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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGGGAGGATGCTCTTAAGGATGGAATGGGAGGAGGCAGTGACTTCCATAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaacatatgtaccctgaaattttccagcaccctcaacatttttttgtttgaactttttttttaaaaaaaaacagaattattcatgctaacttttatggttaacag

Basic information

species Oryza sativa
transcript LOC_Os04g46390.3
intron # 3
splice site 5'
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|84117330|gb|CD151097.1|CD151097
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTAC
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTAC
EST: gi|29639999|gb|CB645008.1|CB645008
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|33653448|gb|CF276062.1|CF276062
EST:     AATCCATTTGACATATTTGAGCAGTTTTTCGGGGGGTGGTGCCTTTNNNN                         NNNAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCAT
genomic: AATCCATTTGACATATTTGAGCAGTTTTTCGGGGG-TGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGG-AGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCAT
EST: gi|29643236|gb|CB648243.1|CB648243
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|13807441|gb|AU181957.1|AU181957
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29643291|gb|CB648298.1|CB648298
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29678521|gb|CB674796.1|CB674796
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|14714017|gb|AU197958.1|AU197958
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29668764|gb|CB665039.1|CB665039
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|33654740|gb|CF277354.1|CF277354
EST:     AATCCATTTGACATATTTGAGCAGTTTTTCGGGGGGTGGTGCCTTTNNNN                         NNNAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCAT
genomic: AATCCATTTGACATATTTGAGCAGTTTTTCGGGGG-TGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGG-AGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCAT
EST: gi|29637040|gb|CB642049.1|CB642049
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29645124|gb|CB650131.1|CB650131
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|4715680|gb|AU056796.1|AU056796
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCNAAGAGTACGCAGACAGAGACGTGGTGAAG
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTC-AAGAGTACGCAGACAGAGACGTGGTGAAG
EST: gi|29657304|gb|CB653579.1|CB653579
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|33657288|gb|CF279902.1|CF279902
EST:     AATCCATTTGACATATTTGAGCAGTTTTTCGGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: AATCCATTTGACATATTTGAGCAGTTTTTCGGGGG-TGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|29614042|gb|CB619055.1|CB619055
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGTGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|218494200|gb|FG946885.1|FG946885
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGT
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGT
EST: gi|58593485|gb|CF991793.1|CF991793
EST:     AAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCACAGAGTACGCAGACAGAGACGTGGTGAA
genomic: AA-TCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCA-AGAGTACGCAGACAGAGACGTGGTGAA
EST: gi|29680639|gb|CB676914.1|CB676914
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|33694058|gb|CF322297.1|CF322297
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATA
EST: gi|88316124|gb|CI620402.1|CI620402
EST:     TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGG                         GGAGTAGCTCAA
genomic: TAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAA

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), 75 (downstream exon)
Score: 297

TATGGGGAGGATGCTCTTAAGGATGGAATGGGAGGAGGCAGTGACTTCCATAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaaca ... tggttaacagGGAGTAGCTCAAGAGTACGCAGACAGAGACGTGGTGAAGATGTGGCGCATACTTTGAAGGTGTCTTTAGAAGATGTGTATAATGGATCTATGAAGAAACT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGGGAGGATGCTCTTAAGGATGGAATGGGAGGAGGCAGTGACTTCCATAATCCATTTGACATATTTGAGCAGTTTTTCGGGGGTGGTGCCTTTGGGGgtaagcaacatatgtaccctgaaattttccagcaccctcaacatttttttgtttgaactttttttttaaaaaaaaacagaattattcatgctaacttttatggttaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG