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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttttctgaaattttctggtgcattagggtttcttttagtgtttatttttttatttaaaaaattgaataattttatgagttgggtttttgggctttag

Basic information

species Glycine max
transcript GLYMA19G17920.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G008623_T01 (Zea mays), 5'ss of exon 3
GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttttctgaaattttctggtgcattagggtttcttttagtgtttatttttttatttaaaa---aattgaataattttatgagttgggtttttgggctttag
||||||| ||||||||||||||||||||||  ||||  ||||| | |||  |   |  | |||  |   || || |      |   |||  ||   ||    ||      | || || |   | ||| ||||   || |  ||||||
GACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTCCTGgtaagatttgcccttatctatcttttttctttggttcagggatgaagttatttggcttgcccaagtcctgactggatcacgatttgatttggtggttggttctttag

upper sequence: GLYMA19G17920.1 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G028346_T01 (Zea mays), 5'ss of exon 1
------------------------------------------GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttttctgaaattttctggtgcattagggtttcttttagtgtttatttttttatttaaaaaattgaataattttatgagttgggtttttgggctttag
                                          ||||||| ||||||||||||||||||||||  ||||  ||||| | |     || |  ||       | ||   |||       |   || |||   |   | |||  |||| |   ||   ||  |||   || |  ||||||
TTCTATGATTCTTATTGATCAAGCCACGGTGTTTGTGAAAAGGACTGTTGTTGGGATCAAGTGCAAAGATGGCATTGTTCTGgtaagataagattggaccttctcatcccctttcagttct-----gaagttgtttgagttgctcaaatcttgactggatt-gcgatgtggtggttggtcctttag
















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|298166742|gb|HO010181.1|HO010181
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATGGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|151409523|gb|EV279331.1|EV279331
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|151406675|gb|EV276490.1|EV276490
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|151411404|gb|EV281215.1|EV281215
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|192334682|gb|FK025887.1|FK025887
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGCTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|151409103|gb|EV278911.1|EV278911
EST:     GCCTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|192324735|gb|FK018771.1|FK018771
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|192325082|gb|FK017498.1|FK017498
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|8827689|gb|BE211419.1|BE211419
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|26048077|gb|CA784674.1|CA784674
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|192325978|gb|FK016655.1|FK016655
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|298176424|gb|HO026659.1|HO026659
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|16344394|gb|BI969989.1|BI969989
EST:     AGCGGGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: AGCGGGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|16344458|gb|BI970053.1|BI970053
EST:     GCGGGACTGTTA-TGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTNNNGGGTTCNNATAGA
genomic: GCGGGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|254321256|gb|GR827705.1|GR827705
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|16347339|gb|BI972934.1|BI972934
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|20498037|gb|BQ272967.1|BQ272967
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|26047788|gb|CA784463.1|CA784463
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|208110680|gb|GD913200.1|GD913200
EST:     TAACAGCGGGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: TAACAGCGGGACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
EST: gi|6726863|gb|AW311282.1|AW311282
EST:     GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTG                         GGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA
genomic: GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttt ... tgggctttagGGCGTTGAGAAGCTTATTCCGTCGAAAATGATGCTTCCGGGTTCCAATAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTGTTATTGGGATCAAGTGCAAAGATGGGGTTGTGTTGgtaggttttttctgaaattttctggtgcattagggtttcttttagtgtttatttttttatttaaaaaattgaataattttatgagttgggtttttgggctttag

- - - - - - - - - - GCAAAG
- - - - - - - - - - -  AAGATG