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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagcattacactctcttgcaagtccctgttgtaccggaaattatccttgctgacatcacttcttggtctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAGGAAGTGATAAAGGGTGCCTATGCCGTGCCTTCGCTTGCAACTGCAGCGC

Basic information

species Oryza sativa
transcript LOC_Os05g08990.1
intron # 20
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|86478372|gb|CI121005.1|CI121005
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88838558|gb|CI375106.1|CI375106
EST:     TCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: TCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88259382|gb|CI363675.1|CI363675
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|89195040|gb|CI051153.1|CI051153
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|12404996|gb|AU166597.1|AU166597
EST:     TTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: TTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88978056|gb|CI384538.1|CI384538
EST:     TCAGATTGTTCCAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGGCTGGGTGATCTCAACCCACGATCAAA
genomic: TCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATT-GGCTGGGTGATCTCAACCCACGATCAAA
EST: gi|87022785|gb|CI269721.1|CI269721
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88262438|gb|CI366212.1|CI366212
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88266902|gb|CI368678.1|CI368678
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88508075|gb|CI435581.1|CI435581
EST:     AAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: AAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88263378|gb|CI367152.1|CI367152
EST:     GAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: GAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|89189666|gb|CI049205.1|CI049205
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|86437465|gb|CI119187.1|CI119187
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88262244|gb|CI365820.1|CI365820
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGATATTATTTCTTTCAGA-                         AATCCTGTGGAGCTTGAGGATTGGCTTGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|86487083|gb|CI129716.1|CI129716
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCTACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88262431|gb|CI366205.1|CI366205
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|86865746|gb|CI335445.1|CI335445
EST:     GTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: GTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|87022805|gb|CI269741.1|CI269741
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|88971448|gb|CI017762.1|CI017762
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|87029369|gb|CI250302.1|CI250302
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|86481762|gb|CI124395.1|CI124395
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
EST: gi|86481706|gb|CI124339.1|CI124339
EST:     ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAG                         AATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG
genomic: ACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAG

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: 66 (upstream exon), 48 (downstream exon)
Score: 4

GGTGTGTTGCACTGGGTTGCCGAACCTTCTCCAGGTGTTAACCCGCTCAAAGTGGAAATCAGATTGTTCGAGAAATTATTTCTTTCAGAGgtatagcatt ... tctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAGGAAGTGATAAAGGGTGCCTATGCCGTGCCTTCGCTTGCAACTGCAGCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccctgttgtaccggaaattatccttgctgacatcacttcttggtctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAGGAAGTGATAAAGGGTGCCTATGCCGTGCCTTCGCTTGCAACTGCAGCGC
                          tgctgac  putative branch site (score: 4)
                aaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagcattacactctcttgcaagtccctgttgtaccggaaattatccttgctgacatcacttcttggtctacattagAATCCTGTGGAGCTTGAGGATTGGCTGGGTGATCTCAACCCACGATCAAAGGAAGTGATAAAGGGTGCCTATGCCGTGCCTTCGCTTGCAACTGCAGCGC

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