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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaaactatttcatttagcttgcttgcatctttgtgagtacatgtactgaagtgtcattctggggtgcttattggaattgctactgttgtatgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG

Basic information

species Oryza sativa
transcript LOC_Os02g56850.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G806449_T02 (Zea mays), 3'ss of exon 4
-------------------------------acaaactatttcatttagcttgcttgcatctttgtgagtacatgtactgaagtgtcatt---ctggggtgcttattg-----gaattgctactgttgtatgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG----------------------------
                               || ||       ||  |   || ||      | |  |  |      || | |   || |   || |  ||   ||||     ||| ||    | |  ||  | |||||||| | ||||||||||||||||| || || || || ||||||||||| ||||||| |||  |||||||||||                            
gttagtcatgttactgtcttattatgatagaactaatgtgggtatccaaaatggttctgaagtggctatcatggaatctaaggacacacttgccttgattgtagattgtatgtgaactgtagttttgttacaaatgcagGATTCGAAGAATTTTGGGTGGGAGATTAACGGAGATATTAACTTCAATTGGAAAACGCTATTGGAAAATAAGGTCATGTTTAAATCTCTACCATGACTGT

upper sequence: LOC_Os02g56850.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM5G806449_T01 (Zea mays), 3'ss of exon 3
-------------------------------acaaactatttcatttagcttgcttgcatctttgtgagtacatgtactgaagtgtcatt---ctggggtgcttattg-----gaattgctactgttgtatgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG
                               || ||       ||  |   || ||      | |  |  |      || | |   || |   || |  ||   ||||     ||| ||    | |  ||  | |||||||| | ||||||||||||||||| || || || || ||||||||||| ||||||| |||  |||||||||||
gttagtcatgttactgtcttattatgatagaactaatgtgggtatccaaaatggttctgaagtggctatcatggaatctaaggacacacttgccttgattgtagattgtatgtgaactgtagttttgttacaaatgcagGATTCGAAGAATTTTGGGTGGGAGATTAACGGAGATATTAACTTCAATTGGAAAACGCTATTGGAAAATAAG
















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|88416046|gb|CI594158.1|CI594158
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|88392434|gb|CI612908.1|CI612908
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|117220740|gb|CT845514.1|CT845514
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|88723894|gb|CI745591.1|CI745591
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTCGGGTGGGAAATCA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCA
EST: gi|29675048|gb|CB671323.1|CB671323
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|88694888|gb|CI738926.1|CI738926
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGA
EST: gi|88417209|gb|CI576283.1|CI576283
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
EST: gi|88726529|gb|CI750184.1|CI750184
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACA
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACA
EST: gi|2443112|gb|C74883.1|C74883
EST:     TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAG                         GATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG
genomic: TGCCTAAAAAGATACTGGTGTATGGTTCATCTTTCCGCGGAGAATTTGAGgtaactgatc ... atgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgaagtgtcattctggggtgcttattggaattgctactgttgtatgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG
                                            tatgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaaactatttcatttagcttgcttgcatctttgtgagtacatgtactgaagtgtcattctggggtgcttattggaattgctactgttgtatgattgcagGATGCAAAGAATTTTGGGTGGGAAATCAATGGGGACATTAACTTCAACTGGAAAAGGCTGCTGGAAAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA