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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaactgagaactcaagtctttatttgacattttgtatacaggcgccagactggtgtataaatgtaaattttatgtttacaatgtttcttgttttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATGGTAATGGAGAATCTCTTTTACAAGAGAAACATATCCAGGGTATATGATC

Basic information

species Glycine max
transcript GLYMA20G01680.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G01680.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G71010.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagaactgagaactcaagtctttatttgacatttt-gtatacaggcgccagactggtgtataaatgtaaattttatgtttacaatgtttcttgttttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATGGTAATGGAGAATCTCTTTTACAAGAGAAACATATCCAGGGTATATGATC
      | ||| ||   | |     || |||  || | | |  | |     | |   |||     |||| |||  |   |||  |||| |  |||||      | ||||| |  | ||| | || |||||||| || || ||||| || ||| ||||||| |||||||||||||| ||||| ||||  ||||| ||| | |||||||
---gttagtgacaatataggagggaatgtgaacttgtaggactctgaaatgaaataagtgagc--atgtgaatgattgatttggaatgatatttgtt------gtagGTCTCAATTAAACATCCGAAAGGTGGAAAAGAGACAAAGATGGATTTGATGGTGATGGAGAATCTCTTCTACAACAGAAGAATATCTAGGATCTATGATC

upper sequence: GLYMA20G01680.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv01s0011g04790.t01 (Vitis vinifera), 3'ss of exon 9
gtgagaactgagaactcaagtctttatttgacattt-tgtatacaggcgccagactggtgtataaatgtaaattttatgtt--tacaat----gtttcttgttttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATGGTAATGGAGAATCTCTTTTACAAGAGAAACATATCCAGGGTATATGATC
               |     | || ||||| ||||    ||  ||   |  |  ||||||  ||||   ||| || |  |  |   ||     ||| ||| |    |||||||||||||||||| | |  |||||||| |||||||||||||| ||| ||||||| |||||||| || |||| ||||||||| || || || || |||||||
-------------gttaggcccattctttgatatttgcacatgtagatacatgggtggtgtgcaaatactaatgttgttctcttgtgattttgatttattggtccaatggcagGTCACTGTCAAAAATCTGAAAGGTGGAAAGGAAACAAAAATGGATTTGATGGTGATGGAGAACCTTTTTTTCAAGAGAAATATCTCAAGAGTCTATGATC
















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|193422232|gb|FK391469.1|FK391469
EST:     TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAG                         GTCACTGTCAAATACCCAAAAGGTGGCAAGGAAAC-AAAATAGATCTGATG
genomic: TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAGgtgagaactg ... ttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
EST: gi|208067622|gb|GD865710.1|GD865710
EST:     TTGTCTTGCCAAAATTCTTGGTATTTATCAG                         GTCACTGTCAAATAACCCAAAAGGTGG
genomic: TTGTCTTGCCAAAATTCTTGGTATTTATCAGgtgagaactg ... ttggtggcagGTCACTGTCAAATA-CCCAAAAGGTGG
EST: gi|6724683|gb|AW309016.1|AW309016
EST:     TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAG                         GTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
genomic: TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAGgtgagaactg ... ttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
EST: gi|208052189|gb|GD853474.1|GD853474
EST:     TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAG                         GTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
genomic: TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAGgtgagaactg ... ttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
EST: gi|192324896|gb|FK015377.1|FK015377
EST:     TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAG                         GTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
genomic: TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAGgtgagaactg ... ttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
EST: gi|208125235|gb|GD923695.1|GD923695
EST:     TCAACTCAGGGGGGCCAACTTGTCTTGCCGAAATTCTTGGTATTTATCAG                         GTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
genomic: TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAGgtgagaactg ... ttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
EST: gi|193702471|gb|FK640919.1|FK640919
EST:     TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAG                         GTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG
genomic: TCAACTCAGGAGGGCCAACTTGTCTTGCCAAAATTCTTGGTATTTATCAGgtgagaactg ... ttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactggtgtataaatgtaaattttatgtttacaatgtttcttgttttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATGGTAATGGAGAATCTCTTTTACAAGAGAAACATATCCAGGGTATATGATC
                                    tttcttgtttt  CT-rich tract
        tataaatgtaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagaactgagaactcaagtctttatttgacattttgtatacaggcgccagactggtgtataaatgtaaattttatgtttacaatgtttcttgttttggtggcagGTCACTGTCAAATACCCAAAAGGTGGCAAGGAAACAAAAATAGATCTGATGGTAATGGAGAATCTCTTTTACAAGAGAAACATATCCAGGGTATATGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA