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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaggggtctctattcctgttgtttcgattaagatcattacaaggttggtttccttgtacctatttgcaatcaatgacagtgttccccattgtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAGAGGCGTTAATTCCAAACTGGCAAGCTCACTTCACCACCATTTGGTTGAG

Basic information

species Oryza sativa
transcript LOC_Os12g04210.1
intron # 2
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|88566902|gb|CI497619.1|CI497619
EST:     CGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAG                         AGATTTGAATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
genomic: CGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAGgtgatgtttc ... gtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
EST: gi|88560777|gb|CI491472.1|CI491472
EST:     CCGTTTGCTGNCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAG                         AGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
genomic: CCGTTTGCTGGCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAGgtgatgtttc ... gtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
EST: gi|88287981|gb|CI512658.1|CI512658
EST:     CCGTTTGCTGGGGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAG                         AGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
genomic: CCGTTTGCTGGCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAGgtgatgtttc ... gtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
EST: gi|88293254|gb|CI500540.1|CI500540
EST:     CCGTTTGCTGGCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAG                         AGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
genomic: CCGTTTGCTGGCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAGgtgatgtttc ... gtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
EST: gi|88566060|gb|CI496777.1|CI496777
EST:     ACGCTGGGGAANACAAGTATGAAGGGCCTGAGTTCAG                         AGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
genomic: ACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAGgtgatgtttc ... gtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
EST: gi|89161882|gb|CI102230.1|CI102230
EST:     CCGTTTGCGGGCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAG                         AGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGGTATCTGGTGGCAAG
genomic: CCGTTTGCTGGCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAGgtgatgtttc ... gtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
EST: gi|88285873|gb|CI512530.1|CI512530
EST:     CCNTTTNCTGGCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAG                         AGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG
genomic: CCGTTTGCTGGCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAGgtgatgtttc ... gtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAG

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: 23 (upstream exon), 28 (downstream exon)
Score: 1

AAGGTGATGGCGGCTCTGCTGACTATGATGTTACTAATGCTTGTTATCACCCGTTTGCTGGCGACGCTGGGGAAGACAAGTATGAAGGGCCTGAGTTCAGgtgatgtttc ... gtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAGAGGCGTTAATTCCAAACTGGCAAGCTCACTTCACCACCATTTGGTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttccttgtacctatttgcaatcaatgacagtgttccccattgtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAGAGGCGTTAATTCCAAACTGGCAAGCTCACTTCACCACCATTTGGTTGAG
                                    ttccccattgttttt  CT-rich tract
                                          attgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaggggtctctattcctgttgtttcgattaagatcattacaaggttggtttccttgtacctatttgcaatcaatgacagtgttccccattgtttttgcagAGATTTGGATCCTCGGTTACAGGTTGCACTGAAAGGATATCTGGTGGCAAGAGGCGTTAATTCCAAACTGGCAAGCTCACTTCACCACCATTTGGTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - -ctgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttccc