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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agattttattacttttaattaatgagtcagtctttcttttttatgttaaacacttttttggccttggaaatgctcatgcttctgctgctgtatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTTAACCTTGCAAAATCACTTTTTGGCATTGAAATTGAGCCAGCTGATGGTC

Basic information

species Glycine max
transcript GLYMA09G33490.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G65620.1 (Arabidopsis thaliana), 3'ss of exon 8
agattttattacttttaattaatgagtcagtctttcttttttatgttaaacacttttttggccttggaaatgctcatgcttctgctgctgtatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTTAACCTTGCAAAATCACTTTTTGGCATTGAAATTGAGCCAGCTGATGGTC
        ||  || |  ||    ||  |||  | |  || ||| ||      |||    | ||||   || || || ||   | |   || | || ||||||||||| ||||| |  ||||| ||||||||||||||||||||||| || |  || || ||  |||||||||| ||||| ||||| ||||| |||||| 
-------gttctttgtccttctgtagctagtgatgcaattatatattg----ttttgaaagtcttg---atccttat-ctctcgttttggtctttc-tagGAAGAACTACGTCCATACTTCTCACTGCCAAAGGTTATGGATGGACTTTTCAGTCTAGCTAAGACACTTTTTGGAATTGATATTGAACCAGCAGATGGTT

upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 8
agattttattacttttaattaatgagtcagtctttcttttttatgttaaacacttttttggccttggaaatgctcatgcttctgctgctgta---tctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTTAACCTTGCAAAATCACTTTTTGGCATTGAAATTGAGCCAGCTGATGGTC
 | |   ||| ||| |  ||  || ||   | |||| |  || |    ||  | |  ||     | || |  || ||   | |  || | ||   ||  | |||| ||||| || |||| ||||||  |||||||||| |||| ||| || || | |||||| ||    |||||||| ||||| |||||||||||||||||||
-gttgaaattgcttattctttgtgggtt--tttttcctgattgtaaataagccctcatttctgatagagaaacttatttattttttgttttaaaatccaacagGAGGAACTACGCCCCTATTTCTCATTGCCAAAGGTCATGGGTGGTCTTTTCAGCCTTGCTAAGATGCTTTTTGGAATTGACATTGAGCCAGCTGATGGTC

upper sequence: GLYMA09G33490.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 3'ss of exon 11
agattttattacttttaattaatgagtcagtctttcttttttatgttaaacacttttttggccttggaaa----tgctcatgcttctgctgctgtatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT-AACCTTGCAAAATCACTTTTTGGCATTGAAATTGAGCCAGCTGATGGTC
       ||| || ||  ||  || ||   | || ||  ||     ||| | | |  ||     | || |    |  | ||  || || |     |||  | |||| ||||| || |||| ||||||  |||||||||| |||| ||| |  ||| | |||||| ||    |||||||| ||||| |||||||||||||||||| 
----aaaattcctatttctttgtgggttttttttcctgattgtaaataagcccctcatttctgatagagaaacttatttatttttttgttttaaaatccaacagGAGGAACTACGCCCCTATTTCTCATTGCCAAAGGTCATGGGTGGTCCTTTTCAGCCTTGCTAAGATGCTTTTTGGAATTGACATTGAGCCAGCTGATGGT-

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|193554261|gb|FK513418.1|FK513418
EST:     TTACCTATTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
EST: gi|193718071|gb|FK656031.1|FK656031
EST:     TTACCTATTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
EST: gi|193703380|gb|FK636494.1|FK636494
EST:     TTACCTATTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
EST: gi|151410408|gb|EV280223.1|EV280223
EST:     TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
EST: gi|207728609|gb|GD707737.1|GD707737
EST:     TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
EST: gi|193726753|gb|FK656887.1|FK656887
EST:     TTACCTATTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
EST: gi|192308087|gb|FK000415.1|FK000415
EST:     TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
EST: gi|298198857|gb|HO042220.1|HO042220
EST:     TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
EST: gi|6502048|gb|AW203421.1|AW203421
EST:     TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAAGAACTTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAA-GAACT-GCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCT
EST: gi|254336791|gb|GR842970.1|GR842970
EST:     TTACCTATTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
EST: gi|308098840|gb|HO760681.1|HO760681
EST:     TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAG                         GAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT
genomic: TTACCTTTTGGAGTGAGAGGCTACGTGAGTCAAAATATGATATTAATGAGgtttctctct ... tatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaacacttttttggccttggaaatgctcatgcttctgctgctgtatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTTAACCTTGCAAAATCACTTTTTGGCATTGAAATTGAGCCAGCTGATGGTC
      actttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agattttattacttttaattaatgagtcagtctttcttttttatgttaaacacttttttggccttggaaatgctcatgcttctgctgctgtatctcatagGAAGAACTGCGTCCCTTTTTCTCTCTGCCAAAGGTTATGGATGGACTCTTTAACCTTGCAAAATCACTTTTTGGCATTGAAATTGAGCCAGCTGATGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgctgc