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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttaaacattatgtactaattcatgtactagtctataatatgacagataaatggttcagtcagtcctaaaaaaaagatggctcagttctgtttctgacccagaagtatgcatttgctgaaagatcgcatcttttgcgactgtggcccatgggtcattttaatgagaagttttctttctctcagGTCATCCGGAAACTTGGGTTTTTGACATTCTGGAATCCAAGTGGTCTGTTTGTGTAGTACCTCCTAGTTCCTCAATTACCACAAAGAAA

Basic information

species Oryza sativa
transcript LOC_Os11g43590.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g43590.4 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G070553_T02 (Zea mays), 3'ss of exon 11
gtaagtttaaacattatgtactaattcatgtactagtctataatatgacagataaatggttcagtcagtcctaaaaaaaagatggctcagttctgtttctgacccagaagtatgcatttgctgaaagatcgcatcttttgcgactgtggcccatgggtcat-tttaatgagaagttttctttctctcagGTCATCCGGAAACTTGGGTTTTTGACATTCTGGAATCCAAGTGGTCTGTTTGTGTAGTACCTCCTAGTTCCTCAATTACCACAAAGAAA
                                   ||   |   |   |   |  || |||  ||   ||     |||    || | ||||||  ||| | | |   | | |||| | || |  ||||    ||  ||||| ||| |||   ||||    | | |||  | |||   |   |  |||||| || || ||||| |||||||| ||  | || || ||||  ||||||||||||||||| ||||||||||||||||| || |||||||||
-----------------------------------gtaagttccacc-cttttgcattgttt-gtatatcacgggaaattagtgacacagttccatttatcaacagtatgcatgcttctg-tataagaatttataatttgctactatgg---atggacggtatctaacaaaaagaaat---tacctcagGGCACCCTGAAACATGGGTTTTCGATGTCCTTGAGTCCAGATGGTCTGTTTGTGTAGTGCCTCCTAGTTCCTCAATCACTACAAAGAAA


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttgcgactgtggcccatgggtcattttaatgagaagttttctttctctcagGTCATCCGGAAACTTGGGTTTTTGACATTCTGGAATCCAAGTGGTCTGTTTGTGTAGTACCTCCTAGTTCCTCAATTACCACAAAGAAA
                           ttttaat  putative branch site (score: 3)
                                        ttttctttctctc  putative PPT
                        tcattttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttaaacattatgtactaattcatgtactagtctataatatgacagataaatggttcagtcagtcctaaaaaaaagatggctcagttctgtttctgacccagaagtatgcatttgctgaaagatcgcatcttttgcgactgtggcccatgggtcattttaatgagaagttttctttctctcagGTCATCCGGAAACTTGGGTTTTTGACATTCTGGAATCCAAGTGGTCTGTTTGTGTAGTACCTCCTAGTTCCTCAATTACCACAAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA