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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtctcatgtgttttgaattggctgtggtgtttgttggcactcttgagaattgcataagaaagtctttgtgtgttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGGCGGTGTACGTTTGTTGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG

Basic information

species Glycine max
transcript GLYMA11G08350.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os09g36800.1 (Oryza sativa), 3'ss of exon 2
--gtaggtctcatgtgttttgaattggctgtggtgtttgttggcactcttgagaattgcataagaaagtctttg--tgtgttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGGCGGTGTACGTTTGTTGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG
  |   || |  |      | ||  |      | |  |    |   |  |   | |   ||  |   ||  ||   ||  | |  ||   |||  || || ||||| || || ||||||||  ||||||| ||||| ||||||||||| |||||||||||  | || ||||| || ||||| |||||||| |
gtgcgtgtgtggttcagacttaagcgttctgagagactaccagttgttgtttcagtccaatttgggtgtacttaactgcttgcggcttgcagGGCACACTGATGAAGGTTTTCGACAAGGCAGTCGAGTCCCGGCTGGACCGGCGGTGCACGTTTGTTGCGTTGGGAGGTGGCGTTATTGGGGACATGTGCG

upper sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G051129_T01 (Zea mays), 3'ss of exon 1
gt-aggtctcatgtgttttgaattgg-ctgtggtgtttgt-tggcactcttgagaattgcataaga--aagtctttgtgtg-------ttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGGCGGTGTACGTTTGTTGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG
|| || || | ||||||||  |  |  ||   ||||   |  |   || ||     ||| |||     || |   ||  ||       |   |  |  |||| || || ||||| || |||||||||||  ||||||| ||  | ||||| ||||| || ||||| || || ||||||||||| ||||| ||||||||||
gtgagctcgcttgtgttttccagcgttcttctgtgtgaatgcgtttctttttcagtttgtatagatttaactgactgcctgacttggctgtgatgggcagGACACGCTGATGAAGGTGTTTGACAAGGCAGTCGAGTCCCGTTTTGACCGCCGGTGCACATTTGTAGCACTGGGTGGTGGTGTCATTGGGGACATGTGTG

upper sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G573867_T01 (Zea mays), 3'ss of exon 2
gtagg-tctcatgtgttttgaattggctgtggtgtttgttggcactcttgagaattgcataagaaagtctttgtgtgttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGGCGGTGTACGTTTGTTGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG
||  | || | |||||||   |  | |    |||  ||  |    | |||     || ||||       |   |||| ||  |    |||| || || ||||| || |||||||||||  ||||||| ||| | ||||| ||||| || ||||| || || ||||||||||| || || ||||||||||
gtgagctcgcttgtgtttcccagcgtcctgtgtgaatgc-gtttgttttgcagtctgtataacctgacttggctgtggtcggc----agGACACGCTGATGAAGGTGTTTGACAAGGCAGTCGAGTCCCGGTTTGACCGCCGGTGCACATTTGTAGCACTGGGTGGTGGTGTCATCGGGGACATGTGTG

upper sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G66120.2 (Arabidopsis thaliana), 3'ss of exon 2
--gtaggtc-tcatgtgttttgaattggctgtggtgtttgttggcactcttgagaattgca--taagaaagtctttgtgtgttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGGCGGTGTACGTTTGTTGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG
    | ||  || ||  |||||| ||  ||||  | |      | |   ||   ||| |    | |   || || | | | |||   |  ||||||||||| ||||||||||| ||||||||||| ||||| || || ||  | || ||||| |||||||| ||||| || |||||||| ||||| |||||||
gtacatgttatcttggattttgatttccctgtt-tataataaagaatcattagtaatcgtgagttattgagactcttt-tattc--tttctagGATACTCTCATGAAAGTCTTCGACAAGGCCATTGAGTCTCGCCTAGATAGACGATGTACATTTGTTGCCCTTGGAGGCGGTGTGATAGGCGATATGTGTG

upper sequence: GLYMA11G08350.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g03820.t01 (Vitis vinifera), 3'ss of exon 2
gtaggtctcatgtgttttgaattggctgtggtgtttgttggcactcttgagaattgcataagaaagtctttgtgtgttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGGCGGTGTACGTTTGTTGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG
|||||| |  |    ||| ||||  |  |  ||| | |  |   |  |   | |||||| |  |  |  |||  | |     |  ||||| || || |||||||| ||||||||||| || ||||| ||| | ||  | || ||||| ||||||||  ||||||||||||| ||||| ||||||||||
gtaggtatattcaagtttcaattaacgatt-tgtgtttaagatgtgattgtagttgcatta--atttaattgcttttatgtattgtagGACACACTAATGAAAGTTTTTGACAAGGCAATTGAGTCACGGTTGGATAGACGTTGTACATTTGTTGCCGTTGGTGGTGGTGTTATTGGTGACATGTGTG

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|21256948|gb|BQ453836.1|BQ453836
EST:     TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATG                         GATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCG
genomic: TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATGgtaggtctca ... caactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCG
EST: gi|24205560|gb|BU964813.1|BU964813
EST:     TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATG                         GATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGG
genomic: TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATGgtaggtctca ... caactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGG
EST: gi|151408017|gb|EV277832.1|EV277832
EST:     ACCTGATGGTGAGCAGTACAAGGGACATG                         GATACTCTTATGAAAGTCTTTTGACAAGGGCCATCGAGTCGCGGCTCGAC
genomic: ACCTGATGGTGAGCAGTACAA-GGACATGgtaggtctca ... caactgatagGATACTCTTATGAAAGTC-TTTGACAA-GGCCATCGAGTCGCGGCTCGAC
EST: gi|213594369|gb|DB967981.1|DB967981
EST:     TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATG                         GATACTCTTATGAAAGTCTTTG
genomic: TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATGgtaggtctca ... caactgatagGATACTCTTATGAAAGTCTTTG
EST: gi|192306954|gb|FG999973.1|FG999973
EST:     TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATG                         GATACTCTTATGAAAGTCTTTGACAAAGCCATCGAGTCGCGGCTCGACCGG
genomic: TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATGgtaggtctca ... caactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGG
EST: gi|213600921|gb|DB968843.1|DB968843
EST:     TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATG                         GATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCG
genomic: TTTCTGTGGAGAGTGTAATTTTACCTGATGGTGAGCAGTACAAGGACATGgtaggtctca ... caactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttggcactcttgagaattgcataagaaagtctttgtgtgttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGGCGGTGTACGTTTGTTGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG
                        ataagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtctcatgtgttttgaattggctgtggtgtttgttggcactcttgagaattgcataagaaagtctttgtgtgttcaactgatagGATACTCTTATGAAAGTCTTTGACAAGGCCATCGAGTCGCGGCTCGACCGGCGGTGTACGTTTGTTGCTCTTGGTGGTGGTGTGATTGGCGACATGTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG