117
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|88392654|gb|CI625476.1|CI625476
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|29675440|gb|CB671715.1|CB671715
EST:     GCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: GCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|88393098|gb|CI616582.1|CI616582
EST:     GAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: GAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|33813054|gb|CF332417.1|CF332417
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|33688490|gb|CF316729.1|CF316729
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|58689757|gb|CK078444.1|CK078444
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|88332298|gb|CI656167.1|CI656167
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|86849751|gb|CI301639.1|CI301639
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|88325004|gb|CI645019.1|CI645019
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|88353244|gb|CI654510.1|CI654510
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
EST: gi|88338304|gb|CI655493.1|CI655493
EST:     CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCNNNNNNNNGGCAG                         CGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT
genomic: CGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCT

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), 75 (downstream exon)
Score: 35

AGCACCTTCCCGTGCCTTCCTCGTATCCAAACTCTCCTTTACCCCAATCTCGTGAGCGGCGACGAACTTTGCCACCGATTTCGATCCTTTTTTTTGGCAGgtaaatctta ... tttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCTGACGGAGTCGGATCTGAAGGGGAAGAAGGTGTTCCTCCGCGCCGATCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattgcaaggccgtcgtgcgaatttttgagattttcggggtcggatttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCTGACGGAGTCGGATCTGAAGGGGAAGAAGGTGTTCCTCCGCGCCGATCTG
                    aatttttgagatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatcttacctcatctcccctgatcgctccgatttatggattgcaaggccgtcgtgcgaatttttgagattttcggggtcggatttggtgcagCGTGTAGTGACGCGAGAGAGAAATGGCGAGCAAGAGGAGCGTGGGCACCCTGACGGAGTCGGATCTGAAGGGGAAGAAGGTGTTCCTCCGCGCCGATCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG