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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttcaaattcacgctaaaagtagatgtacatgattttcctattccttttatgttatgtttttagctaggtctctttgtcttacagtgctcccacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGAAAATCACTAATCCCGTACATGTG

Basic information

species Glycine max
transcript GLYMA06G12130.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G12130.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G21760.1 (Arabidopsis thaliana), 3'ss of exon 4
------------------------------ttcaaattcacgctaaaagtagatgtacatgattttcctattccttttatgttatgtttttagctaggtctctttgtc----ttacagtgctcccacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGAAAATCACTAATCCCGTACATGTG
                                 | ||||  ||   ||||   |||      || |    |     | |  |  ||| ||    ||  | | ||  |     | ||  ||   |  | |||||||||||||||||||||| ||||||||||||||||||||| ||||||||||||| || || ||||| || ||  | 
gtaatctttctttcttcatcctcttgcttcacgacattctagcgccaagtgattgttttcttttgtatgctctgactaacatcgtgtcttgttatatctttattgattaaagtaactatgtatcttcttctcagGTCTTTATGTGAGTAGGAATACTTACATTCGAGCTGGAATTGCTGAGTGGAAGATTACAAATCCAGTTCACATT

upper sequence: GLYMA06G12130.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv18s0001g02630.t01 (Vitis vinifera), 3'ss of exon 5
ttcaaattcacgctaaaagtagatgtacatgattttcctattccttttatgttatgtttttagctaggtctctttgtcttacagtg--------ctcccacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGAAAATCACTAATCCCGTACATGTG
        ||| |  | | |   |||     |  |   |     ||| |  ||||  || |   |  | |  | |||| |  |  |         |  ||||| |||||||||||||||||||| || || |||||||| ||||||||||| ||||||| | | || ||||| || ||||||
-------ccactcctacaatctctgtgtgaaacctgggttcatatttcagattatcattgtt-ttgtgaccttctgtcctgaaaggaaattcgcttttcacatatcagGTCTTTATGTGAGTAGGAACACCTACATTCGTGCTGGAGTTGCAGAGTGGAGAGTTACCAATCCAGTTCATGTG
















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|193463932|gb|FK427856.1|FK427856
EST:     TGTTACGACCAAGGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: TGTTACGACCAAGGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|208265521|gb|GE062713.1|GE062713
EST:     GTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: GTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|208142228|gb|GD934932.1|GD934932
EST:     GTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: GTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|6455802|gb|AW186477.1|AW186477
EST:     TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|193342258|gb|FK308534.1|FK308534
EST:     GTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: GTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|193591004|gb|FK546851.1|FK546851
EST:     GGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: GGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|9565579|gb|BE475088.1|BE475088
EST:     TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAACTGGA
genomic: TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGA
EST: gi|207835308|gb|GD805935.1|GD805935
EST:     GTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: GTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|298197496|gb|HO044975.1|HO044975
EST:     TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|9987749|gb|BE661857.1|BE661857
EST:     GGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACCTGATG                         G-CTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGG
genomic: GGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGAC-TGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGG
EST: gi|207735387|gb|GD710230.1|GD710230
EST:     GGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: GGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|151409014|gb|EV278822.1|EV278822
EST:     TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|26059085|gb|CA801999.1|CA801999
EST:     TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|151394446|gb|EV264317.1|EV264317
EST:     TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: TGGCTCATGGCGGAAAATGTGGCTGTTACGACCAAGGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
EST: gi|21602646|gb|BQ612977.1|BQ612977
EST:     AAATGTGGCTGTTACGACCAAGGTTGCGGACTGATG                         GTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA
genomic: AAATGTGGCTGTTACGACCAAGGTTGCGGACTGATGgtaagaacaa ... cacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgttatgtttttagctaggtctctttgtcttacagtgctcccacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGAAAATCACTAATCCCGTACATGTG
                              gtcttac  putative branch site (score: 3)
                                       tgctccc  putative PPT
      ttatgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttcaaattcacgctaaaagtagatgtacatgattttcctattccttttatgttatgtttttagctaggtctctttgtcttacagtgctcccacatctcagGTCTTTATGTGAGTAGAAATACTTACATTCGAGCTGGAGTTGCTGAGTGGAAAATCACTAATCCCGTACATGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - ttcacgc
- - - - - - - - - - - - -tacatga
- - - - - - - - - - - - - - - - - - - - - - - - -tgttatg