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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctattttctgatccaagtacttagctgagtcgtatgatttaccatacatttttttgtggtcccaccctgattgtcaatttgtttgcatctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTTCACAG

Basic information

species Oryza sativa
transcript LOC_Os06g49110.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g49110.1 (Oryza sativa), 3'ss of exon 7
lower sequence: PP1S450_21V6.2 (Physcomitrella patens), 3'ss of exon 6
ttctattttctgatccaagtacttagctgagtcgtatgatttaccatacatttt-tttgtggtcccaccctg------attgtcaatttgtttgcatctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTTCACAG
     |      ||  ||  ||||| |||| |   |||| |  | |   |       ||     |||  |||      ||  | |   ||      ||      ||||||| |||||||| || || |||||| ||||||| ||||||||||| ||  |||||
-----tccatcaattaaa--acttaactgaattcaatgaatagctaaggaaaagacctgacacaccatactgcaaatcatgcttaccatggacatgtcctaatacagGAGTGATTATGAACGACGAGACAGTTCATCAACTTTGCAAGCAGGCCGTAGCACAG
















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:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29616370|gb|CB621382.1|CB621382
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29619108|gb|CB624120.1|CB624120
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29666981|gb|CB663256.1|CB663256
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29660427|gb|CB656702.1|CB656702
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29617546|gb|CB622558.1|CB622558
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29621569|gb|CB626580.1|CB626580
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29673911|gb|CB670186.1|CB670186
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29641824|gb|CB646831.1|CB646831
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATG
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATG
EST: gi|29687455|gb|CB683730.1|CB683730
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGNAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAA
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAA
EST: gi|29672090|gb|CB668365.1|CB668365
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29661434|gb|CB657709.1|CB657709
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCCAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29641133|gb|CB646140.1|CB646140
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAAC
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAAC
EST: gi|29679002|gb|CB675277.1|CB675277
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29619411|gb|CB624423.1|CB624423
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGC
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGC
EST: gi|29637162|gb|CB642171.1|CB642171
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29624060|gb|CB629071.1|CB629071
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29682583|gb|CB678858.1|CB678858
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATG
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATG
EST: gi|29619315|gb|CB624327.1|CB624327
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|9788971|gb|BE530981.1|BE530981
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29643724|gb|CB648731.1|CB648731
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAAACAGTT-ATCAACTGTGCAAGCAGGCTGTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAA-CAGTTTATCAACTGTGCAAGCAGGCTGTT
EST: gi|29655802|gb|CB652077.1|CB652077
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGT
EST: gi|29637541|gb|CB642550.1|CB642550
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29681299|gb|CB677574.1|CB677574
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGA
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGA
EST: gi|29688148|gb|CB684423.1|CB684423
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGACACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
EST: gi|29660273|gb|CB656548.1|CB656548
EST:     TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATG                         GAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT
genomic: TCTGGACCCTTATTCATCTGATGGTCATGATGGCATTGTCAGGGAAGATGgtaaggaaaa ... ctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacatttttttgtggtcccaccctgattgtcaatttgtttgcatctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTTCACAG
                     ccctgat  putative branch site (score: 4)
     tttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctattttctgatccaagtacttagctgagtcgtatgatttaccatacatttttttgtggtcccaccctgattgtcaatttgtttgcatctcgtaccagGAGTAATTATGAATGATGAAACAGTTTATCAACTGTGCAAGCAGGCTGTTTCACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT