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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGGGCATCTCAGAATATTTCATTGGCCGAGCATGAATGTGCTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaagtgcaagcataattattttcctttattatttgcaaaagaatcccaggatattctcatctgttgaacaagtgttgttgtaaatggcgcaat...

Basic information

species Oryza sativa
transcript LOC_Os07g09000.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g09000.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G158489_T03 (Zea mays), 5'ss of exon 2
GATGGGCATCTCAGAATATTTCATTGGCCGAGCATGAATGTGCTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaagtgcaa-gcataattattttccttt--attatttgcaaaagaatccca-ggatattctcatctgttgaac-aagtgttgttgtaaa-tggcgcaat
||||| |||||||||||||| |||||||| ||||| || ||||| || ||||| ||||| |||||||| |||||||| |||||||||||||||| ||  ||     || |||| | | || |  |||  |||  |  || | |||| |||   ||||  ||||   |  | | || ||||  |||||| |||      
GATGGACATCTCAGAATATTCCATTGGCCAAGCATAAAAGTGCTTTTGGATGAGCCCAAAGCTCATAAATCCTTCCGAGACATGGATATCAGgtcagaacagacctaaagcattacttttatttttttaattgctcacagaggaatgccataaatatcatcattactatagctaaatgtttatgtaaaatgg------
















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|58674632|gb|CK063319.1|CK063319
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|117233168|gb|CT848021.1|CT848021
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|30228290|gb|CB966181.1|CB966181
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTTGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|58683603|gb|CK072290.1|CK072290
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGC
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGC
EST: gi|29640028|gb|CB645037.1|CB645037
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|58687497|gb|CK076184.1|CK076184
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|58684449|gb|CK073136.1|CK073136
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|29627838|gb|CB632849.1|CB632849
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|88395653|gb|CI590668.1|CI590668
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|58695857|gb|CK084544.1|CK084544
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|58666737|gb|CK055423.1|CK055423
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGC
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGC
EST: gi|33796125|gb|CF323928.1|CF323928
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
EST: gi|29674145|gb|CB670420.1|CB670420
EST:     CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAG                         CTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT
genomic: CTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAAT

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: 75 (upstream exon), 69 (downstream exon)
Score: 32

GATGGGCATCTCAGAATATTTCATTGGCCGAGCATGAATGTGCTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaa ... cctcttgtagCTTAGATTCAGAATTTTTAGTTTCCACATCCACTGATGGTTCTGCAAGAATATGGAAGATAGATGAGGGGGTACCATTGGTCAATTTGACTCGATCTGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGGGCATCTCAGAATATTTCATTGGCCGAGCATGAATGTGCTCTTAGATGAACCCAAGGCTCATAAGTCCTTCCGGGACATGGATATCAGgttagggcaagtgcaagcataattattttcctttattatttgcaaaagaatcccaggatattctcatctgttgaacaagtgttgttgtaaatggcgcaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaagaa