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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgcagaatcggaagccgttattcctttcataatccatttttactgagtaatgaaagatctgacaatttattggtccatattgatttattttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT

Basic information

species Glycine max
transcript GLYMA13G40130.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G40130.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv06s0004g02890.t01 (Vitis vinifera), 3'ss of exon 10
atgcagaatcggaagccgttattcctttcataatccatttttactgagtaatgaaagatctgacaatttattggtccatattga---tttattttaact--gcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT
   ||  |   ||| || || ||  |   ||    ||| |  |    || || ||  ||    ||| | ||      ||| |||   | | ||||   |   ||| ||||||| |||||||| ||||| |||||||| |||||||||||||||| ||| || 
---catgaa-agaaaccctttttaatccaatgcatcatgtccatattgttataaagcataatgcaaat-ataaacttatagtgaaactctgtttttctttgacagTCTGATGGGTTCCCCACACTTCTATTCTTCCCAGCAGGAAACAAGAGTTCTGATCCA
















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|209714609|gb|BW662245.1|BW662245
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|8403249|gb|BE058883.1|BE058883
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|193717911|gb|FK655983.1|FK655983
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|26059696|gb|CA802610.1|CA802610
EST:     CCAGGGCTAAG                         CCTGCTGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: CCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|6567366|gb|AW234977.1|AW234977
EST:     TTGTGATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCGCCACTCTTCTCTTCTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTT
EST: gi|6846143|gb|AW348433.1|AW348433
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|254316462|gb|GR827999.1|GR827999
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|4289796|gb|AI437977.1|AI437977
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|192331238|gb|FK020977.1|FK020977
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|192331239|gb|FK020978.1|FK020978
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|21285376|gb|BQ473247.1|BQ473247
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGG
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGG
EST: gi|208225225|gb|GE022242.1|GE022242
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|13240110|gb|BG359419.1|BG359419
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|21285317|gb|BQ473188.1|BQ473188
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTC
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTC
EST: gi|254316461|gb|GR827998.1|GR827998
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|6725175|gb|AW309574.1|AW309574
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|192326874|gb|FK015131.1|FK015131
EST:     TTGTAATAGCCAAGGTGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|33387977|gb|CA851184.1|CA851184
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|6069456|gb|AW099142.1|AW099142
EST:     CAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: CAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|31464264|gb|CD406292.1|CD406292
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|23731199|gb|BU763711.1|BU763711
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|209714608|gb|BW662244.1|BW662244
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
EST: gi|7029455|gb|AW459238.1|AW459238
EST:     TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAG                         CCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT
genomic: TTGTAATAGCCAAGATGGATGGAACAACAAATGAGCATCCCAGGGCTAAGgtaaacacaa ... ttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtaatgaaagatctgacaatttattggtccatattgatttattttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT
                                           ttttaac  putative branch site (score: 2)
                                       tttatttt  CT-rich tract
                                atattgatttatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgcagaatcggaagccgttattcctttcataatccatttttactgagtaatgaaagatctgacaatttattggtccatattgatttattttaactgcagCCTGATGGATTCCCCACTCTTCTCTTCTTCCCGGCAGGAAACAAGAGTTTTGACCCT

- - - - - - - - - - - -cctttca
- - - - - - - - - - - - - - - - - - - - -tactgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgaca