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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcagcatctattttggttattgatccaccaagtgcaagttgtttactccaaaatatttcagaataaggctactgacattgctttgatgtattctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGCCTACTTCATGTTGATATCAGTATGCTCGGCTATATCAGTGGCAGCTTTT

Basic information

species Oryza sativa
transcript LOC_Os11g44940.1
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|3106808|gb|D42533.1|D42533
EST:     CTTCATCGTCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
genomic: CTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|86847458|gb|CI287028.1|CI287028
EST:     TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
genomic: TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|13420403|gb|AU174493.1|AU174493
EST:     TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
genomic: TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|88294668|gb|CI602388.1|CI602388
EST:     TGGGGCGCCGAGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTAAAAGGGAAAATGTTCCCAGC
genomic: TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|88369565|gb|CI582760.1|CI582760
EST:     TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
genomic: TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|88468854|gb|CI696856.1|CI696856
EST:     TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
genomic: TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|58597504|gb|CK008032.1|CK008032
EST:     TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
genomic: TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|58590843|gb|CF989151.1|CF989151
EST:     TGGGGCGCCGAGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAG
genomic: TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAG
EST: gi|86601370|gb|CI251744.1|CI251744
EST:     GCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
genomic: GCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|86906360|gb|CI294483.1|CI294483
EST:     TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGT-CCCAGC
genomic: TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|5038677|gb|AU070787.1|AU070787
EST:     TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
genomic: TGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
EST: gi|86601410|gb|CI253738.1|CI253738
EST:     CGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAA                         GTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC
genomic: CGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGC

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

CCGGGGTCGCGGCGGCGAGGCTGGCGCACGTCCTCTGCTTCGCCACCGCCTGGGGCGCCGCGCTCTGGGTCACCTTCATCGGCGGCATCGTCATGTTCAAgtaaagagct ... attctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGCCTACTTCATGTTGATATCAGTATGCTCGGCTATATCAGTGGCAGCTTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actccaaaatatttcagaataaggctactgacattgctttgatgtattctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGCCTACTTCATGTTGATATCAGTATGCTCGGCTATATCAGTGGCAGCTTTT
                                            tattcttt  CT-rich tract
     aaaatatttcagaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcagcatctattttggttattgatccaccaagtgcaagttgtttactccaaaatatttcagaataaggctactgacattgctttgatgtattctttaagGTATTTGCCAAGGCACCAGTTTGGGAGTCTACAAGGGAAAATGTTCCCAGCCTACTTCATGTTGATATCAGTATGCTCGGCTATATCAGTGGCAGCTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
tgcagca
- - - - - - - - - - - gatccac
- - - - - - - - - - - - - - - - gtgcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaataag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctttg