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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtttaagattgctaacatcctttttgattcctagggtacttctactattgattttctgtggtgctatattgtatgtactaactgtctattgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTGGAGCATGAATACTTCAAAGACATTAAATTTGTGCCCTGATTCCATATCT

Basic information

species Glycine max
transcript GLYMA09G03470.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G03470.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0045g00310.t01 (Vitis vinifera), 3'ss of exon 8
-----cgtttaagattgctaacatcctttttgattcctagggtacttctactattgattttctgtggtgctatattgtatgtactaactgtctattgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTGGAGCATGAATACTTCAAAGACATTAAATTTGTGCCCTGATTCCATATCT
       | |  |  |  ||| |  | | |   ||       || | |  |  ||  || | | |         || ||   | |   ||| | || | |||||||  ||||| ||| |||||||||||| |||||| || |||||||| ||| | |||||||| ||||||||||| |||   |||||||||||||| ||| | |
tcacaaatatgtggatcttaataggcatataattttaagaactagtgcagcagtt--ttgtttataccatccgcttatacaaatt---tgtatgttattttccagAAAATGCTGTGCCTGGATCCCAGCAGAAGAATAACTGCCAGGAGTGCTCTTGAGCATGAGTACTTCAAAGATATTGGGTTTGTGCCCTGATTGCATGTGT
















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|192309059|gb|FK001835.1|FK001835
EST:     TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCT                         AGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
genomic: TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCTgtaagtgcaa ... tgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
EST: gi|18038899|gb|BM307193.1|BM307193
EST:     ATCTTGATGCAGCTGGTCTTAATCTTCTTTCT                         AGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
genomic: ATCTTGATGCAGCTGGTCTTAATCTTCTTTCTgtaagtgcaa ... tgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
EST: gi|9563850|gb|BE473359.1|BE473359
EST:     TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCT                         AGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
genomic: TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCTgtaagtgcaa ... tgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
EST: gi|193499843|gb|FK464760.1|FK464760
EST:     TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCT                         AGTATGCTTTGCTTGGATCCCAGCAAAAG
genomic: TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCTgtaagtgcaa ... tgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAG
EST: gi|192330929|gb|FK023102.1|FK023102
EST:     TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCT                         AGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
genomic: TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCTgtaagtgcaa ... tgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
EST: gi|192312081|gb|FK003858.1|FK003858
EST:     TAGCAAATGTGGTTCCAAATCTTGACGCAGCTGGTCTTAATCTTCTTTCT                         AGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
genomic: TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCTgtaagtgcaa ... tgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTG
EST: gi|193356410|gb|FK323123.1|FK323123
EST:     TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCT                         AGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCG
genomic: TAGCAAATGTGGTTCCAAATCTTGATGCAGCTGGTCTTAATCTTCTTTCTgtaagtgcaa ... tgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctattgattttctgtggtgctatattgtatgtactaactgtctattgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTGGAGCATGAATACTTCAAAGACATTAAATTTGTGCCCTGATTCCATATCT
                               tactaac  putative branch site (score: 0)
                    tatattgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgtttaagattgctaacatcctttttgattcctagggtacttctactattgattttctgtggtgctatattgtatgtactaactgtctattgtattccagAGTATGCTTTGCTTGGATCCCAGCAAAAGAATTACCGCCAGGAGCGCTGTGGAGCATGAATACTTCAAAGACATTAAATTTGTGCCCTGATTCCATATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - tgctaac
- - - - - - - - - - - - -tgattcc
- - - - - - - - - - - - - - - - - - - -cttctac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgtcta