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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacgaatataagatgaatactccgtattctatatgacgatatctgctcattcgtcgagaatttttcaatattttttcttgattatgctgtctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGAAGGGCCAAGGAGAGGAACCAGCGGAGAGCAAGAGCAGTAGTTCTTCACA

Basic information

species Oryza sativa
transcript LOC_Os01g62060.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62060.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G370044_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------tacgaata--taagatgaa---tactccgtattctatatgacgata-tctgctcattcgtcgagaatttttcaatatttttt---cttgattatgctgtctgtg-------agcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGAAGGGCCAAGGAGAGGAACCAGCGGAGAGCAAGAGCAGTAGTTCTTCACA
                                                   | || ||  |||| ||      || ||  |||  |  |     || ||  |||  ||||   ||  |  |  |  | || |   | | ||||| || |   ||       |||||||||||||||||| |||||||||||||| ||||||||||  ||||||||||||   |  ||| | ||  | |||  |   ||||          |  |||
gtaggccgtaggcggcactcttgcaagcaagcgattaatcgagattatttcaagagtagttaagttgtcgtccacgccaaattaaagctactactagtcgactcgatcgtatcgatctcattgacctcttcttggcattattatactatacatgctgctatagcagTGTGGAAGGAGCTGGAGAAGGAGAACAGGGAGTTCTTCGAGACGTACAAGAAGTATCTGGGACAAGAGTCGGCGCTGCAGAAGAATCCATCCGATGGACA

upper sequence: LOC_Os01g62060.3 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA19G35810.1 (Glycine max), 3'ss of exon 2
----tacgaatataagatgaatactccgtattctatatgacgatatctgctcattc-gtcgagaatttttcaatattttttcttgattatgctgtctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGAAGGGCCAAGGAGAGGAACCAGCGGAGAGCAAGAGCAGTAGTTCTTCACA
    |   ||  |||  ||    |   || |||| | |  |  | | |  | ||||  ||    | |     | |    | | ||  | || |    | ||||||| ||||||||| | |||||||||||||  ||||||||||   | |||| || | ||  || ||||  | |  |||||||  |||  ||          ||
atgttgttaaagtaatgtgttgtcaatgttttctctctctctctctttttttattctatctgtgaat----gacacacgtgcatgcatgtgat-cgcgcgagcagTTTGGAAGGAGTTAGAGAAGGAGAACAAGGAGTTCTTCGAGGCATACACGAGGAGCAGAGCAGAGAGAGCTTCGGAGAGAGAGACAAGGCAAAGGATCCA
















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|86530502|gb|CI170708.1|CI170708
EST:     ACGCCAACATCAAGCCCGTCATCACCTCCACCG                         TGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
genomic: ACGCCAACATCAAGCCCGTCATCACCTCCACCGgtaattcgct ... ctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
EST: gi|88281566|gb|CI402962.1|CI402962
EST:     GGAGAAGCACGCCAACATCAAGCCCGTCATCACCTCCACCG                         TGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
genomic: GGAGAAGCACGCCAACATCAAGCCCGTCATCACCTCCACCGgtaattcgct ... ctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
EST: gi|88517933|gb|CI444822.1|CI444822
EST:     CCGTCATCACCTCCACCG                         TGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
genomic: CCGTCATCACCTCCACCGgtaattcgct ... ctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
EST: gi|88478182|gb|CI415453.1|CI415453
EST:     GAGAAGCACGCCAACATCAAGCCCGTCATCACCTCCACCG                         TGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
genomic: GAGAAGCACGCCAACATCAAGCCCGTCATCACCTCCACCGgtaattcgct ... ctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
EST: gi|86534394|gb|CI174600.1|CI174600
EST:     GGAGACGCTGGAGAAGCACGCCAACATCAAGCCCGTCATCACCTCCACCG                         TGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
genomic: GGAGACGCTGGAGAAGCACGCCAACATCAAGCCCGTCATCACCTCCACCGgtaattcgct ... ctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
EST: gi|88482346|gb|CI419617.1|CI419617
EST:     GGAGACGCTGGAGAAGCACGCCAACATCAAGCCCGTCATCACCTCCACCG                         TGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA
genomic: GGAGACGCTGGAGAAGCACGCCAACATCAAGCCCGTCATCACCTCCACCGgtaattcgct ... ctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcattcgtcgagaatttttcaatattttttcttgattatgctgtctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGAAGGGCCAAGGAGAGGAACCAGCGGAGAGCAAGAGCAGTAGTTCTTCACA
                              tcttgat  putative branch site (score: 4)
           agaatttttcaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacgaatataagatgaatactccgtattctatatgacgatatctgctcattcgtcgagaatttttcaatattttttcttgattatgctgtctgtgagcagTGTGGAAGGAGCTTGAGAAGGAGAACAGCGAGTTCTTCGCCACGTACAAGAAGGGCCAAGGAGAGGAACCAGCGGAGAGCAAGAGCAGTAGTTCTTCACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG