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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGAAGCATGTGCACATTCATTCTTTGATGAATTGCGAGAACCCCACGCAAGGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatttctaggcagatatacctttcatgaacaaaaatactaagttaagatgaaaagaccgacttatgtgcctgcttgttcatttgcag

Basic information

species Oryza sativa
transcript LOC_Os02g14130.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g14130.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G151916_T01 (Zea mays), 5'ss of exon 11
CGAAGCATGTGCACATTCATTCTTTGATGAATTGCGAGAACCCCACGCAAGGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaat---ttctaggcagatatacctttcatgaacaaaaatactaagttaagatgaaaagaccgacttatgtgcctgcttgttcatttgcag---------------------------------------------------------------------------------------------------
 ||||| ||||||||| ||||||||||||| |||||||| || || || ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||||| |   ||| || | |||| |  ||          |  | ||   |||  || || | ||| |   |||||      |||  | |||||                                                                                                    
TGAAGCGTGTGCACATCCATTCTTTGATGAGTTGCGAGAGCCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagtagtagtttcgagactgatacagattaatgctttgcatgtgct---ttactattaacaaaccaaagcatgtggggaactgt--agttgcaattggtaattccagcatgcattccacaatgtcacaaaacagctaaacgtaaatgtctgtatataagtgagataccaacatttttgcctattaatttgcag

upper sequence: LOC_Os02g14130.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G121790_T01 (Zea mays), 5'ss of exon 11
CGAAGCATGTGCACATTCATTCTTTGATGAATTGCGAGAACCCCACGCAAGGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatttctaggcagatatacctt--tcatgaacaaaaatactaagttaagatgaaaagaccgacttatgtgcctgcttgttcatttgcag------
 ||||| ||||||||| |||||||||| || ||||||||||| || || ||||||||||||||||| ||||| || ||||||||||||||||| || |||||||| | |||| || | || | || ||  |  |   ||       |   || |    || ||  | |   |||||   | |||   |  || ||      
TGAAGCGTGTGCACATCCATTCTTTGACGATTTGCGAGAACCACATGCGAGGTTGCCAAATGGACGGCCATTTCCTCCACTGTTCAACTTTAAACAGGAAgtaagcagtttcaagactgagacacattaatgctttgcatgtgattttctttcaacaaaataggacaaaacatgtggg-gattggggaactgtagtcgcgt
















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|58665556|gb|CK054242.1|CK054242
EST:     GTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATATATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: GTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|24468658|gb|CA305607.1|CA305607
EST:     GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATATATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|29660511|gb|CB656786.1|CB656786
EST:     GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|88233437|gb|CI233286.1|CI233286
EST:     GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|89183773|gb|CI046338.1|CI046338
EST:     TGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: TGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|89173615|gb|CI041508.1|CI041508
EST:     ATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: ATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|29665852|gb|CB662127.1|CB662127
EST:     GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|29631169|gb|CB636178.1|CB636178
EST:     GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|88834708|gb|CI077991.1|CI077991
EST:     CTGTTCAACTTTAAGCAAGAA                         CTAGCGAATTGATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: CTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|86414532|gb|CI068935.1|CI068935
EST:     CAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATTNATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: CAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
EST: gi|58677693|gb|CK066380.1|CK066380
EST:     GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAA                         CTAGCGAATATATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT
genomic: GGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCT

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: 73 (upstream exon), 48 (downstream exon)
Score: 2

CGAAGCATGTGCACATTCATTCTTTGATGAATTGCGAGAACCCCACGCAAGGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatt ... tcatttgcagCTAGCGAATTTATCGCCAGAGCTCATCAACAGGTTGATACCAGAGCATGCTCGGTGACATTGTGGGTTCAATTTCTTGCCTGCTGCCGGACCATAGGACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGAAGCATGTGCACATTCATTCTTTGATGAATTGCGAGAACCCCACGCAAGGTTGCCAAATGGACGTCCATTCCCCCCACTGTTCAACTTTAAGCAAGAAgtaagtaatttctaggcagatatacctttcatgaacaaaaatactaagttaagatgaaaagaccgacttatgtgcctgcttgttcatttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA