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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggaagactcgttcctgttattgttcattagttttgatactctattattggtttcattataaattttccccgtatatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCAAGTTCTGCTTGAGGAGGCTAAAGAAAGTTACTCGGAGGAGAAAGTGATT

Basic information

species Glycine max
transcript GLYMA16G27430.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27430.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g03280.t01 (Vitis vinifera), 3'ss of exon 2
gtacggaagactc-gttcctgttattgt-tcattagttt--tgatactctatta----ttggtttcattataaattttccccgtatatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCAAGTTCTGCTTGAGGAGGCTAAAGAAAGTTACTCGGAGGAGAAAGTGATT
|||  || |  |  | ||  |  ||  | |  || ||||  | |||| ||   |    |   |||   |  |||  ||    || | |||| ||| || ||||  |  ||||||||||| |||||||| ||||||||||| || |||||  |||| |||||||| || || |||||  | |||||    ||  | 
gtagtgatgtttttgctcagggcatcatcttcttggtttcttcatacccttccacccatcattttggctcaaaaaattgtttgt-tgtgtggcagAGGATACACGGGGTCAAAGCTTTCAAACAATATCGAATGTGAAATATTTCAAGTATTGCTGGAGGAGGCGAAGGAGAGTTATCCAGAGGACGTCGTAGTG
















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|213619568|gb|DB963734.1|DB963734
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|193535354|gb|FK489994.1|FK489994
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCT
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCT
EST: gi|298193921|gb|HO040569.1|HO040569
EST:     GTTGTACTTCAAACTGATAACACCATTCTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|207731652|gb|GD707125.1|GD707125
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|31307006|gb|CD392209.1|CD392209
EST:     GTTGTACTTCAAACTGATAACACCATTCTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|298192839|gb|HO033273.1|HO033273
EST:     GTTGTACTTCAAACTGATAACACCATTCTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|192332213|gb|FK023862.1|FK023862
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|298183620|gb|HO028833.1|HO028833
EST:     GTTGTACTTCAAACTGATAACACCATTCTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|298173803|gb|HO017139.1|HO017139
EST:     GTTGTACTTCAAACTGATAACACCATTCTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|254317987|gb|GR832155.1|GR832155
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|298196424|gb|HO041167.1|HO041167
EST:     GTTGTACTTCAAACTGATAACACCATTCTGTACGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|254331451|gb|GR845923.1|GR845923
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|192311583|gb|FK004838.1|FK004838
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|192316022|gb|FK007125.1|FK007125
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|254325388|gb|GR838269.1|GR838269
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|192317805|gb|FK009397.1|FK009397
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|208055228|gb|GD854519.1|GD854519
EST:     TTGTACTTCAAACTGATAACACCATTTTGTTATGACCGTTTGAGTAGGAG                         GGGGTACGAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCC
genomic: TTGTACTTCAAACTGATAACACCATTTTG-TATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTAC-AAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCC
EST: gi|298193545|gb|HO034151.1|HO034151
EST:     GTTGTACTTCAAACTGATAACACCATTCTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAA-GCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|151401187|gb|EV271001.1|EV271001
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|254325389|gb|GR838270.1|GR838270
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|254323438|gb|GR840135.1|GR840135
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|298178466|gb|HO024201.1|HO024201
EST:     GTTGTACTTCAAACTGATAACACCATTCTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|193670198|gb|FK609452.1|FK609452
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCT
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCT
EST: gi|193548257|gb|FK505250.1|FK505250
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|192318020|gb|FK009472.1|FK009472
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|254317988|gb|GR832156.1|GR832156
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
EST: gi|254347363|gb|GR853612.1|GR853612
EST:     GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAG                         GGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA
genomic: GTTGTACTTCAAACTGATAACACCATTTTGTATGACCGTTTGAGTAGGAGgtacggaaga ... tatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttgatactctattattggtttcattataaattttccccgtatatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCAAGTTCTGCTTGAGGAGGCTAAAGAAAGTTACTCGGAGGAGAAAGTGATT
  ttttgat  putative branch site (score: 4)
           tctattattggtttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggaagactcgttcctgttattgttcattagttttgatactctattattggtttcattataaattttccccgtatatgtgacagGGGGTACAAAGATTCAAAGCTTTCGAACAATATTGAATGTGAAATCTTCCAAGTTCTGCTTGAGGAGGCTAAAGAAAGTTACTCGGAGGAGAAAGTGATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA