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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaaattcatttctcgtttcattatctgaagatttctttggcactaccatgattatttgactgcaaccattctttttggaggaatatttctgttacaaattcgaattcagcttccattgaatactacttttttcacaataactagctaagatatgctcctaattttgtttag

Basic information

species Oryza sativa
transcript LOC_Os01g51920.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51920.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G425249_T01 (Zea mays), 5'ss of exon 5
ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaaattcatttctcgtttcattatctgaagatttctttggcactaccatgattatttgactgcaaccattctttttggaggaatatttctgttacaaattcgaattcagcttccattgaatactacttttttcacaataactagctaagatatgctcctaattttgtttag
|   ||||||||||||||||||||| ||||| ||||| | || ||||||||| |   |  ||| |  | |||| ||        | | | | | | | | |  ||  |   | |||| |   |   |||    |||  ||  |     ||  ||                                                                        
ATGTTGATGAGCAGAAGCGTTTTGTTAAGACCTACCTGAACATTTCTGgtaattctgagctcactgttggtttaat-------ggttctgtattgtagttcagtg-ctgcataactgtacgtaaattttcatcaggggtacgtacagaacgcatca----------------------------------------------------------------------
















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|87037984|gb|CI192606.1|CI192606
EST:     CTGATGAGCAGAAGCGTTTTGCGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: CTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|86497719|gb|CI140352.1|CI140352
EST:     ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|325494505|gb|JG459029.1|JG459029
EST:     ACACTGATGAGCAGAAGCGTAATGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAACAGGTGGAGAACCTTCTCC
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCC
EST: gi|58672419|gb|CK061105.1|CK061105
EST:     ACACTGATGAACAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|58588260|gb|CF986568.1|CF986568
EST:     ACACTGATGAACAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|86500529|gb|CI143162.1|CI143162
EST:     ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|29634653|gb|CB639662.1|CB639662
EST:     TGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTC--                         T--GTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: TGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|86495212|gb|CI137845.1|CI137845
EST:     ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|86851235|gb|CI312636.1|CI312636
EST:     ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|86496165|gb|CI138798.1|CI138798
EST:     ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|40488156|gb|BX898760.1|BX898760
EST:     ACACTGATGAACAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAACAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|86499149|gb|CI141782.1|CI141782
EST:     GTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: GTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|86500222|gb|CI142855.1|CI142855
EST:     ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|33676093|gb|CF304332.1|CF304332
EST:     ACACTGATGATCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
EST: gi|87024609|gb|CI259324.1|CI259324
EST:     TACCTAAGCAATTCTG                         TAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG
genomic: TACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTG

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), 72 (downstream exon)
Score: 83

ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaa ... ttttgtttagTAAGTGAAGAACCTGATGCGGAAGAGGTGGAGAACCTTCTCCAAAGCATTGAGAAATACACGCTCGCCAGTCATCTAGTTTGGGGCCTCTGGGGAATAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACACTGATGAGCAGAAGCGTTTTGTGAAGACGTACCTAAGCAATTCTGgtaagtgcaaattcatttctcgtttcattatctgaagatttctttggcactaccatgattatttgactgcaaccattctttttggaggaatatttctgttacaaattcgaattcagcttccattgaatactacttttttcacaataactagctaagatatgctcctaattttgtttag

- - - - GAGCAG
- - - - - - AGAAGC
- - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - -  AAGCAA