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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaactttttttaaaaaaaatgaaaaatctcgtcttttatatatgttgttatgttgtagtgtggaacatctaggcgactctaacctcgtgatattattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATAAGTGGGAAGTACTTCAGCAACTGCAATTTAGAGACCCCAAGCTCACAGG

Basic information

species Oryza sativa
transcript LOC_Os10g40030.11
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40030.11 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G464885_T01 (Zea mays), 3'ss of exon 7
gtgaactttttttaaaaaaaatgaaaaatctcgtcttttatata--tgttgttatgttgtagtgtggaacatctaggcgactctaacctcgtgatattattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATAAGTGGGAAGTACTTCAGCAACTGCAATTTAGAGACCCCAAGCTCACAGG
                      | |   | ||  || |||| |   || ||     ||      |    ||   |  | | || ||| | ||   ||  ||||| ||||||||||||||||||| ||||| ||| | ||||||||||| |  || |||||||| |||||||||| ||| ||  || |||  | ||| |||||||| |
----------------------gtaggttttcacctcttattttactgctggcgcatttgcagatcatgcactgatcctaatc-aactttgtttcatcttttttcagGGTGCTGCAACGACATGCTATGTTGCAATGCATCCTCAAGTGAGGGGGATAAGTGGAAAGTACTTCACCAATTGTGATGTAGCCAACCCGAGCTCACAAG

upper sequence: LOC_Os10g40030.11 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv16s0050g00750.t01 (Vitis vinifera), 3'ss of exon 1
-----gtgaactttttttaaaaaaaatgaaaaatctcgtcttttatatatgttgttatgttgtagtgtggaacatctaggcgactctaacctcg-tgatattattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATAAGTGGGAAGTACTTCAGCAACTGCAATTTAGAGACCCCAAGCTCACAGG
        || |||   |        || |||            |   || ||   |  ||  | |||  || |  |  ||   ||| |  ||  | ||  | |||  ||||| |||||||| ||||| ||||||||||||||||| || || |  ||  | || ||  | || ||     |||| ||  |||  |  || | | ||||||
agttctcaaattttggctctgtttggtggaaagga--------aaagaatatttcaaacttccattgtacaa-acttgagc--ttctgatttctcttatggtgtttgatagGGAGCTGCAACCACATGCTATGTGGCATTACATCCACAGGTGAAGGGGGTGAGCGGCCAATATTTTTCTGACTGTAACATAGCCAAACCCACCGCACAGG
















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|88521223|gb|CI448894.1|CI448894
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88277301|gb|CI398103.1|CI398103
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|29656761|gb|CB653036.1|CB653036
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88475803|gb|CI413074.1|CI413074
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|86842409|gb|CI335295.1|CI335295
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|86835581|gb|CI348038.1|CI348038
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88465137|gb|CI517306.1|CI517306
EST:     CTGTGGTGGACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|86864259|gb|CI334058.1|CI334058
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88531802|gb|CI460315.1|CI460315
EST:     CTGTGGTGAACACCATTGGAAGAATGGTATGTAAAACTGTAGAACAG                         GGTGCTNCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88506009|gb|CI433515.1|CI433515
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAAT
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGG-TGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAAT
EST: gi|38477927|gb|CF962060.1|CF962060
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|3764142|gb|AU030642.1|AU030642
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88280407|gb|CI401605.1|CI401605
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCNACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88277245|gb|CI398047.1|CI398047
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|86832996|gb|CI333595.1|CI333595
EST:     CTGTGGT-AACACCATT-GAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88462690|gb|CI517219.1|CI517219
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|86870124|gb|CI318040.1|CI318040
EST:     CTGTGGTGAACACCAGTTGNAAAAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCA-TTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88478793|gb|CI416064.1|CI416064
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTNCAACGACATNTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88525522|gb|CI452377.1|CI452377
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88286185|gb|CI522485.1|CI522485
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|86863517|gb|CI345235.1|CI345235
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|86865757|gb|CI335450.1|CI335450
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|86841577|gb|CI336520.1|CI336520
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAAGCTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAA-CTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|86598223|gb|CI354840.1|CI354840
EST:     CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
EST: gi|88277264|gb|CI398066.1|CI398066
EST:     CTGTGGTGGACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAG                         GGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA
genomic: CTGTGGTGAACACCATTGGAAGAATCGTATGTAAAACTGTAGAACAGgtgaactttt ... tattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgttgtagtgtggaacatctaggcgactctaacctcgtgatattattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATAAGTGGGAAGTACTTCAGCAACTGCAATTTAGAGACCCCAAGCTCACAGG
                            ctctaac  putative branch site (score: 2)
                                            ttatttttt  putative PPT
                                       tgatattatttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaactttttttaaaaaaaatgaaaaatctcgtcttttatatatgttgttatgttgtagtgtggaacatctaggcgactctaacctcgtgatattattttttagGGTGCTGCAACGACATGTTATGTGGCATTACATCCTCAAGTTACTGGAATAAGTGGGAAGTACTTCAGCAACTGCAATTTAGAGACCCCAAGCTCACAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA