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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC

Basic information

species Oryza sativa
transcript 13113.m00246
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 8
gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgc--atagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
||  |  |||||| |  ||||    ||  || |||||   | || |||   |  | ||    ||| ||  ||| || ||   ||| |   |||||||||||||||||||||||| | ||||| || |||||||| ||||||||  |||| || || |||||||| || ||||| |||||||||||||||||||
gttgg-gatataattatcatg----ataactaattat---agtactttaaaatgaactcttaataattgtttcttgcaa---cttttgcaaagGTTCTTCGCCCATTTCTTCTTAGGAGGCTCAAGTCTGATGTAGAAAAGGGTCTACCTCCGAAGAAGGAAACCATACTTAAAGTTGGAATGTCTCAGATGC

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 5
gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaa--cctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
||  |  |||||  |  | || |||          ||  || ||  ||   |  |   ||  ||| ||  |||  | ||   ||| |   ||||||||||||||||| |||||| | ||||| || |||||||| ||||||||  |||| || || || ||||| || ||||| |||||||||||||||||||
gttgg-gatatagttttcgtgatcacca-------attttagtaccttaaaatgaactctttataattgtttctcgcaa---cttttgcaaagGTTCTTCGCCCATTCCTTCTTAGGAGGCTCAAGTCTGATGTAGAAAAGGGCCTACCTCCAAAGAAAGAAACAATTCTTAAAGTTGGAATGTCTCAGATGC

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 8
gtgagtaatataac--tcccatgctcaatggctcattatgctaataatttgggaca-acctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
|| | | | | |||  ||   || |   |||       |  |  |||| ||| ||| |  ||     ||||||        |   | ||| ||||| || ||||||||||| ||||||||| | || || |||||||| || || || || || |||||||||||||| |||||||| || ||||| || ||||
gtaaattacagaaccttcttttgattgttggaagtccttaatgttaatctggcacataattgtcattttcattttc-----tatgtatatcaagGTCCTCCGCCCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGGTTGCCACCGAAAAAGGAAACTATTCTTAAGGTAGGCATGTCCCAAATGC

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 8
gtgagtaatataac--tcccatgctcaatggctcattatgctaataatttgggaca-acctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
|| | | | | |||  ||   || |   |||       || |  |||| ||| ||| |  ||     ||||||        |   | ||| ||||| || || |||||||| ||||||||| | || || |||||||| || ||||| || || |||||||||||||| ||||| || || ||||| || ||||
gtaaattacagaaccttcttttgattgttggaagtccttgatgttaatctggcacataattgtcattttcattttc-----tatgtatatcaagGTCCTCCGACCATTTCTCCTTCGAAGGTTGAAGTCAGATGTTGAGAAAGGATTGCCACCAAAAAAGGAAACTATTCTTAAAGTAGGCATGTCCCAAATGC

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
                   | |||| |   | || | | | ||  | |  |    | |       ||||| |       || ||| || ||||||| || |||||||||||||| ||| | ||||| ||||| || || || ||||| || |||||||| || || || || ||||| |||||||| ||||
--------------gtatgtactca-tattttatcaaggttattctctaagtt--cttatgctaatcatttac-----ctcatctttgtagGTTCTGCGACCATTTCTTCTTCGGAGGTTAAAATCAGATGTAGAGAAAGGCTTACCTCCAAAAAAGGAGACAATACTCAAAGTTGGCATGTCTCAAATGC

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
    |||      | ||||| |         ||||  | | ||  | |           | ||| | | |    |  ||   ||| |  |||||||||| ||||||||||||||||| || || || |||||||| || || || || || || ||||| || || ||||| ||||| |||||||||||||
----gtatggatgcacccattcct-----tgcattgagtttattctgttctgtgtgagtcgtaggttaattgctttcatgtatctttttagGTTCTTCGACCATTTCTTCTTCGAAGACTAAAGTCAGATGTTGAGAAAGGTTTGCCACCGAAGAAGGAGACCATACTTAAAGTTGGTATGTCTCAGATGC

upper sequence: LOC_Os01g27040.1 (Oryza sativa), 3'ss of exon 8
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 8
gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgta-aattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
                                          || ||     || | |  |||  |||  ||||   ||  ||| |    ||||  | |||||||||||  |  || | || || || ||||||||||  ||||||||||| || ||||| || ||||| || ||||| |||||||||||||
-----------------------------------------gtactt--atccagcatttataaatcaaccatgagtaacactttttctcagGTCTTACGCCCATTTCTCTTAAGACGTCTCAAGTCGGATGTTGAAAGAGGATTACCCCCAAAGAAGGAGACAATCCTCAAAGTTGGGATGTCTCAGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctaataatttgggacaacctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC
 tgctaat  putative branch site (score: 2)
                                          ttcttctat  putative PPT
                                   atgtaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtaatataactcccatgctcaatggctcattatgctaataatttgggacaacctgcatagttcattcatgtaaattcttctatgaagGTTCTTCGCCCATTTCTTCTTCGAAGGCTTAAATCTGATGTTGAAAAGGGATTACCCCCCAAAAAGGAAACTATCCTTAAGGTTGGAATGTCTCAGATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG