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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccagagatgaccagttgatactgaactgaacaaaatgatgtgcaatgtttattgcattaattaatgatcaatcttatatgatctgttgcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTA

Basic information

species Oryza sativa
transcript LOC_Os09g12660.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 8
tttccagagatgaccagttgatactgaactgaacaaaatgatgtgcaatgtttatt--gcattaattaatg-atcaatcttatatgatctgttgcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTA
||  | |   | |  |||||||| || ||  || || |||   ||   | ||| ||  | ||| |||  |  |||  || || ||  | | ||| || |||||||||||||| | || ||| ||||||||||   ||||||||| || ||||| || ||||||||||| |||||||| ||||| || || || ||||| ||||
ttgactgctcttag-agttgataatggac-aaaaaatatgcactgatgtttttgttatgtattcattggttcatccttcctaaatagtttattgttt-tacagATAATCAATTTTGATAATGTCCAAGAAGCAGTAAGGGAGACAGAAGGATATTTTATCAAAAGTGGAATTGTCACGGTGATTAAAGATGCTTTAATTCCTA

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 8
----tttccagagatgaccagttgatactgaactgaacaaaatgatgtgcaatgtttattgcattaattaatgatcaatcttatatgatctgttgcttgtac--agATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTA
    ||||     ||     ||||  | |  | ||     | | |||||  |||||    |   || || |     |||||   ||| | |||| |   |||  |||| || ||    |||||| ||||||||||| ||||||| || ||||| || ||||| |||||||| |||||||| || |||||||| || ||||| ||||
atgttttcttttcatactgtgttgcca-tacattgttttcattcatgtgacatgtta--cgagatattttaaatctaatct---atggtttgtttccaatactcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 8
tttccagagatgaccagttgatactgaactgaacaaaatgatgtgcaatgtttattgcattaattaatgatcaatcttat--atgatctgttgcttgtac--agATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTA
     | | ||| |   ||   ||| ||   | | | ||  |     ||||    ||     |   ||  | ||||| ||  ||  | |||| |   | |  |||| || ||    |||||| ||||||||||| ||||||| || ||||| || ||||| |||||||| |||||||| || |||||||| || ||||| ||||
--gataaaaatggct--ttctcactaaatatatccatattttcattcatgtgacatgttacgagatattttaaatctaatctatcgtttgtttccaattctcagATTATTAACAGTGACAATGTCCAAGAAGCTGCAAGGGAAACAGATGGGTATTTCATAAAAAGTGGGATTGTCACAGTAATCAAGGATGCTTTAATTCCTA

upper sequence: LOC_Os09g12660.2 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G48300.1 (Arabidopsis thaliana), 3'ss of exon 7
tttccagagatgaccagttgatactgaactga-acaaaatgatgtgcaatgtttattgcattaattaatgatcaatcttatatgatctgttgcttg-tacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTA
        | |      |  ||   ||||  | |||  ||| |  ||  |||| ||  | |    |  |  | ||   | | || | ||   ||||  |||||| || ||   ||||||  | ||||| ||  | || |||||||||||||| ||||| || || || ||||| || || ||||| |||||||||||||| |
--------gttagtgtttatatttggaacacacacaggatgtttagctttgttcat-acttgctctgctcttaaaatgtgtttgttgtggaccttggcacagATCATAAACAGCGACAACGTGCAAGAGGCAGCGAGAGAGACTGATGGATATTTCATAAAGAGCGGAATTGTAACGGTTATCAAAGACGCCTTAATCCCAA

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|86858990|gb|CI275175.1|CI275175
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|86496727|gb|CI139360.1|CI139360
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|24468914|gb|CA305863.1|CA305863
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|87009864|gb|CI277365.1|CI277365
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|88222446|gb|CI222402.1|CI222402
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|88222920|gb|CI220666.1|CI220666
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|87018057|gb|CI275871.1|CI275871
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|89164207|gb|CI101295.1|CI101295
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|88967313|gb|CI002497.1|CI002497
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|58683758|gb|CK072445.1|CK072445
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|88957454|gb|CI095395.1|CI095395
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|29675781|gb|CB672056.1|CB672056
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|86494922|gb|CI137555.1|CI137555
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|218485015|gb|FG946141.1|FG946141
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|86504993|gb|CI147626.1|CI147626
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|87010148|gb|CI279245.1|CI279245
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|86500004|gb|CI142637.1|CI142637
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|86504994|gb|CI147627.1|CI147627
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
EST: gi|86500640|gb|CI143273.1|CI143273
EST:     TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAG                         ATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC
genomic: TCAGAAAAGCAATAATTGACAAGAATGCTCGTATTGGAGAAAATGTTAAGgtatttcata ... gcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgtttattgcattaattaatgatcaatcttatatgatctgttgcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTA
                aattaat  putative branch site (score: 3)
             attaattaatgatcaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccagagatgaccagttgatactgaactgaacaaaatgatgtgcaatgtttattgcattaattaatgatcaatcttatatgatctgttgcttgtacagATAATCAATGTCGACAATATCCAAGAAGCTTCAAGGGAGACTGATGGATACTTCATCAAAAGTGGCATTGTCACTGTGATCAAGGACGCCTTAATCCCTA

- - - - - - - - - -gatactg
- - - - - - - - - - - - - - - gaacaaa
- - - - - - - - - - - - - - - - - - - -gatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatctg