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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGATGAAACTCAAGAAACTGGACTTGCAATACACTTTTCTCACAACAGAAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttcctgtatacaagcattgattaattgtgtttgaattagtatatgccatattacaacgagatgtcctcaacag

Basic information

species Oryza sativa
transcript LOC_Os01g63420.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63420.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G035314_T01 (Zea mays), 5'ss of exon 3
TTCGATGAAACTCAAGAAACTGGACTTGCAATACACTTTTCTCACAACAGAAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttcctgtatacaagcattgattaattgtgtt---tgaattagtat---atgccatattacaacg-agatgtcctcaacag
|||   |   || |||||||||||| |||| |||||||| ||||| || |||||||| |||||| |||| || ||||| ||||| |||||  |||| |||||||  |||          |  ||   |||   || |    | | | | |||    ||  || | ||||   | |||  ||| ||||
TTCTGCGTCGCTTAAGAAACTGGACCTGCAGTACACTTTCCTCACCACTGAAGATCACTGTCAGCTTATCGCTAAATGCCCCAACCTACTGGTTCTCGAGgtaacttttttgtagctttaatatcagttatccgtctaaaataagtgactatctagtgttatctgacaagatacatgctctcgacag

upper sequence: LOC_Os01g63420.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G125411_T01 (Zea mays), 5'ss of exon 2
TTCGATGAAACTCAAGAAACTGGACTTGCAATACACTTTTCTCACAACAGAAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttcctgtatacaagcattgattaattgtgttt---gaattagtatatgccatattacaacg--------agatgtcctcaacag
||| |  |  || ||||||||||||||||| | |||||| ||||| || ||||| || |||||| ||||||| ||||| ||||| |||    |||| |||||||| |||  || | |     | | |||| | |||| |    ||| |||   |  |  ||| ||||         |||||  ||| ||||
TTCCACAATGCTTAAGAAACTGGACTTGCAGTTCACTTTCCTCACCACTGAAGACCACTGTCAGCTTATTGCTAAATGCCCCAACCTAAGTGTTCTCGAGgtaatgtttt-tggacatctttaat-attactcgtgtgtctaaaataagtgactatctaatttcaactgacaaggtagatgctctcgacag
















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|5056094|gb|AU075473.1|AU075473
EST:     AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
genomic: AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
EST: gi|58679194|gb|CK067881.1|CK067881
EST:     AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
genomic: AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
EST: gi|58682067|gb|CK070754.1|CK070754
EST:     AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
genomic: AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
EST: gi|218479840|gb|FG954721.1|FG954721
EST:     AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
genomic: AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
EST: gi|58652978|gb|CK041658.1|CK041658
EST:     AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
genomic: AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
EST: gi|29674615|gb|CB670890.1|CB670890
EST:     AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
genomic: AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
EST: gi|58687112|gb|CK075799.1|CK075799
EST:     AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTCGTTGGTGATACATGC
genomic: AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
EST: gi|3768208|gb|AU032235.1|AU032235
EST:     AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
genomic: AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
EST: gi|58682547|gb|CK071234.1|CK071234
EST:     GATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
genomic: GATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
EST: gi|58661283|gb|CK049963.1|CK049963
EST:     AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAG                         GTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC
genomic: AAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGC

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), 73 (downstream exon)
Score: 88

TTCGATGAAACTCAAGAAACTGGACTTGCAATACACTTTTCTCACAACAGAAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttc ... tcctcaacagGTGAGGAACGTGATAGGAGATAGAGGGCTAGAAGTTGTTGGTGATACATGCAAGAAGCTACGAAGACTCCGAATTGAGCGGGGTGATGATGATCCAGGTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCGATGAAACTCAAGAAACTGGACTTGCAATACACTTTTCTCACAACAGAAGATCATTGTCAGATTATTGCAAAATGTCCCAATCTACTAATTCTTGAGgtaatatttcctgtatacaagcattgattaattgtgtttgaattagtatatgccatattacaacgagatgtcctcaacag

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