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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgatattgtactgtagtagccattattttctcctgttcataagctaacattttcttgatgttagtatttctgatggaaactggcatttgtgttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTCTGATCTGATGGCCAACATTAACATGGCAGATACTGTTCCTTCCTGTGAT

Basic information

species Oryza sativa
transcript LOC_Os11g43860.1
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|88430920|gb|CI571910.1|CI571910
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|66926808|gb|CX113656.1|CX113656
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|88425469|gb|CI567189.1|CI567189
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|33677911|gb|CF306150.1|CF306150
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTT
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|58586056|gb|CF984364.1|CF984364
EST:     CCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: CCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|88338768|gb|CI660539.1|CI660539
EST:     GCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: GCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|88719264|gb|CI742774.1|CI742774
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|87023581|gb|CI286332.1|CI286332
EST:     GATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: GATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|58687350|gb|CK076037.1|CK076037
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|58662427|gb|CK051113.1|CK051113
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|33664264|gb|CF295231.1|CF295231
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|88364505|gb|CI644583.1|CI644583
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|88573161|gb|CI664732.1|CI664732
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|88301866|gb|CI667712.1|CI667712
EST:     GCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: GCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
EST: gi|58591783|gb|CF990091.1|CF990091
EST:     AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCG                         GAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC
genomic: AAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTC

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: 61 (upstream exon), 44 (downstream exon)
Score: 4

CATCCACACCAAAAGCAAGAACCCCAAGAACCGCAGATAAAAAGGGGAGCAAGAAGAACTTTGCTCCGATCCGCCGCCGCCATCTGCTCCCTCCACCCCGgtaatctgcc ... gttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTCTGATCTGATGGCCAACATTAACATGGCAGATACTGTTCCTTCCTGTGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacattttcttgatgttagtatttctgatggaaactggcatttgtgttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTCTGATCTGATGGCCAACATTAACATGGCAGATACTGTTCCTTCCTGTGAT
               ttagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgatattgtactgtagtagccattattttctcctgttcataagctaacattttcttgatgttagtatttctgatggaaactggcatttgtgttgtaacagGAACTGGGAATACTGCAGTTCTCGTCTTATACTAGGCTACTAGCACTCCTCTGATCTGATGGCCAACATTAACATGGCAGATACTGTTCCTTCCTGTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT