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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctgtgccaaacaggccctacataggaaaattatcaatgtgaattactgatcagccaattgttcctacaacactttaactgaatgttttttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGCCACTTGCAATTCAATAACCAAGCAGACCGGATCCACAACGCCATCCTCC

Basic information

species Oryza sativa
transcript LOC_Os01g16900.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G404855_T01 (Zea mays), 3'ss of exon 7
agctgtgccaaacag--gccctacataggaaaattatcaatgtgaattactgatcagccaattgttcctacaacactttaactgaatgtttt--ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGCCACTTGCAATTCAATAACCAAGCAGACCGGATCCACAACGCCATCCTCC
  ||   ||  | ||  | |   |||        ||| ||  |       |  | |    |  ||| ||| |    |||| ||| || | |   || |    |||||||||| |||||||| |||||||||||||||||||| ||||||||||||||||||||||||||  || ||||||||||||||||||||||||||||||
--cttaacctgaaagttgtctggcatgttcctgctattaacatttcggtatattgatattacagttactatat--atttacctggatttgtggattgtttttagAACCTTGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGATGTTGCGCCACTTGCAATTCAACGACAAAGCAGACCGGATCCACAACGCCATCCTCC

upper sequence: LOC_Os01g16900.3 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G120857_T02 (Zea mays), 3'ss of exon 7
agctgtgccaaacaggccctacataggaaaattatcaatgt---gaattactgatcagccaattgttcctacaacactttaactgaatgtttt--ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGCCACTTGCAATTCAATAACCAAGCAGACCGGATCCACAACGCCATCCTCC
         |||   | |   |||    |  || | ||  |   ||  || || |    || ||  |        ||     ||| || | ||  || |  | ||||||| || |||||||| |||||||||||||||||||| ||| ||||||||||| ||||||||||  || ||||||||||||||||||||||||||||||
-----cctaaaagttgtctggcatgttcatgttgttaacatctcgatgtattggtattacagttactatatatttacccggtctgtatttgttggttgtttctagAACCTCGCGAACCCGACTGCTCTTATGCTGAGTGCTGTCATGTTGTTGCGCCACATGCAATTCAACGACAAAGCAGACCGGATCCACAACGCCATCCTCC
















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|27920689|gb|CB096497.1|CB096497
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|55410982|gb|CV723358.1|CV723358
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|88975256|gb|CI023507.1|CI023507
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|29640079|gb|CB645088.1|CB645088
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|218503212|gb|FG950056.1|FG950056
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|27554418|gb|CA998318.1|CA998318
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|41883639|gb|BX928526.1|BX928526
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|16579226|gb|BI813321.1|BI813321
EST:     -TTGTCTGCCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGC-AACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|33799865|gb|CF325799.1|CF325799
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGATGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|29673427|gb|CB669702.1|CB669702
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|29616639|gb|CB621651.1|CB621651
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|87036093|gb|CI189540.1|CI189540
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|88226248|gb|CI226164.1|CI226164
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|86415795|gb|CI029806.1|CI029806
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|29639682|gb|CB644691.1|CB644691
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|55410961|gb|CV723337.1|CV723337
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|29619531|gb|CB624543.1|CB624543
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|29664535|gb|CB660810.1|CB660810
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|86495897|gb|CI138530.1|CI138530
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|88829336|gb|CI074206.1|CI074206
EST:     CTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: CTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|88247463|gb|CI247312.1|CI247312
EST:     TGGCAGAAGCTGTTCACGATTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|27554444|gb|CA998344.1|CA998344
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|29616640|gb|CB621652.1|CB621652
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|4714232|gb|AU058199.1|AU058199
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         ACCCTTGCAANCC-GACCGCTCTAATGCTGAGTGCTGTAATGATGTT-CGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|29671573|gb|CB667848.1|CB667848
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|86255505|gb|CI065182.1|CI065182
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|86900281|gb|CI296324.1|CI296324
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|89181212|gb|CI045295.1|CI045295
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
EST: gi|88974956|gb|CI023219.1|CI023219
EST:     TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAG                         AACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC
genomic: TTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGC

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: 73 (upstream exon), 73 (downstream exon)
Score: 66

CTGCAACATTGGTGAAGGTGGCATTTGTCTGGCAGAAGCTGTTCACGGTTCTGCTCCTGATATTGCTGGCAAGgtgagttaga ... ttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGCCACTTGCAATTCAATAACCAAGCAGACCGGATCCACAACGCCATCCTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgatcagccaattgttcctacaacactttaactgaatgttttttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGCCACTTGCAATTCAATAACCAAGCAGACCGGATCCACAACGCCATCCTCC
                                       tgttttttttcccc  CT-rich tract
                                   tgaatgtttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctgtgccaaacaggccctacataggaaaattatcaatgtgaattactgatcagccaattgttcctacaacactttaactgaatgttttttttccccagAACCTTGCAAACCCGACCGCTCTTATGCTGAGTGCTGTTATGATGTTGCGCCACTTGCAATTCAATAACCAAGCAGACCGGATCCACAACGCCATCCTCC

- ctgtgcc
- - - - - - caggccc
- - - - - - - - - - - - aggaaaa
- - - - - - - - - - - - - - - - - -caatgtg
- - - - - - - - - - - - - - - - - - - - - - ttactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgaatg