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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacacttgtcgtttcagttagttactgaagatggctgtgtttgtaggatcccaatctatcttatacaagtactgattttgttttatattctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAATGTTATGGAGTTTCTAATTCTGGCTGGAGATCACCTTTACCGCATGGACT

Basic information

species Oryza sativa
transcript LOC_Os08g25734.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 2
-caacacttgtcgtttcagttagttactgaagatggctgtgtttgtaggatcccaatctatcttata-caagtactgattttgttttatattctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAATGTTATGGAGTTTCTAATTCTGGCTGGAGATCACCTTTACCGCATGGACT
   |  |     |     |   | ||||  | |||   || ||  |||    |    |||  |||   || ||| ||||||| ||||||||| |   ||||||||||||||||||||||||| |||||||| ||| | ||||||||||||||||| ||||| ||||||||||| ||||| |||||||| ||||| |||||||
atcatgccataagcaaatgcatgctactctacatgaa-gttttgctagcccacttcactagtttacgtcatgtattgattttcttttatattttt-tctcagGGTACTGCAGATGCTGTAAGGCAGTACTTGTGGTTGTTTGAGGAGCATAATGTGATGGAATTTCTAATTCTTGCTGGCGATCACCTGTACCGGATGGACT

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G163437_T01 (Zea mays), 3'ss of exon 2
-caacacttgtcgtttcagttagttactgaagatggctgtgtttgtaggatcccaatctatctta-tacaagtactgattttgttttatattctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAATGTTATGGAGTTTCTAATTCTGGCTGGAGATCACCTTTACCGCATGGACT
   |  | |   |     |   | || |  | | ||   | ||  |||    |    ||| |||| | |||||||||||||| ||||||||| |   ||||||||||||||||||||||||| || ||||| ||| |||||||||| |||||||| ||||||||||||||||| ||||| |||||||| ||||| ||||| |
atcatgccttaagcaaatgcatgctaatctaca-ggaaattttgttagcgcacttcactagcttactccaagtactgattttcttttatattttt-tctcagGGTACTGCAGATGCTGTAAGGCAATACTTGTGGTTATTTGAGGAACATAATGTGATGGAGTTTCTAATTCTTGCTGGCGATCACCTGTACCGGATGGATT

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 2
-------caacacttgtcgtttcagttagttactgaagatggctgtgtttgtag--gatcccaatctatcttatacaagtactgattttgttttatattctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAATGTTATGGAGTTTCTAATTCTGGCTGGAGATCACCTTTACCGCATGGACT
       || |||| | | |  |  | | ||   | |  | ||  || |    |  | |  |  |  || | ||      ||  | || || | ||      |   |||||||||||||||||||| || ||||| || ||||| ||||| ||||| |||||| |||| ||  |  |||||||||| || ||  | || || ||||| |
gtaatgccagcact-gccttgactctaaattttggtaccttgcgatgataactgttgttgtcccttgatttgatgttttaacaaacttggtgtgatc-----attgcagGGTACTGCAGATGCTGTGAGGCAGTATTTGTGGCTTTTTGAAGAGCACAATGTTTTGGAATTCTTGGTTCTGGCTGGTGACCATTTGTATCGAATGGATT

upper sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 2
-----caacac-ttgtcgtttcagttagttactgaagatggct-gtgtttgtaggatcccaatctatcttatacaagtactgattttgttttatattctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAATGTTATGGAGTTTCTAATTCTGGCTGGAGATCACCTTTACCGCATGGACT
      | ||| ||| | | |  |    | | |   |||  || | | |  |    |  |        | ||   | |  | |      ||  | |  | |   |||||||||||||||||||| || ||||| || ||||| ||||| ||||| |||||| |||| ||  |  |||||||||| || ||  | || || ||||| |
gtaatgaccacattgccttgtttgactctaaattttgatacctcgcgatgatgacttttcttgtcccttgattttattttttaacaaacttggtgtgatcattgcagGGTACTGCAGATGCTGTCAGGCAGTATTTGTGGCTTTTTGAAGAGCACAATGTTTTGGAATTCTTGGTTCTGGCTGGTGACCATTTGTATCGAATGGATT

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|58678083|gb|CK066770.1|CK066770
EST:     TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAG                         T
genomic: TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAGgtatcatact ... ctgacctcag-
EST: gi|58678083|gb|CK066770.1|CK066770
EST:     TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAG                         T
genomic: TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAGgtatcatact ... ctgacctcag-
EST: gi|15847618|gb|BI795908.1|BI795908
EST:     TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAG                         GGTACT-CAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT
genomic: TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAGgtatcatact ... ctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT
EST: gi|29614233|gb|CB619246.1|CB619246
EST:     TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAG                         GGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT
genomic: TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAGgtatcatact ... ctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT
EST: gi|88544256|gb|CI474337.1|CI474337
EST:     TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAG                         GGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT
genomic: TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAGgtatcatact ... ctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT
EST: gi|29681248|gb|CB677523.1|CB677523
EST:     TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAG                         GGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT
genomic: TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAGgtatcatact ... ctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT
EST: gi|58668409|gb|CK057095.1|CK057095
EST:     TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAG                         GGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT
genomic: TTGAAGTCCTCGCTGCACAGCAGAGCCCAGATAATCCTAACTGGTTTCAGgtatcatact ... ctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatcccaatctatcttatacaagtactgattttgttttatattctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAATGTTATGGAGTTTCTAATTCTGGCTGGAGATCACCTTTACCGCATGGACT
                                           ttctgac  putative branch site (score: 2)
                            tgattttgttttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacacttgtcgtttcagttagttactgaagatggctgtgtttgtaggatcccaatctatcttatacaagtactgattttgttttatattctgacctcagGGTACTGCAGATGCTGTAAGACAGTACTTATGGCTATTTGAGGAGCATAATGTTATGGAGTTTCTAATTCTGGCTGGAGATCACCTTTACCGCATGGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA