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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTACAAGTCTCGTGATGTTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaacgaatataattcattttctgtttcatgtgtattaatatcttgagttgacttaatactctttgttccttcag

Basic information

species Oryza sativa
transcript LOC_Os06g49110.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv18s0001g02550.t01 (Vitis vinifera), 5'ss of exon 4
GTCTACAAGTCTCGTGATGTTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaacga-atataattcattttctgtttcatgtgtattaatatcttga-gttgacttaatactct--ttgttccttcag------
||    ||| | || ||||||||||| |||||| ||||||| ||||| |||||||| ||||| ||||||||  ||   |   ||  | ||   ||| ||  |    |  | | ||||  ||  ||   | |  |  | |  ||||| |||         
GTTGCAAAGGCCCGGGATGTTGGTGTAAACAGTGTTGTGCTCTTTCCTAAAGTTCCAGATGCCTTGAAGgttcttattctccatccagtttcctttttgaattccataaaatgatataatggtgtcatcattgtcatgtaattgtttcttgcacactag

upper sequence: LOC_Os06g49110.2 (Oryza sativa), 5'ss of exon 4
lower sequence: PP1S219_94V6.4 (Physcomitrella patens), 5'ss of exon 5
GTCTACAAGTCTCGTGATGTTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaacgaatataattcattttctgtttcatgtgtattaatatcttgagt-tgacttaatactctttgttc-cttcag----------------------
|| |||||| |  | ||||||||||| |||||| |||| || ||||| ||||| ||||||||  ||||||||  ||   ||   ||||| ||||| | |   || || |   ||| || | || | |  | | |   |   ||| || ||                       
GTGTACAAGGCAAGAGATGTTGGTGTCAACAGTGTTGTTCTTTTTCCCAAAGTCCCTGATGCTCTGAAGgtaagtc--tgacagtaatttattttttctccaatctgaa--gataactcgtgtgtaagatgaaatgatgaattcgctgcaattgagtatcgtaattttatcca
















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|29681115|gb|CB677390.1|CB677390
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29644874|gb|CB649881.1|CB649881
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGG
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGG
EST: gi|29616370|gb|CB621382.1|CB621382
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29619108|gb|CB624120.1|CB624120
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29613357|gb|CB618370.1|CB618370
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAA-GTTCCTGATGCATTGAAG                         TCTCAATCTGGAGA
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGA
EST: gi|29666981|gb|CB663256.1|CB663256
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29660427|gb|CB656702.1|CB656702
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29617546|gb|CB622558.1|CB622558
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29621569|gb|CB626580.1|CB626580
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29673911|gb|CB670186.1|CB670186
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29641824|gb|CB646831.1|CB646831
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29687455|gb|CB683730.1|CB683730
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29672090|gb|CB668365.1|CB668365
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29661434|gb|CB657709.1|CB657709
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29645158|gb|CB650165.1|CB650165
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGA
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGA
EST: gi|29641133|gb|CB646140.1|CB646140
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29679002|gb|CB675277.1|CB675277
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29619411|gb|CB624423.1|CB624423
EST:     TTGGTGTTAACAGATTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29667711|gb|CB663986.1|CB663986
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29615586|gb|CB620598.1|CB620598
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29637162|gb|CB642171.1|CB642171
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29624060|gb|CB629071.1|CB629071
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29682583|gb|CB678858.1|CB678858
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29619315|gb|CB624327.1|CB624327
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|9788971|gb|BE530981.1|BE530981
EST:     GGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: GGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|58612032|gb|CK039744.1|CK039744
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTC
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTC
EST: gi|29643724|gb|CB648731.1|CB648731
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29655802|gb|CB652077.1|CB652077
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29637541|gb|CB642550.1|CB642550
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29681299|gb|CB677574.1|CB677574
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29688148|gb|CB684423.1|CB684423
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
EST: gi|29660273|gb|CB656548.1|CB656548
EST:     TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAG                         TCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT
genomic: TTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaac ... gttccttcagTCTCAATCTGGAGATGAGGCATACAATGATAATGGTTTGGTTCCACGGACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTACAAGTCTCGTGATGTTGGTGTTAACAGTTTTGTGCTGTTTCCAAAAGTTCCTGATGCATTGAAGgtatttcaacgaatataattcattttctgtttcatgtgtattaatatcttgagttgacttaatactctttgttccttcag

- - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG