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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggcatatttagaatatgaaagggaaaaaaaaaagaaagttgcagttcagacatgcaccggcagaaaaatcactgaacttcctgttgatttcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCTCAAAGAAAAGCTACCTGCTGAATAAATTCTGGTGGGAATTAATGTATGC

Basic information

species Oryza sativa
transcript LOC_Os02g58030.1
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58030.1 (Oryza sativa), 3'ss of exon 20
lower sequence: GRMZM2G015090_T01 (Zea mays), 3'ss of exon 17
gggcatatttagaatatgaaagggaaaaaaaaaagaaagttgcagttca----gacatgcaccggcagaaaaat-cactgaacttcctgttgatttcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCTCAAAGAAAAGCTACCTGCTGAATAAA--TTCTGGTGGGAATTAATGTATGC
       ||  ||  |  | |  |||| ||||  ||||  |  |||| |    |||||    |  |   | |||   || | | |||||||| |||| | ||||||||| | || |||||| |||||||||||||||||||| |||| ||||| |||||||||||  | ||  ||||||||   || | |    || || ||| || 
-----ctttgtgacaaaaagaatgaaataaaagggaaatatatagttgacggagacattggtcaacgttacaatatgcttagcctcctgttgctttcttgtgcagCATAAGACGAACTCTGTTGGAGCGAGGAACGAAAGCAGTTCTCAAGTACCTCAAAGAAAAATTGCCGTCTGAATAATATTTATAGAACAAACTATTGT-TG-
















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|88270323|gb|CI385581.1|CI385581
EST:     CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|87007099|gb|CI277174.1|CI277174
EST:     CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|88557769|gb|CI488203.1|CI488203
EST:     CCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|88271595|gb|CI387648.1|CI387648
EST:     CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGCCGGACTCTGATGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|88457382|gb|CI534380.1|CI534380
EST:     GATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: GATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|88835733|gb|CI370838.1|CI370838
EST:     CCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|88263721|gb|CI366622.1|CI366622
EST:     CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|88271454|gb|CI387507.1|CI387507
EST:     CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|88266303|gb|CI377205.1|CI377205
EST:     CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|109713039|gb|CI105647.1|CI105647
EST:     CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
EST: gi|86495873|gb|CI138506.1|CI138506
EST:     CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAG                         CATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT
genomic: CTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCT

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

GGTTTGCTTGAGCCTAACCTGCAAGTCTTGAAACTTGATGGAAATCCCCTCAGGAGgtaagaagta ... tcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCTCAAAGAAAAGCTACCTGCTGAATAAATTCTGGTGGGAATTAATGTATGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagacatgcaccggcagaaaaatcactgaacttcctgttgatttcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCTCAAAGAAAAGCTACCTGCTGAATAAATTCTGGTGGGAATTAATGTATGC
                                     tgttgat  putative branch site (score: 6)
                                           tttcgtct  CT-rich tract
                 agaaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggcatatttagaatatgaaagggaaaaaaaaaagaaagttgcagttcagacatgcaccggcagaaaaatcactgaacttcctgttgatttcgtctgcagCATACGGCGGACTCTGCTGGAGCGAGGAACGAAAGCAATTCTGAAGTATCTCAAAGAAAAGCTACCTGCTGAATAAATTCTGGTGGGAATTAATGTATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - -aagggaaa
- - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - gttgcag
- - - - - - - - - - - - - - - - - - - - - - - - - acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccggcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaatca