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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatacaggcaagaatcctttgacatttgattttgagattgatttattttccatagacatttttcttcaatcaaccaataccatttatgcactaccagCCATTTCATTTGGAGCTAAATTTCTTCAATAAAGAGAACCGAGTTCTTCATTATCCCGTCAGGGCTTTCTATGTGGATGGACCCAATCTTATGGCACATA

Basic information

species Glycine max
transcript GLYMA01G39110.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39110.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os09g24260.1 (Oryza sativa), 3'ss of exon 12
gttatacaggcaagaatcctttgacatttgattttgagattgatttattttccatagacatttttcttcaatcaaccaataccatttatgcactaccagCCATTTCATTTGGAGCTAAATTTCTTCAATAAAGAGAACCGAGTTCTTCATTATCCCGTCAGGGCTTTCTATGTGGATGGACCCAATCTTATGGCACATA
              | |  |   | | | ||| ||   | |  |||| ||      |       |||  || |     ||  | | | |  ||| ||||||||| ||| ||||||| |||||||||||  | |||||||| ||  |||| ||||| || || ||||||||| ||||||||   || || ||||| || |
-----------gtaacttgtactataatggatattatcacttgtttactt------gttgccactctctaacctttttatttcttcttt-tact-ccagCCATTCCATCTGGAGCTGAATTTCTTCAACCAGGAGAACCGCGTGGTTCAATATCCAGTTAGAGCTTTCTATTTGGATGGATTTAACCTAATGGCCCACA

upper sequence: GLYMA01G39110.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G150772_T01 (Zea mays), 3'ss of exon 10
gttatacaggcaagaatcctttga-catttgattttgagattgatttattttccatagacatttttcttcaatcaaccaataccatttatgcactaccagCCATTTCATTTGGAGCTAAATTTCTTCAATAAAGAGAACCGAGTTCTTCATTATCCCGTCAGGGCTTTCTATGTGGATGGACCCAATCTTATGGCACATA
              || | || ||  | || |||||   ||| | ||  | ||  |     || ||||  || |||  | |     || ||||   ||||||||| ||| | ||||| ||||||||||| || || | ||| ||| |||| ||||| || || ||||||||| ||||||||                   
------------gtaaccgttagagtaatttatttttttatttacttgctctcttt-----ttgttctctaaacaattagT--TGATTTTGCAACTCCAGCCATTCCATCTAGAGCTGAATTTCTTCAACAAGGAAACCCGTGTTGTTCAGTATCCAGTTAGAGCTTTCTATTTGGATGGAT------------------

upper sequence: GLYMA01G39110.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G150772_T02 (Zea mays), 3'ss of exon 12
gttatacaggcaagaatcctttga-catttgattttgagattgatttattttccatagacatttttcttcaatcaaccaataccatttatgcactaccagCCATTTCATTTGGAGCTAAATTTCTTCAATAAAGAGAACCGAGTTCTTCATTATCCCGTCAGGGCTTTCTATGTGGATGGACCCAATCTTATGGCACATA
              || | || ||  | || |||||   ||| | ||  | ||  |     || ||||  || |||  | |     || ||||   ||||||||| ||| | ||||| ||||||||||| || || | ||| ||| |||| ||||| || || ||||||||| ||||||||   || || ||||| ||||
------------gtaaccgttagagtaatttatttttttatttacttgctctcttt-----ttgttctctaaacaattagt--tgattttgcaactccagCCATTCCATCTAGAGCTGAATTTCTTCAACAAGGAAACCCGTGTTGTTCAGTATCCAGTTAGAGCTTTCTATTTGGATGGATTTAACCTGATGGCCCATA

upper sequence: GLYMA01G39110.1 (Glycine max), 3'ss of exon 12
lower sequence: AT3G50590.1 (Arabidopsis thaliana), 3'ss of exon 13
gttatacaggcaagaatcctttgacatttgattttgagattg-atttattttccatagacatttttcttcaatcaaccaataccatttatgcactaccagCCATTTCATTTGGAGCTAAATTTCTTCAATAAAGAGAACCGAGTTCTTCATTATCCCGTCAGGGCTTTCTATGTGGATGGACCCAATCTTATGGCACATA
                        ||| | | | |    | |  ||| |||||  |||    |  | |       ||  ||   ||| ||   ||  |||||||||||||||||||| ||||||||||||||    ||  |||||||||||||||| || ||| | || ||| | || || |  || || ||||| || |
-----------------------gcatgtaactgttgtttagtgtttcttttctgtagtatctgatttatgcctgactgattggatt-at---ctgacagCCATTTCATTTGGAGCTGAATTTCTTCAATAAGCCAAATAGAGTTCTTCATTATCCTGTGAGGTCCTTTTATATCGAGGGCCTTAACCTCATGGCTCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttattttccatagacatttttcttcaatcaaccaataccatttatgcactaccagCCATTTCATTTGGAGCTAAATTTCTTCAATAAAGAGAACCGAGTTCTTCATTATCCCGTCAGGGCTTTCTATGTGGATGGACCCAATCTTATGGCACATA
               atttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatacaggcaagaatcctttgacatttgattttgagattgatttattttccatagacatttttcttcaatcaaccaataccatttatgcactaccagCCATTTCATTTGGAGCTAAATTTCTTCAATAAAGAGAACCGAGTTCTTCATTATCCCGTCAGGGCTTTCTATGTGGATGGACCCAATCTTATGGCACATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA