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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccctcccagcttctcatgcatgttgctctttcttcatatcaaacagtccactagttgtgcattcatatacttttgcggtctgtctgatctattt...

Basic information

species Oryza sativa
transcript LOC_Os12g02390.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G347541_T01 (Zea mays), 5'ss of exon 10
TGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccctcccagcttctcatgcatgttgctctttcttcatatcaaa---cagtc-cactagttgtgcattcatatacttttgcggt-----ctgtctgatctattt-----------
||||||||| | ||||| | |||||| ||||| ||||||||||| |||||||| ||||| || ||| ||||||| |||||||||||||| ||||||||||||||||  || ||        |  |     |||  || || |  |  ||   ||||   |  |  | ||  || | |||    ||   |     || ||   | | |||           
TGCCAGTGCGAAGAATGCAGATGCAAAAACACGTGGGGAAGCTACGAGTGCGGCTGCAGCGGGGGCCTGCTTTACATGAAGGAGCATGACACATGCATAAgtatgtagcttccgcacatgtacactgtcagcttattgttgagttggaagctcagtagtagcaactatgttttaacatagacatgaacttgacactctcaagtgtgtttgtcgtactcag

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G389362_T01 (Zea mays), 5'ss of exon 11
TGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccctcccagcttctcatgca-tgttgctctttcttcatatcaaacagtccactagttgtgcattcatatacttttgcggtctgtctgatctattt
|| || ||||| ||||| |||||||| ||||||||||||||||||||||| || |||||||| ||||||||||| |||||||||||||||||||||||||||||||    |||   | | |   || | |     | |  |    |||  |  |     |  | || ||| ||  || || |   |        |   || 
TGTCAATGCAAAGAATGCAAATGCAAAAACACATGGGGAAGCTATGAGTGTGGCTGCAGTGGAGGCTTGCTTTACATGAAGGAGCATGATACATGCATAAgtatgtgtaaccctcatacacgcacactatcagcttattattgagtcactctttttttcatgt-tgaattaattaaccttagacttagaggctgtaagtta

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT2G30290.2 (Arabidopsis thaliana), 5'ss of exon 11
TGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccctcccagcttctcatgcatgttgctctttcttcatatcaaacagtccactagttgtgcattcatatacttttgcggtctgtctgatctattt
||||| ||    || || |||||||| |||||||||||||||||||| ||  ||||||| ||  |||||||||| || |  || || || |  ||||||||||| |  | | ||     |||| |||  |    ||||     | | ||   | ||||| |  |  | |  | |||                        
TGCCAATGTCGCGATTGCAAATGCAAAAACACATGGGGAAGCTATGAATGTAGTTGCAGCGGAAGCTTGCTTTACATAAGAGAACACGACATTTGCATAAgtatattacactca-----tcattcatcatat--tttcgaataaacgaatcattcactaatcattaacttgtgtacag----------------------

upper sequence: LOC_Os12g02390.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv08s0058g01360.t01 (Vitis vinifera), 5'ss of exon 10
TGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccctcccagcttctcatgcatgttgctctttcttcatatcaaacagtccactagttgtgcattcatatacttttgcggtctgtc-tgatctattt----
||| | ||    || || ||||||||||| || |||||||| ||||||||| | |||||||||   ||  | || |||   || |||||  | || ||||||  ||   |  | |  |        || |   |||| |  || | ||  |  | | |      | | | ||| || | | |  |    |   ||  |       
TGCAATTGTCCAGAGTGCAAATGCAAGAATACCTGGGGAAGTTATGAGTGCAGCTGCAGTGGCAATTTATTGTACATGCGAGAACATGACGCCTGTATAAgtgagtatttttctgaatgct---tctgctttcctttttcgatgt-aaggatcctagtgagaaagaaataata-acctgtccaattcaccaccataaaacccaag

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|86598375|gb|CI354992.1|CI354992
EST:     CGGCTTGCTTTATATGAAGGAGCATGATACATGCATAA                         GCAAAAATGCAGCAACAGATGTAGGATGGAACTTCTTGT-GGTGATCTTCT
genomic: CGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccct ... ctatattcagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
EST: gi|58673963|gb|CK062649.1|CK062649
EST:     CGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAA                         GCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
genomic: CGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccct ... ctatattcagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
EST: gi|88955756|gb|CI092045.1|CI092045
EST:     TATGAAGGAGCATGATACATGCATAA                         GCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
genomic: TATGAAGGAGCATGATACATGCATAAgtatgtccct ... ctatattcagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
EST: gi|2312600|gb|C28755.1|C28755
EST:     CGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAA                         GCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
genomic: CGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccct ... ctatattcagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
EST: gi|88837810|gb|CI079170.1|CI079170
EST:     GGAGCATGATACATGCATAA                         GCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
genomic: GGAGCATGATACATGCATAAgtatgtccct ... ctatattcagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
EST: gi|88960134|gb|CI382012.1|CI382012
EST:     CAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAA                         GCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
genomic: CAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccct ... ctatattcagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
EST: gi|86494648|gb|CI137281.1|CI137281
EST:     CGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAA                         GCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT
genomic: CGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccct ... ctatattcagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCT

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), 72 (downstream exon)
Score: 30

TGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccct ... ctatattcagGCAAAAATGCAGCAACAGAGGTAGGATGGAACTTCTTGTGGGTGATCTTCTTTGGCCTAGTGGTAGCCGGCATTGCAGGATACGCAGTATACAAGTACAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCAGTGCAAGGAATGTAAATGCAAGAACACATGGGGAAGCTATGAGTGCGGTTGCAGTGGCGGCTTGCTTTATATGAAGGAGCATGATACATGCATAAgtatgtccctcccagcttctcatgcatgttgctctttcttcatatcaaacagtccactagttgtgcattcatatacttttgcggtctgtctgatctattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctccc