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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaagtcaaaaagggtgttgataccacttttgtatcatataatctgcaaccttctagctgttttgtatatattgatatgtggattgattttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGGATTAAAACTTGAACAGTTTATATTTGATGCATTTCCATATGCTCCTACG

Basic information

species Glycine max
transcript GLYMA08G09170.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os04g52370.2 (Oryza sativa), 3'ss of exon 12
ataaagtcaaaaagggtgttgataccacttttgtatcatataatctgcaaccttctagctgttttgtatatat----tgatatgtggattgattttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGGATTAAAACTTGAACAGTTTATATTTGATGCATTTCCATATGCTCCTACG
      |    |||   ||     |||  |||  | | |  || || || | |||   || || | | | ||     ||| || |  |    |||| ||| ||||||||||||||| |||||||| || |||||||| ||||| ||  ||||||| || || |||||||||| |||||| || || ||    ||  | ||  | 
---ctcttcctaagaaagtgagagccatgtttaaaac-tgcaagctccatcattcattctattgtatttgtagcacatgaaatttacaaaacttttgtgtccagTTATCATCTTGCTGAGAAGAAGATCCCTTCCATCCATGGGTACGCAATGGGCTTGAAGCTTGAACAGTATATATTCGACGCGTTCAGTTACTCCCCATCC

upper sequence: GLYMA08G09170.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv01s0011g01420.t01 (Vitis vinifera), 3'ss of exon 12
ataaagtcaaaaagggtgttgataccacttttgtatcatataatctgcaaccttctagctgttttgtatatattgatatgtggattg-attttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGGATTAAAACTTGAACAGTTTATATTTGATGCATTTCCATATGCTCCTACG
 |    |  ||    ||| |   |  | ||||     ||| |   | |||      | |    || |  ||||| || |      || ||| |  ||| ||||| ||||| ||||||||||||||  |||| |  || ||||| ||||||||||||||||| || ||||||||||||||||||||||||||||| ||| | 
-tcttatgcaattttgtggttgcatgatttttcatctataaatgtttcaattactcaaccacattttgaatattaatctacactctggattgtgagtgtagTTACCATCTAGCAGAGAAGAAAATCGCTTCAACCCACGGATACACAATGGGATTAAAACTAGAGCAGTTTATATTTGATGCATTTCCATATGCCCCTTCA
















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|208191545|gb|GD992781.1|GD992781
EST:     ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCAT                         TTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
genomic: ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCATgtatgtgtgt ... ttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
EST: gi|254342038|gb|GR853175.1|GR853175
EST:     ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCAT                         TTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
genomic: ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCATgtatgtgtgt ... ttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
EST: gi|4313957|gb|AI461076.1|AI461076
EST:     ACTCTGGATTTTCTGAATCAAGTGGCAAATGGCCTTGAAAAAGACAGCAT                         TTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
genomic: ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCATgtatgtgtgt ... ttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
EST: gi|8282791|gb|BE020352.1|BE020352
EST:     GAAAAAGACAGCAT                         TTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
genomic: GAAAAAGACAGCATgtatgtgtgt ... ttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
EST: gi|208215335|gb|GE011090.1|GE011090
EST:     ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCAT                         TTATCATCTTGCAGAAGAAAGAAAATAACCTT
genomic: ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCATgtatgtgtgt ... ttatgtgcagTTATCATCTTGCAGA-GAA-GAAAATA-CCTT
EST: gi|298176684|gb|HO026805.1|HO026805
EST:     ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCAT                         TTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
genomic: ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCATgtatgtgtgt ... ttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
EST: gi|151397105|gb|EV266978.1|EV266978
EST:     ACTCTGGATTTTCTGAATCAAGTGGCAAATGGCCTTGAAAAAGACAGCAT                         TTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
genomic: ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCATgtatgtgtgt ... ttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG
EST: gi|254329705|gb|GR839258.1|GR839258
EST:     ACTCTGGATTTTCTGAATCAAGTGGCAA-TGGCCTTGAAAAAGACAGCAT                         TTATCATCTTGCAGAGAAGAAA-TACCTTCCATACATGGATATACA-TGGG
genomic: ACTCTGGATTTTCTGAACCAAGTGGCAAATGGCCTTGAAAAAGACAGCATgtatgtgtgt ... ttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaccttctagctgttttgtatatattgatatgtggattgattttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGGATTAAAACTTGAACAGTTTATATTTGATGCATTTCCATATGCTCCTACG
                ttttgtatatattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaagtcaaaaagggtgttgataccacttttgtatcatataatctgcaaccttctagctgttttgtatatattgatatgtggattgattttatgtgcagTTATCATCTTGCAGAGAAGAAAATACCTTCCATACATGGATATACAATGGGATTAAAACTTGAACAGTTTATATTTGATGCATTTCCATATGCTCCTACG

- - - - - - -gggtgtt
- - - - - - - - - - - -accactt
- - - - - - - - - - - - - - - - - - - - - atctgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatatg