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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTGATATCAGTTGATGATGGAATTAGGCCAGGGACCACAGCATCTGGATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagcactcttagcttttttttctgctgacactactattgcaaccaggctttgtttgtccattgcttgttacattgtgtatgtgttttttttttttaatttaacgaatctatgtag

Basic information

species Oryza sativa
transcript LOC_Os02g57260.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57260.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM5G848768_T02 (Zea mays), 5'ss of exon 9
GTTGTGATATCAGTTGATGATGGAATTAGGCCAGGGACCACAGCATCTGGATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagcactcttagcttttttttctgctgacactactattgcaaccaggctttgtttgtccattgcttgttacattgtgtatgtgttttttttttttaatttaacgaatctatgtag
||||||||||||||||||||||| |||||||||||||||||||||||||||||||| || || |||||||||||    |||||||| || |||||||||||||||||              ||||||||| |||| || || ||||| | ||  |||         ||   || |  |  ||           | | |  |||   ||  || || |||||
GTTGTGATATCAGTTGATGATGGGATTAGGCCAGGGACCACAGCATCTGGATTGGCGAAACTGAAACCAGTTTTTAAAAAGGATGGGACTACAACTGCAGgtattgc--------------ttttttctggtgaccctccttttgcagctagatttt---------ttctctgctgaaacgt-----------tatctgataaaccaatcaaactgtgtag
















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|29661674|gb|CB657949.1|CB657949
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29641413|gb|CB646420.1|CB646420
EST:     AAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: AAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29661675|gb|CB657950.1|CB657950
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|27577585|gb|CB000280.1|CB000280
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|88307931|gb|CI646366.1|CI646366
EST:     ATTGGCAAAGCTTAAACCAGCTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTATTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29670433|gb|CB666708.1|CB666708
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29670870|gb|CB667145.1|CB667145
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|218505530|gb|FG967454.1|FG967454
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29664436|gb|CB660711.1|CB660711
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|27577745|gb|CB000440.1|CB000440
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|86479233|gb|CI121866.1|CI121866
EST:     TTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: TTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29642434|gb|CB647441.1|CB647441
EST:     CAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: CAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29663748|gb|CB660023.1|CB660023
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29646005|gb|CB651012.1|CB651012
EST:     GCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: GCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29663747|gb|CB660022.1|CB660022
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29687731|gb|CB684006.1|CB684006
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|38471798|gb|CF955929.1|CF955929
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|87026915|gb|CI259568.1|CI259568
EST:     TTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: TTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29683240|gb|CB679515.1|CB679515
EST:     CACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: CACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29667870|gb|CB664145.1|CB664145
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|33681865|gb|CF310104.1|CF310104
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29683241|gb|CB679516.1|CB679516
EST:     CACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: CACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29664437|gb|CB660712.1|CB660712
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29676716|gb|CB672991.1|CB672991
EST:     GCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: GCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|25800239|gb|CA756200.1|CA756200
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29645372|gb|CB650379.1|CB650379
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
EST: gi|29670912|gb|CB667187.1|CB667187
EST:     ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAG                         GCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA
genomic: ATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGA

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: 68 (upstream exon), 74 (downstream exon)
Score: 98

GTTGTGATATCAGTTGATGATGGAATTAGGCCAGGGACCACAGCATCTGGATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagc ... atctatgtagGCAACTCTAGTCAAGTGAGCGATGGTGCTGGAGCTGTTCTTCTCATGAGGAGGGACGTAGCGATGAAGAAGGGACTTCCTATTCTTGGTGTTTTCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTGATATCAGTTGATGATGGAATTAGGCCAGGGACCACAGCATCTGGATTGGCAAAGCTTAAACCAGTTTTCCGGAAGGATGGTACCACAACTGCAGgtattgcagcactcttagcttttttttctgctgacactactattgcaaccaggctttgtttgtccattgcttgttacattgtgtatgtgttttttttttttaatttaacgaatctatgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG