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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattatgtactttaagaaatacacaagttaaaacacattggccaatcctatgtctttctattccattgcattaaggtcctctttaatttctgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGGTGGTCCTCTGATGACTTCGAAGTTTACAAGGAAGGCTTGGCGCAACTGC

Basic information

species Oryza sativa
transcript LOC_Os12g01430.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01430.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G467086_T01 (Zea mays), 3'ss of exon 7
---------------------------------------------------------------------------------------tattatgtactttaagaaatacacaagttaaaacacattggccaatcctatgtctttctattccattgcattaaggtcctctttaatttctgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGGTGGTCCTCTGATGACTTCGAAGTTTACAAGGAAGGCTTGGCGCAACTGC
                                                                                       ||   | || | |    | |  ||  |  ||   |||    |  ||  |||   |||||||||||||| ||| || |   |||  || ||| | ||||||||| |||||||||| || ||||| |||||||| || |||||||| || || |||||    |||||||| ||||||||||| |||||||||  ||| ||  
gtacagtattactgtgtgatggctgttatatgtttgattttgaagatatgccataattcattatgtaacttatgattaatctaaagttaggctctattgtgctcagtttacgtgaaaatcgacacctactcattttatccttttctattccattgtattgag-tatccttcgatctctctcttgcagCGGCTGCTTGGGATACAAATGGCGACATTCCGTCTATACCTTGTGTGTCGCTGGTCGGGCGATGACTTTGAAGTTTACAAAGAAGGCTTGATGCACCTAG
















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|88518129|gb|CI445783.1|CI445783
EST:     CACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: CACAAACTCTGgtatgtactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|88470955|gb|CI408226.1|CI408226
EST:     CCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: CCAGAAGCAGCACAAACTCTGgtatgtactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|218485998|gb|FG965622.1|FG965622
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCTGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtatgtactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|88460678|gb|CI534550.1|CI534550
EST:     AGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: AGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtatgtactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|33686640|gb|CF314879.1|CF314879
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtatgtactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|88517348|gb|CI445002.1|CI445002
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtatgtactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|88517910|gb|CI444799.1|CI444799
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtatgtactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|88517360|gb|CI445014.1|CI445014
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtatgtactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
EST: gi|88518778|gb|CI445521.1|CI445521
EST:     TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTG                         CGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG
genomic: TAGTATGTGAAGAAGGGAAGCCCATTTCACCAGAAGCAGCACAAACTCTGgtatgtactg ... tgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctatgtctttctattccattgcattaaggtcctctttaatttctgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGGTGGTCCTCTGATGACTTCGAAGTTTACAAGGAAGGCTTGGCGCAACTGC
                                   ctttaat  putative branch site (score: 4)
                               tcctctttaatttct  CT-rich tract
                                    tttaatttctgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattatgtactttaagaaatacacaagttaaaacacattggccaatcctatgtctttctattccattgcattaaggtcctctttaatttctgtattgcagCGGTTGCTTGGGATGCAGATGGCAACATTCCGACTGTACCTTGTCTGCCGGTGGTCCTCTGATGACTTCGAAGTTTACAAGGAAGGCTTGGCGCAACTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - acacaag
- - - - - - - - - - - - - - -aaaacaca