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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttatgaattgcatagtccctgatattggatttattataccatttaatgccttttgtagaccatgttgatgactctggacaaaatatgcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC

Basic information

species Glycine max
transcript GLYMA02G42680.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G42680.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G169516_T05 (Zea mays), 3'ss of exon 5
gtttgttttatgaattgcata---gtccctgatattgga--tttattataccatttaatgccttttgtagaccatg--ttgat--gactctggac-aaaatatgcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC
||    | |   |||| ||||        ||||   |||  |  || |||   |   | |    ||  ||  ||||  | | |   | |||| |  |  | |||||||||||| |  |||||||||| ||||| || ||||| |||||||| |||||||| ||  | || ||||||||||| || ||| |||| |||||||| || |
gtgccatgttcaaattacatacatacatttgattcgggaaatcaatgatattctggcagggtactttaagtgcatgaatagctcaaattctgaattactaaatgcagTGCCCTCTTCTGTGCAAAGAGTTCATTATTGATGCTTGGCAACTTTACTATGCACGGTCCAAGGGTGCAGATGCTGTTCTTCTAATAGCTGCTGTATTAC

upper sequence: GLYMA02G42680.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G04400.1 (Arabidopsis thaliana), 3'ss of exon 5
--gtttgttttatgaattgcatagtccctgatattggatttattataccatttaatgccttttgtagaccatgttgatgactctggacaaaatat-gcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC
   |||  || |  ||||     |    || |       |||||||       ||  | || ||||  |||||||  |         |||| ||| |||||| ||  | || |||||||| ||  |  ||||| |||||||  ||||||||||||| |||||||| ||||||||||| ||  | ||||||||||| ||| 
gtattttcttaacaaattctggtgcttttggtgc----gttattat----caaaacactttgtgtaatccatgttttt---------caaattattgcagTGTCCACTATTATGCAAAGAGTTTGTTGTAGATCCATGGCAGATCTACTATGCTCGGACTAAAGGCGCAGATGCAGTACTGCTTATTGCTGCTGTATTGG

upper sequence: GLYMA02G42680.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0057g01240.t01 (Vitis vinifera), 3'ss of exon 5
-------------gtttgttttatgaattgcatagtccctgatattggatttatta------taccatttaatgccttttgt---agaccatgttgatgactctggacaaaatatgcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC
               ||||| |    | | |  | ||  | || |   ||||||        | | ||  ||||  |||| |   |     || |  | || |  | |  || ||| |||||||| || |||||||||||||  || |||||||||||||| |||||||||||||||| ||||| ||||||||| | ||| |||||||||||||||| |
gtctgctcttctaaattgttctcc--actcctcaatctattatttataatttatccacatgcttctatagaatggtttttttttaaagttgtgcttctaacacaaggctcaa-atgtagTGCCCTCTGCTGTGCAAAGAATTTGTCGTAGATGCATGGCAAATCTACTATGCTCGAACCAAAGGGGCAGATGCAATTCTTCTAATTGCTGCTGTTTTAC

upper sequence: GLYMA02G42680.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S330_9V6.2 (Physcomitrella patens), 3'ss of exon 4
gtttgttttatgaattgcatagtccctgat--attggatttattataccatttaatgc-cttttgtagaccatgttgatgactctggacaaaatatgcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC
   |  | ||||  |||| | ||    |     | | ||  | | |   |  | |||  ||| ||| |||  || | |   || | |    ||| |  |||||||  | |||||||||||||||||||| ||||| |||||| ||||| | || ||   ||  ||||||||||| ||||| ||||| || || ||  |||
tcattgtgtatgccttgcttggttgaggggcggtcgtatcaacttttggaacttatgttcttctgttgacactgataagttcttttgttggaatttctagTGCCCGCTTTTGTGCAAAGAATTCATCATTGATGCGTGGCAAATCTACAAGGCCCGTGTTAGCGGTGCAGATGCTGTCCTCTTAATAGCAGCAGTGCTGC

upper sequence: GLYMA02G42680.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24439 (Selaginella moellendorffii), 3'ss of exon 4
gtttgttttatgaattgcatagtccctgatattggatttattataccatttaatgccttttgtagaccatgttgatgactctggacaaaatatgcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC
                                      ||| | || |  |  || |||||  ||   |  |  ||||   ||  |      |||||||||| ||| ||||||| |||||||| || ||||| |||||||||||||||||||||| ||||||||| ||||| || ||||| |||||||||||  | |
-------------------------------------gtatcaaacgagct--tgacttttccagttgacatgtatga---tgtgctg---ttgcagTGCCCGTTGCTGTGCAAGGAATTCATTATTGATGCCTGGCAACTCTACTATGCTCGAATTAAAGGTGCTGATGCCGTTCTTTTGATTGCTGCTGTGCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccatttaatgccttttgtagaccatgttgatgactctggacaaaatatgcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC
                           tgttgat  putative branch site (score: 4)
                                          acaaaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttttatgaattgcatagtccctgatattggatttattataccatttaatgccttttgtagaccatgttgatgactctggacaaaatatgcagTGCCCTTTGTTGTGCAAAGAATTCATCATAGATGCATGGCAACTCTACTATGCTCGAACTAAAGGTGCAGATGCAGTCCTTTTAATTGCTGCTGTTTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT