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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggggtttataacaattttagttaaagctaaagagtttcttgtgctgcatccatgatgtgttattaatcaatttgctttactctcttctatttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCTCACTGAGCCTGTTACTGAAGCAATAGCTTCTGCATTTGCTGCATGGTTA

Basic information

species Oryza sativa
transcript LOC_Os07g26610.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g26610.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G069676_T03 (Zea mays), 3'ss of exon 3
----tggggtttataacaattttagttaaagctaaagagtttcttgtgctgcatccatgatgtgttattaatcaatttgctttactctcttctatttctca-cagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCTCACTGAGCCTGTTACTGAAGCAATAGCTTCTGCATTTGCTGCATGGTTA
            |     ||||  ||||  | |    |     || || | ||    | |  | ||||  || || | |||||  |     || ||  |   |||||||||||||||||||||||||| |||||| ||||| ||||| || || ||||| ||   ||| ||| |||| |||||| | || |||||||||||| | 
aacacacaacccaccctgatttgggttagggtttccaa---cattatg-tacacttgtaagattttatatatgaaat-gctttgattgaggctgttctttggcagTGATATTCGTGGTGTTGCTGTTGCTGGGGTTGAAGGTGAGCCTGTCAACCTCACGGAAGATGTCACTAAAGCTATAGCTGCAGCTTTTGCTGCATGGCTG

upper sequence: LOC_Os07g26610.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA20G32030.1 (Glycine max), 3'ss of exon 2
tggggtttataacaattttagttaaagctaaagagtttcttgtgctgcatccatgatgtgttattaatca-atttgctttactctctt--ctatttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCTCACTGAGCCTGTTACTGAAGCAATAGCTTCTGCATTTGCTGCATGGTTA
     |  ||     ||||  ||||  | |   ||  | |  |    | | |||  || |   | | |   || |   ||| |        || ||   | ||||| ||||||||||| ||||||| ||| || || || ||||| || || |||||||| |||||| | ||||||||||   |||| |||||||||||||||
--aattccatcttcttttttattaagac-agctagcatttattcggtcttacatcttgcgcactgacttgtatataacttattaataaaattaatttaaatagTGACATTCGTGGTGTGGCTGTTGATGGTGTTGAGGGAGAGCCAGTTAACCTCACTGAACCTGTTGCCGAAGCAATAGGAGCTGCTTTTGCTGCATGGTTA

upper sequence: LOC_Os07g26610.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA10G35490.1 (Glycine max), 3'ss of exon 3
tggggtttataacaattttagttaaa---gctaaagagtttcttgtgctgcatccatgatgtgttattaatcaatttgctttactctctt--ctatttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCTCACTGAGCCTGTTACTGAAGCAATAGCTTCTGCATTTGCTGCATGGTTA
        ||     ||||  ||||    ||||     | |   || || |||||   |    | | |  |  || |   |||||        || ||   ||||||| ||||||||||| ||||||| ||| || || || ||||  || || |||||||| |||||| ||||||||||||   |||| |||||||||||||||
--aatcccatcttcctttttattaagatggctagcatttattcggtcctacatcctgtacac-tgacttgt--atatagcttactaataaaattaatttaaacagTGACATTCGTGGTGTGGCTGTTGATGGTGTTGAGGGAGAGCTAGTTAACCTCACTGAACCTGTTGCTGAAGCAATAGGAGCTGCTTTTGCTGCATGGTTA

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|88431706|gb|CI576897.1|CI576897
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88356963|gb|CI620851.1|CI620851
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|86900888|gb|CI304093.1|CI304093
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88740306|gb|CI763814.1|CI763814
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88718727|gb|CI742237.1|CI742237
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88365076|gb|CI616495.1|CI616495
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88298983|gb|CI567986.1|CI567986
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88765250|gb|CI774344.1|CI774344
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88695537|gb|CI737575.1|CI737575
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88392307|gb|CI612781.1|CI612781
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88364874|gb|CI614492.1|CI614492
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88399621|gb|CI583355.1|CI583355
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88736243|gb|CI759751.1|CI759751
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88737211|gb|CI760719.1|CI760719
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88362534|gb|CI623874.1|CI623874
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88298548|gb|CI563543.1|CI563543
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|88761427|gb|CI770983.1|CI770983
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
EST: gi|29660678|gb|CB656953.1|CB656953
EST:     GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAG                         TGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT
genomic: GTTGTCCCATCCTCTGCGAAAGTTGACTTTTTAAAGCTCCAGAATGGCAGgtataacaat ... tttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatccatgatgtgttattaatcaatttgctttactctcttctatttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCTCACTGAGCCTGTTACTGAAGCAATAGCTTCTGCATTTGCTGCATGGTTA
                tattaat  putative branch site (score: 2)
                          tttgctttactctctt  putative PPT
             tgttattaatcaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggggtttataacaattttagttaaagctaaagagtttcttgtgctgcatccatgatgtgttattaatcaatttgctttactctcttctatttctcacagTGATATTCGTGGTGTTGCTGTTGGTGGGGTCGAAGGCGAGCCCGTAAATCTCACTGAGCCTGTTACTGAAGCAATAGCTTCTGCATTTGCTGCATGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - -agctaaa
- - - - - - - - - - - - - - - - - - - cttgtgc
- - - - - - - - - - - - - - - - - - - - - - -tgcatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - atgatgt