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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCCAAGTTCTGGAATGAGTTTGGAAAATCAGTCAAGTTGGGCATCATTGAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttctattctaatgtccactaattgctgtagttatatatgcgagggataatagaactgagtttttatctgtttcag

Basic information

species Oryza sativa
transcript LOC_Os06g50300.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G399073_T02 (Zea mays), 5'ss of exon 14
ATGCCAAGTTCTGGAATGAGTTTGGAAAATCAGTCAAGTTGGGCATCATTGAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttctatt-ctaatgtccactaattg---ctgtagttatatat-----gcgagggataatagaactgagtt----tttatctgtttcag
| ||||||||||||||||||||||| |||||| ||||| |||| ||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||| | |  | ||| | ||||     ||   || || || ||| |     ||  || | || | | ||||  |    |||   ||  ||||
ACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATTGAAGACGCAACTAACAGGAACCGCCTTGCGAAGCTTCTTAGATTTGAAAGgtttgtcctttcctactattttccaaacgctgtagctttaattgtatgtaccgggctgggaaaaaaaaagctgatctgatatttgcttgcctcag

upper sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G141931_T02 (Zea mays), 5'ss of exon 12
ATGCCAAGTTCTGGAATGAGTTTGGAAAATCAGTCAAGTTGGGCATCATTGAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtct-tctattctaat-gtccactaattgctgtagttatatatgcgaggga-taatagaactgagtttttatctgtttcag
| ||||||||||||||||||||||| |||||| ||||| |||| ||||| |||||||| |||||||| ||||| ||||| |||||||| |||||||| ||||| || | || |    ||| ||||     ||  |  |||| |   |   || ||    ||   |  | ||  |   || |||||
ACGCCAAGTTCTGGAATGAGTTTGGCAAATCAATCAAGCTGGGTATCATCGAAGACGCGACTAACAGAAACCGCCTTGCGAAGCTTCTTAGATTTGAGAGgttggtttgtccagcagaattgtcctactcttctttaagttttgggtaaaagagaactgtacctcatatttgctgcttgcttcag
















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|58693264|gb|CK081951.1|CK081951
EST:     GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
EST: gi|87016979|gb|CI286115.1|CI286115
EST:     GAAGACGCAACTAACAGGAACCGTCTCGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
EST: gi|58684599|gb|CK073286.1|CK073286
EST:     GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
EST: gi|32947910|gb|BP184482.1|BP184482
EST:     AAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: AAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
EST: gi|33800491|gb|CF326115.1|CF326115
EST:     GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
EST: gi|58685726|gb|CK074413.1|CK074413
EST:     GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTC
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTC
EST: gi|58689260|gb|CK077947.1|CK077947
EST:     GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
EST: gi|29627895|gb|CB632906.1|CB632906
EST:     GAAGATGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
EST: gi|14192100|gb|AU184311.1|AU184311
EST:     GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
EST: gi|55410371|gb|CV722747.1|CV722747
EST:     GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
EST: gi|29659228|gb|CB655503.1|CB655503
EST:     GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAG                         TACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT
genomic: GAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGAT

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: 69 (upstream exon), 74 (downstream exon)
Score: 124

ATGCCAAGTTCTGGAATGAGTTTGGAAAATCAGTCAAGTTGGGCATCATTGAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttc ... tctgtttcagTACCAAGTCGGAAGGCAAACTTGCCTCTCTTGATGAGTACATTTCAAGGATGAAGCCAGGGCAGAAGGACATCTTTTACATTACCGGAAGCAGCAAGGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCCAAGTTCTGGAATGAGTTTGGAAAATCAGTCAAGTTGGGCATCATTGAAGACGCAACTAACAGGAACCGTCTTGCAAAGCTTCTGAGATTTGAAAGgtttgtcttctattctaatgtccactaattgctgtagttatatatgcgagggataatagaactgagtttttatctgtttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG