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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttcagttcatcttacgaaaccgcttgttgtcaatgttggtctctgattctttctcagcaagtagcatgattgttgtctaacttttgcatcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG

Basic information

species Oryza sativa
transcript LOC_Os04g23890.2
intron # 18
splice site 3'
intron type U2

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|29685192|gb|CB681467.1|CB681467
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29618297|gb|CB623309.1|CB623309
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29619193|gb|CB624205.1|CB624205
EST:     TCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: TCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29679663|gb|CB675938.1|CB675938
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29680790|gb|CB677065.1|CB677065
EST:     ATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: ATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29626656|gb|CB631667.1|CB631667
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29615866|gb|CB620878.1|CB620878
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|33799059|gb|CF325389.1|CF325389
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29685421|gb|CB681696.1|CB681696
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29612811|gb|CB617824.1|CB617824
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29630592|gb|CB635601.1|CB635601
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29620201|gb|CB625213.1|CB625213
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|88306572|gb|CI671324.1|CI671324
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGG
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGG
EST: gi|29619194|gb|CB624206.1|CB624206
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|88578420|gb|CI687351.1|CI687351
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29613428|gb|CB618441.1|CB618441
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|86481914|gb|CI124547.1|CI124547
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29618974|gb|CB623986.1|CB623986
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|29646470|gb|CB651477.1|CB651477
EST:     ACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: ACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
EST: gi|113931112|gb|DQ883893.1|DQ883893
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCT
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCT
EST: gi|88580457|gb|CI697388.1|CI697388
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTG
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTG
EST: gi|33381050|gb|CF196393.1|CF196393
EST:     CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCA                         GAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC
genomic: CTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTC

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: 68 (upstream exon), 73 (downstream exon)
Score: 29

AAAACGAAGAAGGTCACAAGAATTTCTCCCCCCAACATTTGTCTCAGAACCTTCCACTCCATCAAATTCATTTGTTGGTACTGAAGAGTATATCGCTCCAgtaagaatga ... atcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgattctttctcagcaagtagcatgattgttgtctaacttttgcatcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG
                                gtctaac  putative branch site (score: 29)
                                              tcgtttt  putative PPT
                                   taactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttcagttcatcttacgaaaccgcttgttgtcaatgttggtctctgattctttctcagcaagtagcatgattgttgtctaacttttgcatcgttttagGAGGTTATAACGGGTGCAGGGCATACAAGTGCAATCGATTGGTGGGCTCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG