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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaggaactcatttgttgaagatgcttgaaacaataattcagaatttctcatttatccattgcaagacctgaggcactgcttttatctgttatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGACATCGAAGCACATCCGAACAAAGCAGTTCAGAATGTATTGAAATCCTTCC

Basic information

species Oryza sativa
transcript LOC_Os01g50760.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G098569_T01 (Zea mays), 3'ss of exon 10
--gaaggaactcatttgt-tgaagatgcttgaaacaataattcagaatttctcatttatccattgcaagacctgaggcactgcttttatctgttatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGACATCGAAGCACATCCGAACAAAGCAGTTCAGAATGTATTGAAATCCTTCC
  | | | || |||||   ||  | ||||     | |  | || |  ||  | || | | |  | |  |   ||| |  ||    | ||   |   |   ||||  || || ||||| |||||||||||||||||||| |||||||||||||||||||| || || |||| ||| ||||| || | ||| ||||| |||||||
gtggatgtacgcatttacatgtggctgctct---ccaacactctgttttcgttatatgttctgttctggtggtgacgtcctttcctgattgatataaacccagGAGGTTTTCCATGAGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGACATCGAGGCCCAGCCGAGCAAGGCAGTCCAAACTGTTTTGAAGTCCTTCC

upper sequence: LOC_Os01g50760.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G147721_T01 (Zea mays), 3'ss of exon 10
-gaaggaactcatttgttgaagatgcttgaaacaataattcagaatttctcatttatccattgcaagacctgaggcactgcttttatctgttat-actgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGACATCGAAGCACATCCGAACAAAGCAGTTCAGAATGTATTGAAATCCTTCC
    |  | |         |  |||||   ||   |     ||    | |     |     ||     | ||| |  ||  |  |   || ||| | | ||||  || || || |  |||||||||||||||||||| |||||||||||||||||||| || || || | ||| ||||| |||| ||| ||||| |||||||
tctggttaatggcactgaaacaatgctcataatg-tgggcaagtggctgtaccccaagttctgttttgc-tgacgtccttttcctgattgatatgaatccagGAGGTTTTCCAGGCGTACGAGAGGGAGAGTTACAACAAGCTGATTGCCGACATCGAGGCCCAGCCCAGCAAGGCAGTCCAGAGTGTTTTGAAGTCCTTCC
















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|88965695|gb|CI006596.1|CI006596
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86600966|gb|CI356723.1|CI356723
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|88380218|gb|CI516205.1|CI516205
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|27577652|gb|CB000347.1|CB000347
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|4714704|gb|AU055821.1|AU055821
EST:     CTGAATGTGTTGCAAAAGTGANGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|88266799|gb|CI368575.1|CI368575
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86484987|gb|CI127620.1|CI127620
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86852882|gb|CI323191.1|CI323191
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86419076|gb|CI053877.1|CI053877
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86836476|gb|CI348358.1|CI348358
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|33820604|gb|CF336113.1|CF336113
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|87011492|gb|CI279401.1|CI279401
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|33822342|gb|CF336983.1|CF336983
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86535251|gb|CI175457.1|CI175457
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|29620886|gb|CB625897.1|CB625897
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATTTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86527820|gb|CI168026.1|CI168026
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|29682410|gb|CB678685.1|CB678685
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86252127|gb|CI055864.1|CI055864
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86426167|gb|CI071264.1|CI071264
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|89169652|gb|CI110011.1|CI110011
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86834085|gb|CI340224.1|CI340224
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATGAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|8856728|gb|AU094046.1|AU094046
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|88974804|gb|CI023100.1|CI023100
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|29688203|gb|CB684478.1|CB684478
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|89166650|gb|CI103936.1|CI103936
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|88970717|gb|CI385383.1|CI385383
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACCATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|58681411|gb|CK070098.1|CK070098
EST:     CTGAATGTGTTGCCAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86521107|gb|CI161313.1|CI161313
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|29684202|gb|CB680477.1|CB680477
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|88829676|gb|CI074546.1|CI074546
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
EST: gi|86598572|gb|CI355189.1|CI355189
EST:     CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAG                         GCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC
genomic: CTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGAC

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: 72 (upstream exon), 73 (downstream exon)
Score: 85

GAAAATTATGGGAAGCCAGATCCTGAATGTGTTGCAAAAGTGAAGGATCTGTATAAAGAACTTAATCTGGAGgtttgtctta ... tatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGACATCGAAGCACATCCGAACAAAGCAGTTCAGAATGTATTGAAATCCTTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcatttatccattgcaagacctgaggcactgcttttatctgttatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGACATCGAAGCACATCCGAACAAAGCAGTTCAGAATGTATTGAAATCCTTCC
                                   ttttatctgttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaggaactcatttgttgaagatgcttgaaacaataattcagaatttctcatttatccattgcaagacctgaggcactgcttttatctgttatactgcagGCCGTATTTCATGAATACGAGAGGGAGAGTTACAATAAGCTGATTGCCGACATCGAAGCACATCCGAACAAAGCAGTTCAGAATGTATTGAAATCCTTCC

- - - - - - -tgttgaa
- - - - - - - - - - -atgcttg
- - - - - - - - - - - - - - -aacaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgcaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcttt