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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtggaattcaccaatctagttatccctatccacacagttcgtaacaaattcaagatgactgacatctagttccttttataccaacatttctgctgcagTTACTGGCAGGGCAATTAGAGCCTCTTACAGAGCAGCAGCTTGCTGGCATAGCCAACCTGCAACAATCCTCCCAACAGGCTGAAGATGCTCTTTCTCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g59350.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G019907_T01 (Zea mays), 3'ss of exon 5
ttgtggaattcaccaatctagttatccctatccacacagttcgtaacaa-attcaagatgactgacatctagttcc-ttttataccaacatttctgctgcagTTACTGGCAGGGCAATTAGAGCCTCTTACAGAGCAGCAGCTTGCTGGCATAGCCAACCTGCAACAATCCTCCCAACAGGCTGAAGATGCTCTTTCTCAAG
   |  | |||     | || ||  | |  |  ||  | |||  ||| |   ||||| |  |       |  |||  ||||||||||||||| ||| |||||||||||||||| ||  ||||||||||||| || |||||||||| ||| ||| |||||||||| || ||||||||||| ||||||||||||||||||||||
-gataaacttctgtcctgtactttactccgtg-acgaacttctgaactatgctcaagttctcacttgattctttcaattttataccaacattactgttgcagTTACTGGCAGGTCACCTAGAGCCTCTTACTGATCAGCAGCTTGTTGGTATATCCAACCTGCAGCAGTCCTCCCAACAAGCTGAAGATGCTCTTTCTCAAG

upper sequence: LOC_Os01g59350.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G125243_T02 (Zea mays), 3'ss of exon 11
ttgtggaattcaccaatctagttatccctatccacacagttcgtaacaaattcaagatgactgacatctagttcct-----tttataccaacatttctgctgcagTTACTGGCAGGGCAATTAGAGCCTCTTACAGAGCAGCAGCTTGCTGGCATAGCCAACCTGCAACAATCCTCCCAACAGGCTGAAGATGCTCTTTCTCAAG
   |  | |||     |||| ||    ||    ||| | |||  ||| |     |  |   |  |||||| ||| |     |||||||||||||| ||| |||||||||||||||| ||  ||||||||||||| || |||||||||| ||| ||| |||||||||| || ||||||||||| ||||||||||||||||||||||
-gataaacttctgtcctctactttattctgag-acaaacttctgaacgatgctcacgt---tttcatctaattcttacaattttataccaacattactgttgcagTTACTGGCAGGTCACCTAGAGCCTCTTACTGATCAGCAGCTTGTTGGTATATCCAACCTGCAGCAGTCCTCCCAACAAGCTGAAGATGCTCTTTCTCAAG


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaattcaagatgactgacatctagttccttttataccaacatttctgctgcagTTACTGGCAGGGCAATTAGAGCCTCTTACAGAGCAGCAGCTTGCTGGCATAGCCAACCTGCAACAATCCTCCCAACAGGCTGAAGATGCTCTTTCTCAAG
             gactgac  putative branch site (score: 2)
                                           tttctgct  putative PPT
                              ttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtggaattcaccaatctagttatccctatccacacagttcgtaacaaattcaagatgactgacatctagttccttttataccaacatttctgctgcagTTACTGGCAGGGCAATTAGAGCCTCTTACAGAGCAGCAGCTTGCTGGCATAGCCAACCTGCAACAATCCTCCCAACAGGCTGAAGATGCTCTTTCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG