Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACTGATGCTTCCGGTTCTGGCAACAACAATGCAACTGGAGGTCATCGTGGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagttactctatagcttttatatttttttttgtaagatgattacgctaatgttgatacttttacatgctctaccaacagccatattagttttcgag...

Basic information

species Oryza sativa
transcript LOC_Os06g01200.1
intron # 1
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|86527056|gb|CI167262.1|CI167262
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|88484059|gb|CI421330.1|CI421330
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|88281116|gb|CI402314.1|CI402314
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|88331648|gb|CI675996.1|CI675996
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|86493718|gb|CI136351.1|CI136351
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|88520591|gb|CI448245.1|CI448245
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|87015797|gb|CI279549.1|CI279549
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|89196852|gb|CI402606.1|CI402606
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|88225888|gb|CI225804.1|CI225804
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|88222550|gb|CI222506.1|CI222506
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|86497262|gb|CI139895.1|CI139895
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|86493178|gb|CI135811.1|CI135811
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|86421102|gb|CI057091.1|CI057091
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAAGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|86497862|gb|CI140495.1|CI140495
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
EST: gi|86505214|gb|CI147847.1|CI147847
EST:     GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAG                         GGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC
genomic: GGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGC

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: 74 (upstream exon), 68 (downstream exon)
Score: 10

CTACTGATGCTTCCGGTTCTGGCAACAACAATGCAACTGGAGGTCATCGTGGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagtta ... ttgcttgcagGGGCGAGGGACATTGTTTGGAGAAGAGGTGCGCCGCGGCAATGAAGCTAGCCTATTCCGTTCTATTCACCTATCAATGACGAGAAGAAATGTTGGATTTT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACTGATGCTTCCGGTTCTGGCAACAACAATGCAACTGGAGGTCATCGTGGCTACGATGATCTTGACTGAAGAGCATCGGACAAAGAGGGGATGAGGAGgtataagttactctatagcttttatatttttttttgtaagatgattacgctaatgttgatacttttacatgctctaccaacagccatattagttttcgag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG