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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatgcgataatgtatgccacctgctgtctacttttgtgttggacaaattaacatacaatgctactggaattgattcctctgtttcgattcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCCGAGGCGATCTGTGTATTTGAACAATGCAACTACTGTTTAGCTGTTGGCC

Basic information

species Oryza sativa
transcript LOC_Os01g57450.1
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|88460712|gb|CI534584.1|CI534584
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|88428159|gb|CI557053.1|CI557053
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|86507174|gb|CI149807.1|CI149807
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGGAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|86546900|gb|CI187106.1|CI187106
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGGGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|87006957|gb|CI275265.1|CI275265
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|88491095|gb|CI428367.1|CI428367
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAAC-GAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGGTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|86538813|gb|CI179019.1|CI179019
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         TTAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|88384200|gb|CI548541.1|CI548541
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|218498329|gb|FG970102.1|FG970102
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|88478936|gb|CI416207.1|CI416207
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAAGTGAGGTAATGCATCTGGAGCGCAAGGAAGACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|86599519|gb|CI251477.1|CI251477
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|88217788|gb|CI217637.1|CI217637
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|29637929|gb|CB642938.1|CB642938
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|88199468|gb|CI199318.1|CI199318
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGGGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
EST: gi|86542399|gb|CI182605.1|CI182605
EST:     TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAG                         AAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC
genomic: TGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCC

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), 75 (downstream exon)
Score: 62

GCTGCAGGTGCCGACGGGGAGGCAGCAGGGCCAACAGATGAGCTGCACACTGTGCCTGAGGATGAACCTGTGTATCATGATGCACCTGATGTGCAGAAAGgtttgccctt ... ttcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCCGAGGCGATCTGTGTATTTGAACAATGCAACTACTGTTTAGCTGTTGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaattaacatacaatgctactggaattgattcctctgtttcgattcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCCGAGGCGATCTGTGTATTTGAACAATGCAACTACTGTTTAGCTGTTGGCC
     ttaacata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatgcgataatgtatgccacctgctgtctacttttgtgttggacaaattaacatacaatgctactggaattgattcctctgtttcgattcactgcagAAAACTGAGGTAATGCATCTGGAGCGCAAGGAAAACGTGAGAGGCTTGCCCGAGGCGATCTGTGTATTTGAACAATGCAACTACTGTTTAGCTGTTGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - -tgtatgc
- - - - - - - - - - - - tgctgtc
- - - - - - - - - - - - - - - - - - -tgtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - catacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctact