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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatccactagttcatgcctcaattttttttctcctcttttaagttttccaaagagctacattgttgtaaagtgtctaatacaattgattgtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAAGGGAAGTTCAATCATGGCAGGGTCTCTTGCCGCCTCAGCATTCTTCCCA

Basic information

species Oryza sativa
transcript LOC_Os11g43820.1
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|88745380|gb|CI768740.1|CI768740
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88312515|gb|CI585038.1|CI585038
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88689956|gb|CI734035.1|CI734035
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|29637240|gb|CB642249.1|CB642249
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|58668862|gb|CK057548.1|CK057548
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88399649|gb|CI583383.1|CI583383
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|58669806|gb|CK058492.1|CK058492
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88720848|gb|CI744147.1|CI744147
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88695784|gb|CI737361.1|CI737361
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88718369|gb|CI741458.1|CI741458
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88391346|gb|CI598164.1|CI598164
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|58655487|gb|CK044167.1|CK044167
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|58662816|gb|CK051502.1|CK051502
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88422489|gb|CI571471.1|CI571471
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88422742|gb|CI573904.1|CI573904
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88718962|gb|CI742472.1|CI742472
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|88404165|gb|CI575653.1|CI575653
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|58673441|gb|CK062127.1|CK062127
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|58692890|gb|CK081577.1|CK081577
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
EST: gi|33686432|gb|CF314671.1|CF314671
EST:     CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTG                         GTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA
genomic: CCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAA

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: 72 (upstream exon), 65 (downstream exon)
Score: 49

CCTTGCGCCAAGAAAGACGAGCCGCGGCTCAACAGCGGAGTGGAGGGGCGCCGATCTCCATCGCCGAGGAGAGCAGAGCAGGGGAGGGGAGGGGATCCTGgtgagcctcc ... gtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAAGGGAAGTTCAATCATGGCAGGGTCTCTTGCCGCCTCAGCATTCTTCCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccaaagagctacattgttgtaaagtgtctaatacaattgattgtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAAGGGAAGTTCAATCATGGCAGGGTCTCTTGCCGCCTCAGCATTCTTCCCA
                                              tttattc  CT-rich tract
 taatacaattgattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatccactagttcatgcctcaattttttttctcctcttttaagttttccaaagagctacattgttgtaaagtgtctaatacaattgattgtttattcagGTTAGCGCTTTTGGCGTGTGATTGATTTCTAAACGAATTTTGGGCCGTGAAGGGAAGTTCAATCATGGCAGGGTCTCTTGCCGCCTCAGCATTCTTCCCA

-gatccac
- - - - - -ttcatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - agctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgttgt