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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatatagaactagccacatgtctgtctagatttgtactgtgcccaatgtttgtctttcttcattttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAGGTGGATGTATTCATTGGTGGAATTGGAACAGGTGGAACAATATCTGGTG

Basic information

species Oryza sativa
transcript LOC_Os01g74650.1
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|2443060|gb|C74831.1|C74831
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGCAG                       
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCC-AA--AGgtaacatata ... tttcaagc
EST: gi|701729|gb|D48020.1|D48020
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29655936|gb|CB652211.1|CB652211
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|55410639|gb|CV723015.1|CV723015
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29616466|gb|CB621478.1|CB621478
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|28298176|gb|CB238406.1|CB238406
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29663371|gb|CB659646.1|CB659646
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29687246|gb|CB683521.1|CB683521
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|163927355|gb|EG710663.1|EG710663
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGCAG                       
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCC-AA--AGgtaacatata ... tttcaagc
EST: gi|33801701|gb|CF326722.1|CF326722
EST:     TGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: TGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|38480498|gb|CF964587.1|CF964587
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29655935|gb|CB652210.1|CB652210
EST:     CACCTGATGCCTATATGGTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTTTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29672976|gb|CB669251.1|CB669251
EST:     GATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: GATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29677863|gb|CB674138.1|CB674138
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|87008043|gb|CI297021.1|CI297021
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|58690422|gb|CK079109.1|CK079109
EST:     GCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: GCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29616196|gb|CB621208.1|CB621208
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29644300|gb|CB649307.1|CB649307
EST:     TGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: TGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|29684900|gb|CB681175.1|CB681175
EST:     TGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: TGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|38478600|gb|CF962733.1|CF962733
EST:     CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
EST: gi|38481934|gb|CF965999.1|CF965999
EST:     CACCTGATGCCTATATGCTGGAGCAGTTTGACAACCCTGCCAACCCAAAG                         GTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG
genomic: CACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAG

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: 75 (upstream exon), 52 (downstream exon)
Score: 134

AAAAGGGATGAAGGGGGCTGTAGATAAGGCTACAGAGATTTTAAATAAGACACCTGATGCCTATATGCTGCAGCAGTTTGACAACCCTGCCAACCCAAAGgtaacatata ... tttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAGGTGGATGTATTCATTGGTGGAATTGGAACAGGTGGAACAATATCTGGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtctgtctagatttgtactgtgcccaatgtttgtctttcttcattttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAGGTGGATGTATTCATTGGTGGAATTGGAACAGGTGGAACAATATCTGGTG
                            tgtttgtctttcttca  CT-rich tract
                                        ttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatatagaactagccacatgtctgtctagatttgtactgtgcccaatgtttgtctttcttcattttcaagcagGTACATTATGAGACTACTGGGCCAGAAATCTGGGAGGATTCTAAAGGGAAGGTGGATGTATTCATTGGTGGAATTGGAACAGGTGGAACAATATCTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA