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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttactgcaactatcatgtaattcggtacttattacccctcaactgtatggatttgtttatgtgcatggcttttaacacaggctcaatatttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG

Basic information

species Oryza sativa
transcript LOC_Os03g11614.1
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|55408883|gb|CV721259.1|CV721259
EST:     AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
genomic: AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
EST: gi|58684925|gb|CK073612.1|CK073612
EST:     AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAG
genomic: AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAG
EST: gi|86822847|gb|CI251887.1|CI251887
EST:     AACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
genomic: AACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
EST: gi|58598071|gb|CK008599.1|CK008599
EST:     AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAG
genomic: AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAG
EST: gi|5004673|gb|AU069848.1|AU069848
EST:     AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
genomic: AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
EST: gi|8857332|gb|AU094650.1|AU094650
EST:     AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
genomic: AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
EST: gi|7378312|gb|AU088583.1|AU088583
EST:     AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
genomic: AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
EST: gi|86493995|gb|CI136628.1|CI136628
EST:     AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
genomic: AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
EST: gi|58602799|gb|CK013327.1|CK013327
EST:     AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
genomic: AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
EST: gi|32948430|gb|BP185002.1|BP185002
EST:     AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAG                         AACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
genomic: AGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG

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: 42 (upstream exon), 75 (downstream exon)
Score: 295

AAATATTCTTGGTGAGGATTTGGGCCCACTAAGCATGAAGGAGCTGGAGCAGCTTGAGAACCAGATAGAAGTATCCCTCAAACAAATCAGGTCAAGAAAGgtaaaaatgt ... atttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtatggatttgtttatgtgcatggcttttaacacaggctcaatatttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG
                           ttttaac  putative branch site (score: 295)
                                            tatttct  putative PPT
        atttgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttactgcaactatcatgtaattcggtacttattacccctcaactgtatggatttgtttatgtgcatggcttttaacacaggctcaatatttctgcagAACCAAGCACTGCTTGATCAGCTGTTTGATCTGAAGAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - tactgca
- - - - - - - atcatgt
- - - - - - - - - - - - - - - - - - - - - - -ctgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacaggc