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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACCGTTCCTCGCCGTGGCTAACAAAACCAGCAACCCATTGTTCAGGGGGCTCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgtcggcataaacccaaagccactgcacgatttttcgctgaacaccggctgatgacgacgaaacacgtgtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os02g44860.1
intron # 2
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|58680170|gb|CK068857.1|CK068857
EST:     TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
genomic: TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
EST: gi|58675238|gb|CK063925.1|CK063925
EST:     TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
genomic: TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
EST: gi|58684193|gb|CK072880.1|CK072880
EST:     TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
genomic: TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
EST: gi|2443055|gb|C74826.1|C74826
EST:     CAGGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTTCAANA                         GGTCA-TCCATCATCCCAATGAGCAAGCAATTGCAGCAATT
genomic: CAGGG-AACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACT-CAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATT
EST: gi|2442975|gb|C74746.1|C74746
EST:     CAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
genomic: CAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
EST: gi|8336456|gb|BE040905.1|BE040905
EST:     TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGGCAAGCA-GTGCAGCAATTCGCCGGCGT
genomic: TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAG-CAAGCAAGTGCAGCAATTCGCCGCCGT
EST: gi|163928198|gb|EG714326.1|EG714326
EST:     TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
genomic: TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
EST: gi|58683450|gb|CK072137.1|CK072137
EST:     AACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
genomic: AACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
EST: gi|58588140|gb|CF986448.1|CF986448
EST:     CTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCGCGT
genomic: CTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGC-CGT
EST: gi|58599763|gb|CK010291.1|CK010291
EST:     TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
genomic: TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTG
EST: gi|58659317|gb|CK047997.1|CK047997
EST:     TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACA                         GGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCCGT
genomic: TCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCC-GT

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), 67 (downstream exon)
Score: 9

ACCGTTCCTCGCCGTGGCTAACAAAACCAGCAACCCATTGTTCAGGGGGCTCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgt ... gtgtgtgcagGGTCAATCCATCATCCCAATGAGCAAGCAAGTGCAGCAATTCGCCGCCGTGCAACGCAACATCTCAGCACGCATCAGCCAGCAAGCCGCTGACACCGTGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCGTTCCTCGCCGTGGCTAACAAAACCAGCAACCCATTGTTCAGGGGGCTCCAGGGAACAAACTTTGCCTCTGCAGGATCAGGCATTCTCGACTCAACAgtaagcacgtcggcataaacccaaagccactgcacgatttttcgctgaacaccggctgatgacgacgaaacacgtgtgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG