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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagatcttgatgtccatctatctgttgttcactttctctgttacatctggttaataggttatcgtgtgtataataatgttagGCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCATCTGCTCAGCCAGTTACCAAGATGGAGTTTGAATTTGAGAGACGCCGGA

Basic information

species Glycine max
transcript GLYMA15G10940.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G10940.3 (Glycine max), 3'ss of exon 6
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 6
-------------------------gttagatct--tgatgtccat-ctatctgttgttcactttctctgttacatctggtt--aataggttatcgtgtgtataataatgttagGCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCATCTGCTCAGCCAGTTACCAAGATGGAGTTTGAATTTGAGAGACGCCGGA
                         |||| |     || |    || ||  |||    |   | |       | | ||  ||   |  |    |    ||    ||  | | ||||||| || ||||||||||||||||| || || ||||||||||||||||| |||||||| |||||||||||| |||| ||||||||||||||  |  |||
gtactatctgcttgcttaatatcttgttacagtgaatggtacttattctgactgaacctacttataaaaaaaaaaccttattctgaccgaacctatcatgctgcatgttttcagGCTCTTGCAGATCCATATTTTAAAGGTTTAGCCAAGGTTGAGAGAGAACCCTCTGCTCAACCAGTTACCAAGTTGGAATTTGAATTTGAGAGGAGAAGGA

upper sequence: GLYMA15G10940.3 (Glycine max), 3'ss of exon 6
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 6
------------------------------------------------------------------------------gttagatcttgatgtccatctatctgttgttcactttctct-gttacatctggttaataggttatcgtgtgtataataatgt---tagGCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCATCTGCTCAGCCAGTTACCAAGATGGAGTTTGAATTTGAGAGACGCCGGA
                                                                               ||   | ||  | |  ||  | |||   | |   || | | || | |    ||   |  || |||     |||| | |||    |||||| | || ||||| ||||| ||||| |||||||| || || || ||||| |||||||| ||| |||| || ||||||||||| ||||| ||| |  | |
gtacctcatggattgtacaacatgggatcgaatacagttaaatgcatgtttggacgattttgaagttcttttcaaagtcttttctgttattcttaatggaactgaattccttcttttgtagtcataatatgtcgctttgt-atctaaactatattgatgggtgtagGCTTTGGCAGATCCTTATTTCAAAGGTTTGGCAAAAGTGGATAGGGAACCCTCTGCTCAACCAATTACGAAAATGGAGTTTGAGTTTGAAAGAAGGAGAA
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|207737429|gb|GD715977.1|GD715977
EST:     AGCCTAAGGATCGGCCTACTGCAGAAGAG                         GCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCA
genomic: AGCCTAAGGATCGGCCTACTGCAGAAGAGgttagatctt ... ataatgttagGCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCA
EST: gi|193684281|gb|FK621837.1|FK621837
EST:     CATTTGAGCCTAAGGATCGGCCTACTGCAGAAGAG                         GCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCA
genomic: CATTTGAGCCTAAGGATCGGCCTACTGCAGAAGAGgttagatctt ... ataatgttagGCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcactttctctgttacatctggttaataggttatcgtgtgtataataatgttagGCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCATCTGCTCAGCCAGTTACCAAGATGGAGTTTGAATTTGAGAGACGCCGGA
                     ggttaat  putative branch site (score: 4)
                                       tgtataataatgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagatcttgatgtccatctatctgttgttcactttctctgttacatctggttaataggttatcgtgtgtataataatgttagGCTCTAGCGGATCCATATTTTAAAGGCTTGGCAAAGGTTGAGAGAGAACCATCTGCTCAGCCAGTTACCAAGATGGAGTTTGAATTTGAGAGACGCCGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA