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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctaacaactgacacaaccaaagcattgacattattgacattggcattcttgtttgcatctctgaaagagaacattgttagttgcattctggtttctgaattctgggtttttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAAGTGGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCC

Basic information

species Oryza sativa
transcript LOC_Os08g42470.1
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|88344232|gb|CI655626.1|CI655626
EST:     CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAG                         GATAGCTGCAAGGATGGCAAGAGCAGGAGA
genomic: CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAGGAGA
EST: gi|88296417|gb|CI669193.1|CI669193
EST:     CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAG                         GATAGCTGCAAGGATGGCAAGAGCAG
genomic: CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAG
EST: gi|88341700|gb|CI641452.1|CI641452
EST:     CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAG                         GATAGCTGCAA
genomic: CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAA
EST: gi|88330074|gb|CI652466.1|CI652466
EST:     CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAG                         GATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAA
genomic: CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAA
EST: gi|88573763|gb|CI665532.1|CI665532
EST:     CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAG                         GATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAA
genomic: CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAA
EST: gi|58680598|gb|CK069285.1|CK069285
EST:     CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAG                         GATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAA
genomic: CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAA
EST: gi|163926679|gb|EG713695.1|EG713695
EST:     AGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAG                         GATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAA
genomic: AGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAA
EST: gi|88576571|gb|CI670716.1|CI670716
EST:     CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAG                         GATAGCTGCAAGGATGGCAAG
genomic: CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAAGGATGGCAAG
EST: gi|88347521|gb|CI637461.1|CI637461
EST:     CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAG                         GATAGCTGCAAG
genomic: CATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAAG

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: 39 (upstream exon), 25 (downstream exon)
Score: 2

GGAGGATGCCTCATTGGAGAGCTCAGTGTCTGCAGTTCTTGACACCTCTCCATCTGTGGACAGGAAGAGGAAGGCAGCAGAAGACAGTGCACACTCCAAGgtagctaaca ... ttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAAGTGGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagaacattgttagttgcattctggtttctgaattctgggtttttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAAGTGGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCC
                                          tttttgc  CT-rich tract
        attgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagctaacaactgacacaaccaaagcattgacattattgacattggcattcttgtttgcatctctgaaagagaacattgttagttgcattctggtttctgaattctgggtttttgcaagcagGATAGCTGCAAGGATGGCAAGAGCAGGAGAGGGAAGAAGGCCAGCAAAGAAGTGGAGGAGAAGAGCACCACTGAAGATGAGCCTCCAAAAGGGTACATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG