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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatataaggaaacaactgagatgattagatttcacattgcatgtaagggtgccttttctgactatgctacctttgttttgccgtccattcgttttcaatattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGACTACTAAATTTGGTGCATCATCTAGGAT

Basic information

species Glycine max
transcript GLYMA08G20670.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 3
--gtgagtatataaggaaacaactgagatgattagatttcacattgcatgtaagggtgccttttctgactatgctacctttgttttgccgtccattcgttttcaatattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGACTACTAAATTTGGTGCATCATCTAGGAT
  | ||     |    |     || |   ||||   ||      | ||| |  ||    ||||| ||   || ||||     ||||    ||| |  ||| | ||       ||  ||||| ||||| |||||||| || || || || || || |||||||||||||| || ||||| |||||| | ||||| |||||||| ||||| |  ||
gtgcgaaatgttgcttatgtttcttaaccgatt---ttcttggatacat-tctggacttcttttgtggtaat-ctactaacatttt----tccgtgtgttattaa-------agCACCTGGCGATGGTCCAATTGTTCTGGTGTTAGCCCCTACACGTGAACTTGCTGTGCAGATACAGCAAGAGGCAACTAAGTTTGGTGCGTCATCAAAAAT

upper sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 3
---------------------gtgagtat-ataaggaaacaactgagatgattagatttcacattgcatgtaagggtgccttttctgac-tatgctacctttgttttgccgtccattcgttttcaatattttc--agATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGACTACTAAATTTGGTGCATCATCTAGGAT
                     ||   | |    |       | |   ||   |  || |  |  |  || ||    |   | | |  ||  ||  |    | |||      |    || || ||  |||||||  || ||| |||||||| ||||||||  ||||||| ||||||||||||||||||||||| || |||||||||||  |  ||||||||||||||||||| |||||
gtataagtgtctttctaattcgttgatgtcgctaatttctgatttctatctatctatctatctatctatatatatatatatatgcacacacatttttttctagttacaagttttggtctttctctgtattttctcagCTCCAGGAGATGGCCCAATTGTATTAGTTTTAGCTCCAACTCGTGAACTTGCTGTTCAGATACAACAAGAAGCAGCTAAATTTGGTGCATCATCGAGGAT
















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|151407052|gb|EV276867.1|EV276867
EST:     TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAA                         ATCCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTT
genomic: TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAAgtgagtatat ... atattttcagATCC-TGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTT
EST: gi|208245662|gb|GE047026.1|GE047026
EST:     TGTTAATGCTCAGCCAATACTAA                         ATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTG
genomic: TGTTAATGCTCAGCCAATACTAAgtgagtatat ... atattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTG
EST: gi|7925520|gb|AW831546.1|AW831546
EST:     TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAA                         ATCCTGGAGATGGACCAATTGTGCTAGTNTTGGCTCCAACTCGTGAACTTG
genomic: TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAAgtgagtatat ... atattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTG
EST: gi|209700616|gb|BW670334.1|BW670334
EST:     TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAA                         ATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTG
genomic: TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAAgtgagtatat ... atattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTG
EST: gi|213595546|gb|DB968510.1|DB968510
EST:     TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAA                         ATCCTGGAGATGGACCAATTG
genomic: TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAAgtgagtatat ... atattttcagATCCTGGAGATGGACCAATTG
EST: gi|151397571|gb|EV267444.1|EV267444
EST:     TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAA                         ATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTG
genomic: TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAAgtgagtatat ... atattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTG
EST: gi|9986238|gb|BE660346.1|BE660346
EST:     TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAA                         ATCCTGGAGATGG-CCAATTGTGCTAGTTTTGGCTTCCAACTCGTGAACTT
genomic: TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAAgtgagtatat ... atattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCT-CCAACTCGTGAACTT
EST: gi|298192717|gb|HO033151.1|HO033151
EST:     TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATATTAA                         ATCCTGGAGATGGACCA
genomic: TGCTTACTTGTTGCCTGCCATTGTGCATGTTAATGCTCAGCCAATACTAAgtgagtatat ... atattttcagATCCTGGAGATGGACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttctgactatgctacctttgttttgccgtccattcgttttcaatattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGACTACTAAATTTGGTGCATCATCTAGGAT
   ttctgac  putative branch site (score: 2)
                                              tattttc  putative PPT
                                       ttttcaatattttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatataaggaaacaactgagatgattagatttcacattgcatgtaagggtgccttttctgactatgctacctttgttttgccgtccattcgttttcaatattttcagATCCTGGAGATGGACCAATTGTGCTAGTTTTGGCTCCAACTCGTGAACTTGCTGTCCAAATACAACAAGAGACTACTAAATTTGGTGCATCATCTAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA