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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttctttgtactagttttactatatgacatcatcagaataaatgagcactgtaatcgtccgattgtttggaagtcatcaagactcactagaataaatgacaattctacttgcagGTTTGTCCATGTTAGTTCTGCAGGAGTTACAAGACCTGAGAGACCAGGCCTGGATTTAAGTAAACAACCTCCTGCTGTTCGCATGAACAAAGAGCTGGGC

Basic information

species Oryza sativa
transcript LOC_Os02g13970.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G019358_T02 (Zea mays), 3'ss of exon 12
gtttgttctttgtactagttttactata-tgacatcatcagaataaa-------tgagcactgtaatcgtccgattgttt---ggaagtcatcaagactcactagaataaatgacaattctacttgcagGTTTGTCCATGTTAGTTCTGCAGGAGTTACAAGACCTGAGAGACCAGGCCTGGATTTAAGTAAACAACCTCCTGCTGTTCGCATGAACAAAGAGCTGGGC
|||||| || | | ||||||||     | |||||| |  | || | |       |   ||||  | |  | |  ||  ||   ||||   |||| |||| ||| |  |   |     || ||  || ||||| || ||||| |||||||| ||||||||||||||||| ||||| ||  | |||||||| || || || |||||||||||  ||||||||||||| |||
gtttgt-ctatctgctagttttcaggcaatgacataagtaaaacagaatacatatagccacttcattttttcagtttctttatggaaccaatcaggactgactgggcttgcttttc-ttttatatgaagGTTCGTTCATGTGAGTTCTGCGGGAGTTACAAGACCTGAAAGACCGGGGTTAGATTTAAGCAAGCAGCCACCTGCTGTTCGATTGAACAAAGAGCTTGGC

upper sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G019358_T01 (Zea mays), 3'ss of exon 12
gtttgttctttgtactagttttactatatgacatcatcagaataaatgag--cactgtaatcgtccgattgttt---ggaagtcatcaagactcactagaataaatgacaattctacttgcagGTTTGTCCATGTTAGTTCTGCAGGAGTTACAAGACCTGAGAGACCAGGCCTGGATTTAAGTAAACAACCTCCTGCTGTTCGCATGAACAAAGAGCTGGGC
                      |  | || |    | ||||||| ||     ||||  | |  | |  ||  ||   ||||   |||| |||| ||| |  |   |     || ||  || ||||| || ||||| |||||||| ||||||||||||||||| ||||| ||  | |||||||| || || || |||||||||||  ||||||||||||| |||
-------------------gcaatgacataagtaaaacagaatacatatagccacttcattttttcagtttctttatggaaccaatcaggactgactgggcttgcttttc-ttttatatgaagGTTCGTTCATGTGAGTTCTGCGGGAGTTACAAGACCTGAAAGACCGGGGTTAGATTTAAGCAAGCAGCCACCTGCTGTTCGATTGAACAAAGAGCTTGGC

upper sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA05G29330.2 (Glycine max), 3'ss of exon 12
gtttgttctttgtactagttttactatatgacatcatcagaataaatgagcactgtaatcgtccgattgtttggaagtcatcaagactcactagaataaatgacaattctacttgcagGTTTGTCCATGTTAGTTCTGCAGGAGTTACAAGACCTGAGAGACCAGGCCTGGATTTAAGTAAACAACCTCCTGCTGTTCGCATGAACAAAGAGCTGGGC
                          |||  | | |||    |   |   |  |    ||    | ||     ||  |  | ||   |   |   ||| |      |   || |  |||||||| ||||| || || ||||||||||||||||| || || || || || ||| |||||||||| |||||||| |||||  | ||||| || ||||  
-------------------------gtatagccttatctttgtgctt---ctttcccctccattgtttaccctgatatacttaatcttt--tgttatacacctttgtgtcacatttagGTTTGTACATGTGAGCTCAGCAGGAGTTACAAGACCCGAAAGGCCTGGACTAGATCTAAGTAAACAGCCTCCTGCCGTTCGATTAAACAAGGAACTGGAT

upper sequence: LOC_Os02g13970.2 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv10s0003g01640.t01 (Vitis vinifera), 3'ss of exon 12
-------gtttgttct--ttgtactagttttactatatg---acatcatcagaataaatgagcactgtaatcgtccgattgtttggaa-gtcatcaagactcactagaataaatgacaattctacttgcagGTTTGTCCATGTTAGTTCTGCAGGAGTTACAAGACCTGAGAGACCAGGCCTGGATTTAAGTAAACAACCTCCTGCTGTTCGCATGAACAAAGAGCTGGGC
        ||  ||||  || | |||   ||| |  ||    ||||      | |  ||| ||     |   |      |  |||     |  ||     ||  ||   |          || ||||| |||||||| ||||| || ||||| ||||| ||  |||||||||| ||||| || ||  | |||||||| ||||||||||||||| ||||||| ||  |||||
gtttaatattccttctcattttgctaaaattagtccatacacacatttctgtagtttatgtgctggaaagcaggttatcttcttgagtcatgttctgctttccttatcttttgaagttgctccacttgtagGTTTGTACATGTGAGCTCTGCTGGAGTCACCCGACCTGAGAGGCCAGGACTTGACCTTAGTAAACAGCCTCCTGCTGTTCGCTTGAACAAGGAATTGGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgattgtttggaagtcatcaagactcactagaataaatgacaattctacttgcagGTTTGTCCATGTTAGTTCTGCAGGAGTTACAAGACCTGAGAGACCAGGCCTGGATTTAAGTAAACAACCTCCTGCTGTTCGCATGAACAAAGAGCTGGGC
                     gactcac  putative branch site (score: 2)
                                           ttctactt  putative PPT
                               aataaatgacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttctttgtactagttttactatatgacatcatcagaataaatgagcactgtaatcgtccgattgtttggaagtcatcaagactcactagaataaatgacaattctacttgcagGTTTGTCCATGTTAGTTCTGCAGGAGTTACAAGACCTGAGAGACCAGGCCTGGATTTAAGTAAACAACCTCCTGCTGTTCGCATGAACAAAGAGCTGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT