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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttatacattttcccatgctttgcctctaaaaccttgttagttataactattctaagctatccggtatgcctgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCATTTGTTCCACATGATCAAGAGTACTATCTTTCTATTGTATCAGAGAGGC

Basic information

species Oryza sativa
transcript LOC_Os12g37870.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G034083_T02 (Zea mays), 3'ss of exon 2
---gtagttatacattttcccatgctttgcctcta---aaaccttgttagttataactattc-taagctatccgg-----tatgcctg-ttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCATTTGTTCCACATGATCAAGAGTACTATCTTTCTATTGTATCAGAGAGGC------
        || |||| |||||||| |||    |     |||| ||| |   || | |||||  | | || |  |      | |||    ||||  |||| ||||||||||||||||| ||||| |||||||| ||||||||||| |||||||| |||||||| ||||||||||| ||||| |||||||| || ||||      
gtcacgacta-acatattcccatgttttttaccagcacaaactttgattactaaagctatttattatctttatgaatgaatttgctcacttatctaggtcgagATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGCTTGGCA

upper sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G034083_T01 (Zea mays), 3'ss of exon 2
--------gtagttatacattttcccatgctttgcctcta---aaaccttgttagttataactattc-taagctatccgg-----tatgcctg-ttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCATTTGTTCCACATGATCAAGAGTACTATCTTTCTATTGTATCAGAGAGGC
             || |||| |||||||| |||    |     |||| ||| |   || | |||||  | | || |  |      | |||    ||||  |||| ||||||||||||||||| ||||| |||||||| ||||||||||| |||||||| |||||||| ||||||||||| ||||| |||||||| || ||||
gtactgtcacgacta-acatattcccatgttttttaccagcacaaactttgattactaaagctatttattatctttatgaatgaatttgctcacttatctagGTCGAGATGGGTGGCTGCAAAGCTCCAATTACAACCTTCATAGTTGAACCATTTGTGCCACATGACCAAGAGTACTACCTTTCGATTGTATCTGAAAGGC

upper sequence: LOC_Os12g37870.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 3'ss of exon 2
gtagttatacattttcccatgctttgcctctaaaaccttgttagttataactattctaagctatccggtatgcctgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCATTTGTTCCACATGATCAAGAGTACTATCTTTCTATTGTATCAGAGAGGC
   || ||  ||    | |   ||| ||   | ||  |||  | | ||   | |        ||  |   ||  |  | |  |||||||||||||||| |||||||| || || || || || || ||||| || |||||||| ||||| |||||||| || ||||| |||||||| || ||||
---gtgatgaatgcatcaaa--tttacc---agaattttggcactaattcatttctgttaacatgtgaattggattctctttagGTTGAGATGGGTGGTTGCAAGGCACCAATAACCACTTTTATTGTTGAACCGTTTGTTCCCCATGACCAAGAGTATTACCTTTCGATTGTATCTGATAGGC

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|27577556|gb|CB000251.1|CB000251
EST:     CGCCAATTCGTCAAAGAGCGGNTGGGAGTTGCC                         TTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: CGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|29669993|gb|CB666268.1|CB666268
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|88356219|gb|CI627667.1|CI627667
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|569539|gb|D40388.1|D40388
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|3090568|gb|C93555.1|C93555
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|33676456|gb|CF304695.1|CF304695
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
EST: gi|2431459|gb|C73879.1|C73879
EST:     TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAG                         GTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA
genomic: TAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCA

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: 71 (upstream exon), 70 (downstream exon)
Score: 23

CGACATGCTGTTTGGCAAACGTGGGAAGAGTGGCCTTGTGGCCCTCAACCTAGATCTTGCTCAAGTCCGCCAATTCGTCAAAGAGCGGTTGGGAGTTGAGgtagttatac ... tgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCATTTGTTCCACATGATCAAGAGTACTATCTTTCTATTGTATCAGAGAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaaaccttgttagttataactattctaagctatccggtatgcctgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCATTTGTTCCACATGATCAAGAGTACTATCTTTCTATTGTATCAGAGAGGC
               ttataac  putative branch site (score: 23)
           ttagttataactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagttatacattttcccatgctttgcctctaaaaccttgttagttataactattctaagctatccggtatgcctgttatgcagGTTGAGATGGGTGGCTGCAAGGCTCCTATTACAACATTCATAGTTGAGCCATTTGTTCCACATGATCAAGAGTACTATCTTTCTATTGTATCAGAGAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG