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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctattttcttttttttaaataccattactcatggggttcaatttcaaacaattattgacctaactatcattgatatgcaatttttttaatgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCTACGAGGGTTGCTTAACAAACTTTGACATTGGTGACAATGGAGCCGAAGC

Basic information

species Oryza sativa
transcript LOC_Os12g16220.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv02s0033g00260.t01 (Vitis vinifera), 3'ss of exon 3
agctattttcttttttttaaataccattactcatggggttcaatttcaaacaattatt-----gacctaactatcattgATATGCAATTTTTTTAATGCAAGCAGATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCTACGAGGGTTGCTTAACAAACTTTGACATTGGTGACAATGGAGCCGAAGC
            |  |  | | |  ||  ||  ||   |    ||| ||   ||||||     ||   |  |   ||   | | |  |  |  |       | || | |  | | |||    ||||| ||| ||  ||||||||| ||||||| ||| || ||||| |||||||||||||| || || ||  | ||||  |||||
-----------gtaatcaagaaattatggct--tgaattcttttttgaattcattattataaggatggagtttctataagtttactttcgtcctccattgtgtagGTCTTGACTATGCCGGCCAAGTTGGAGTAGGACATTTCTATCACATTTACTATGAAGGTTGTTTAACAAACTTTGAAATAGGGGAAGAGGGAGAAGAAGC

upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 3
agctattttcttttttttaaataccattactcatggggttcaatttcaaacaattattgacctaactatcattgATATGCAATTTTTTTAATGCAAGCAGATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCTACGAGGGTTGCTTAACAAACTTTGACATTGGTGACAATGGAGCCGAAGC
                          | |   ||| |    | | ||   |||   || || | ||  ||||| ||    | | ||| ||  |   | || || | | ||||| || ||||| ||  || |||||||||| ||||||| |||||||||||| || || |||||||| ||||| ||  | ||||  |||||
-------------------------gtaagaaatgagaaatattgtcttccaac--tttactttacattcatttattcatattctttatatggt--gtagGTAAGGACTTTGCATTACAAGTTGGGGTAGCACATTTCTATCACATTTACTACGAGGGTTGTTTGACGAACTTTGAGATTGGAGAAGAGGGAGAAGAAGC

upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv17s0053g00460.t01 (Vitis vinifera), 3'ss of exon 3
agctattttcttttttttaaataccattactcatggggttcaatttcaaacaattattgacctaactatcattgATATGCAATTTTTTTAATGCAA-GCAGATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCTACGAGGGTTGCTTAACAAACTTTGACATTGGTGACAATGGAGCCGAAGC
                | | | |  |  | |  ||   | ||| || | |  |  ||| |  ||   ||   |  | | ||   | | |  ||    | || || | | ||| | || ||||| ||  ||  ||||||||| ||||||| ||||||||||||||||||||||||||| || || ||| | ||||  |||||
---------------gtaataaatgagaaatattgacttccaactttacattac-attcatttattgatttattctttcca---tatatggtgtggtgtagGTAAGGACTTTACCTTCCAAGTTGGGGTAGGACATTTCTATCACATTTACTACGAGGGTTGCTTAACAAACTTTGAGATCGGAGACGAGGGAGAAGAAGC

upper sequence: LOC_Os12g16220.3 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv02s0033g00270.t01 (Vitis vinifera), 3'ss of exon 3
-------------------agctattttcttttttttaaataccattactcatggggttcaatttcaaacaattattgacctaactatcattgATATGCAATTTTTTTA---ATGCAA----GCAGATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCTACGAGGGTTGCTTAACAAACTTTGACATTGGTGACAATGGAGCCGAAGC
                   | ||  |  ||||   ||| || |  | |   |   |  |  ||||      | | ||    ||    |  ||  ||| |  |   | ||   |||  |    | || |||| | | |||    ||||| ||  ||  ||||||||| ||||||| |||||||||||| |||||||||||||| || || ||    ||||  |   |
gttataactgagaaataaaaacttctaactttacattacattcattcatctacaagtatttattt--gttcacttttagtttagtacttgtttttattctttccatatatgcatggtatgttgtagGTATGGACTATGCAAGCCAAGTTGGGGTAGGACATTTCTATCACATTTACTACGAGGGTTGTTTAACAAACTTTGAAATCGGAGAAGGGGGAGAAGCTAC

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|88470882|gb|CI408153.1|CI408153
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88515840|gb|CI443494.1|CI443494
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88547420|gb|CI477710.1|CI477710
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTGT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88532962|gb|CI462297.1|CI462297
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|4716392|gb|AU057508.1|AU057508
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88484916|gb|CI422187.1|CI422187
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88295031|gb|CI522985.1|CI522985
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88555668|gb|CI485944.1|CI485944
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88552997|gb|CI483062.1|CI483062
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88528983|gb|CI457271.1|CI457271
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88542998|gb|CI472362.1|CI472362
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88520930|gb|CI448584.1|CI448584
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|89197834|gb|CI013824.1|CI013824
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88503627|gb|CI431133.1|CI431133
EST:     CTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTTT
genomic: CTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88993999|gb|CI114289.1|CI114289
EST:     TCTTACGAAATCCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|15854562|gb|BI807374.1|BI807374
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCCATGAAAG                         ATATGCCATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88549860|gb|CI479786.1|CI479786
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|55410765|gb|CV723141.1|CV723141
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|117233147|gb|CT848013.1|CT848013
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88546924|gb|CI477184.1|CI477184
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|86895324|gb|CI331241.1|CI331241
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88478471|gb|CI415742.1|CI415742
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88522294|gb|CI450041.1|CI450041
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|9866068|gb|AU101818.1|AU101818
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88486771|gb|CI424042.1|CI424042
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88469147|gb|CI406418.1|CI406418
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|33665681|gb|CF296648.1|CF296648
EST:     CCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: CCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88554679|gb|CI484872.1|CI484872
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
EST: gi|88525405|gb|CI453408.1|CI453408
EST:     TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAG                         ATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT
genomic: TCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCT

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: 74 (upstream exon), 69 (downstream exon)
Score: 2

CTCACTCATAACGAGCTGATCGCAATGTGGGAAAAACTCTCTGGAAAAAGTCTTACGAAATTCCACATACCTGCTGAAGAATTTTTGGCTCCAATGAAAGgtaaaaataa ... atgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCTACGAGGGTTGCTTAACAAACTTTGACATTGGTGACAATGGAGCCGAAGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaacaattattgacctaactatcattgatatgcaatttttttaatgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCTACGAGGGTTGCTTAACAAACTTTGACATTGGTGACAATGGAGCCGAAGC
                         attgatatgcaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctattttcttttttttaaataccattactcatggggttcaatttcaaacaattattgacctaactatcattgatatgcaatttttttaatgcaagcagATATGCAATTTGCTTTTCAAGTGGGAATAACACATTTCTACCACATTTTCTACGAGGGTTGCTTAACAAACTTTGACATTGGTGACAATGGAGCCGAAGC

- - - - - - - - - - - - - - - - - - - - - - -tcaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atatgca