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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGGCTGAGGAGATGGCACCTGCTGCTGCTATAATGAATTTCTTAAACACCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaagaacaattcttgagagaatcaatttatttggtatacttatttcattattttttcagccctgaacttctatgttagtttcttgttgcactttt...

Basic information

species Oryza sativa
transcript LOC_Os09g26400.1
intron # 3
splice site 5'
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|88833722|gb|CI077203.1|CI077203
EST:     CCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: CCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|33808700|gb|CF330235.1|CF330235
EST:     AGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: AGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|33822186|gb|CF336908.1|CF336908
EST:     GATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: GATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|33811910|gb|CF331844.1|CF331844
EST:     ATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: ATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|86494546|gb|CI137179.1|CI137179
EST:     CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|15853332|gb|BI806128.1|BI806128
EST:     GTGGATGGAGACTTAG-ACCCGCTTTGGAAGAATCTCTGCAG                         AATGTGAT-GCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: GTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|88215495|gb|CI215344.1|CI215344
EST:     AGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: AGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|33805222|gb|CF328488.1|CF328488
EST:     CATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: CATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|87026417|gb|CI252371.1|CI252371
EST:     CCATGACAGTGGATGGAGACCTAGAACCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|86505113|gb|CI147746.1|CI147746
EST:     CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|29668875|gb|CB665150.1|CB665150
EST:     CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|87033377|gb|CI188001.1|CI188001
EST:     TTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: TTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|88989954|gb|CI018831.1|CI018831
EST:     ACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: ACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|29663239|gb|CB659514.1|CB659514
EST:     CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|88223604|gb|CI223453.1|CI223453
EST:     CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: CCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
EST: gi|88224649|gb|CI224498.1|CI224498
EST:     AATCTCTGCAG                         AATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG
genomic: AATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCG

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), 64 (downstream exon)
Score: 99

CAGGGCTGAGGAGATGGCACCTGCTGCTGCTATAATGAATTTCTTAAACACCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaaga ... ctattttcagAATGTGATGGCGAATCCTAAGGTGCCTCCAGCTTCAAAGGAAGTCGTTGCGAATCTACCAGTTGTAACCGTGACAGAAGAAATCATAGCTAGATTGGGCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGGCTGAGGAGATGGCACCTGCTGCTGCTATAATGAATTTCTTAAACACCATGACAGTGGATGGAGACCTAGAAGCCGCTTTGGAAGAATCTCTGCAGgtaagaaagaacaattcttgagagaatcaatttatttggtatacttatttcattattttttcagccctgaacttctatgttagtttcttgttgcactttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG