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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTGCGGCGGGCTCGCCGGAGTTGGATCCGGCGGAAGAGAGGATTTCTGGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttcttggattactttggtttttttatgctgtggagctgtaatccctgttgcagttgagctcttctggtcgcccagaagcattattattatcaatt...

Basic information

species Oryza sativa
transcript LOC_Os01g59690.1
intron # 1
splice site 5'
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|88728392|gb|CI751902.1|CI751902
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88408172|gb|CI601650.1|CI601650
EST:     GGGAAGGGTGCCGGGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGGTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88362803|gb|CI614159.1|CI614159
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88306993|gb|CI639423.1|CI639423
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88729174|gb|CI752684.1|CI752684
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTCCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88826727|gb|CI777292.1|CI777292
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88385267|gb|CI630368.1|CI630368
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCA
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCA
EST: gi|88736472|gb|CI759980.1|CI759980
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88300354|gb|CI584773.1|CI584773
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88309838|gb|CI656972.1|CI656972
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88356621|gb|CI617704.1|CI617704
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88730418|gb|CI754031.1|CI754031
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88336952|gb|CI627032.1|CI627032
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCT-GAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88338648|gb|CI644105.1|CI644105
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|29663260|gb|CB659535.1|CB659535
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88318178|gb|CI629459.1|CI629459
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|58596804|gb|CK007332.1|CK007332
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGGACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|218479623|gb|FG945754.1|FG945754
EST:     GTGGTGGCCTT-AG                         GAAATCGCTTCANTTTCGAACGGGCTG-TCAGTTGGCTGGACGATTCATTT
genomic: GTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88426680|gb|CI579509.1|CI579509
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88574256|gb|CI666025.1|CI666025
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|86905496|gb|CI285459.1|CI285459
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|29638826|gb|CB643835.1|CB643835
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88759766|gb|CI769322.1|CI769322
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88314267|gb|CI602599.1|CI602599
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|58674366|gb|CK063052.1|CK063052
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|2310270|gb|C26425.1|C26425
EST:     GGGAAGGGTGCCGCGAAG-TGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88445493|gb|CI587106.1|CI587106
EST:     GGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGTTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGT-GGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88741215|gb|CI764723.1|CI764723
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|117245628|gb|CT848470.1|CT848470
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88358967|gb|CI619471.1|CI619471
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88336656|gb|CI643981.1|CI643981
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88744452|gb|CI767812.1|CI767812
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88439161|gb|CI604446.1|CI604446
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCT-GAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88398600|gb|CI598565.1|CI598565
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
EST: gi|88303306|gb|CI668954.1|CI668954
EST:     GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAG                         GAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT
genomic: GGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTT

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: 57 (upstream exon), 59 (downstream exon)
Score: 6

AAGCTGCGGCGGGCTCGCCGGAGTTGGATCCGGCGGAAGAGAGGATTTCTGGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttctt ... tttgtttcagGAAATCGCTTCAATTTCGAACGGGCTGTTCAGTTGGCTGGACGATTCATTTCAAGAGCAGAAGTGTTTACACCAAGCCGTAGCAGAAGAGGGAATCCTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCTGCGGCGGGCTCGCCGGAGTTGGATCCGGCGGAAGAGAGGATTTCTGGGAAGGGTGCCGCGAAGCTGCTCGACGGCAGGCTCGTGGTGGCCTTGAGgtactttcttggattactttggtttttttatgctgtggagctgtaatccctgttgcagttgagctcttctggtcgcccagaagcattattattatcaatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG