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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtacagttcttcattcaatctagaaatttagttacaagttttcattgatttaatttttaatactatgtaccttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT

Basic information

species Oryza sativa
transcript LOC_Os08g26870.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G146355_T01 (Zea mays), 3'ss of exon 5
gtatgtacagttcttcattcaatctagaaattt----agttacaagttttcattgat-ttaatttttaa-tactatgtaccttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
||| ||| |  | ||  ||  ||   |  | ||    |||   || |||| |||||  |||||   |   |||| | |   |||| |||||||| |||||||||||  |||||||||| |||||||  ||||||||||||
gtacgta-atcttttagtttgattcggtgaattcagaagtaggaattttttattgacattaatgcatgtctactctctcaattttctcagTGGAGATGCCAAGCGTTATTCTGATGGCAGCTATTCATAATGTCCACATT

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G377595_T01 (Zea mays), 3'ss of exon 3
gtatgtacagttcttcattcaatctagaaattt----agttacaagttttcattgat-ttaatttttaa-tactatgtaccttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
||| ||| |  | ||  ||  ||  ||  | ||    |||   || |||| |||||  |||||   |   |||  | |   |||| |||||||| ||||||||||| ||||||||| | | |||||| ||||||||||||
gtacgta-atcttttagtttgattcagtgaattcagaagtaggaattttttattgacattaatgcatgtctaccctctcaattttctcagTGGAGATGCCAAGCGTTCTTCTGATGCCAGTTATTCGTAATGTCCACATT

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G006468_T04 (Zea mays), 3'ss of exon 3
gtatgtacagttcttcattcaatctagaaattt---agttacaagttttcattgat-ttaatttttaat-actatgtaccttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
||| ||| |  | ||  ||  || |   |||||   |||   ||  ||| |||||  |||||   |    ||  | |   |||| |||||||| |||||||| |||||||||||||| |||||||| ||||||||||||
gtacgtaaatcttttagtttgatttgataatttggaagtaggaacctttaattgacattaatgcatgtccaccttctcaattttctcagTGGAGATGCCAAGTGTACTTCTGATGGCGGCTATTCGTAATGTCCACATT

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G148892_T01 (Zea mays), 3'ss of exon 2
gtatgtacagttcttcattcaatctag-aaatttagttacaag---ttttcattgat-ttaatttttaa-tactatgtaccttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
|||  || |  | ||  ||  || | |  |||||||    | |   |||| |||||  |||||   |   |||  | |   |||| |||||||| ||||||||||| ||||||||||| |||||||| |||||||||| |
gtacata-atcttttagtttgatttggtgaatttagaagtaggaattttttattgacattaatgcatgtctaccctctcaattttctcagTGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACAAT

upper sequence: LOC_Os08g26870.4 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G053531_T02 (Zea mays), 3'ss of exon 3
gtatgtacagttcttcattcaatctagaaattt----agttacaagttttcattgat-ttaatttttaa-tactatgtaccttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
||| ||| |  | ||  ||  ||   |  | ||    |||   || |||| |||||  |||||   |   |||  | |   |||| |||||||| ||||||||||| ||||||||||| |||||||| ||||||||||||
gtacgta-atcttttagtttgattcggtgaattcagaagtaggaattttttattgacattaatgcatgtctaccctctcaattttctcagTGGAGATGCCAAGCGTTCTTCTGATGGCAGCTATTCGTAATGTCCACATT

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|29659232|gb|CB655507.1|CB655507
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29660675|gb|CB656950.1|CB656950
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29659550|gb|CB655825.1|CB655825
EST:     GTTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: G-TTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|27920437|gb|CB096245.1|CB096245
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29629367|gb|CB634378.1|CB634378
EST:     GTTTTGAGGATTGAAGATGGAAGTGAAACTTTATTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: GTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29663843|gb|CB660118.1|CB660118
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|3767979|gb|AU032006.1|AU032006
EST:     CCAATCATTGTTT                         TGGAAATNCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: CCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29659488|gb|CB655763.1|CB655763
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29670738|gb|CB667013.1|CB667013
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29675966|gb|CB672241.1|CB672241
EST:     TGTTTTGAGGATTGTAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29671385|gb|CB667660.1|CB667660
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29659844|gb|CB656119.1|CB656119
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29669212|gb|CB665487.1|CB665487
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|58687907|gb|CK076594.1|CK076594
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29664873|gb|CB661148.1|CB661148
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|218495687|gb|FG969804.1|FG969804
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29657113|gb|CB653388.1|CB653388
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29678163|gb|CB674438.1|CB674438
EST:     GGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: GGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29658491|gb|CB654766.1|CB654766
EST:     TTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|58692668|gb|CK081355.1|CK081355
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29629366|gb|CB634377.1|CB634377
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCGGAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29668681|gb|CB664956.1|CB664956
EST:     TTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTTTGATGGCTGCTATTCGGAATGTCCCCATT
genomic: TTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29660157|gb|CB656432.1|CB656432
EST:     GAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTTTGATGGCTGCTATTCGGAATGTCCACATT
genomic: GAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29669928|gb|CB666203.1|CB666203
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29672180|gb|CB668455.1|CB668455
EST:     TTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|33683462|gb|CF311701.1|CF311701
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|58605333|gb|CK033366.1|CK033366
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
EST: gi|29659233|gb|CB655508.1|CB655508
EST:     TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTT                         TGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
genomic: TGTTTTGAGGATTGAAGATGGAAGTGAAACTTTACTTCCAATCATTGTTTgtatgtacag ... cttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttagttacaagttttcattgatttaatttttaatactatgtaccttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT
                             ttttaat  putative branch site (score: 3)
                                          taccttttttc  putative PPT
      ttacaagttttcattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtacagttcttcattcaatctagaaatttagttacaagttttcattgatttaatttttaatactatgtaccttttttcagTGGAAATGCCAAGCGTACTTCTGATGGCTGCTATTCGGAATGTCCACATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT