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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACAACCAAGACAAAGAAGCAAAACAAGCCTGCTGCTTTGCTTCACAAATCTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttgatgctctattattcctaaaatatgattctatttctattggacaatatttgttttcttttggtagctacatttatagttgctgttaaatcca...

Basic information

species Glycine max
transcript GLYMA13G42830.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G42830.1 (Glycine max), 5'ss of exon 2
lower sequence: LOC_Os01g51020.1 (Oryza sativa), 5'ss of exon 3
AACAACCAAGACAAAGAAGCAAAACAAGCCTGCTGCTTTGCTTCACAAATCTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatc---ttgatgctctattattcctaaaatatgat-tctatttctattggacaatatttgttttcttttggtagctacatttatagttgctgttaaatcca
 |||||||||||| ||||||| ||||||||||||    |    ||||| |||||||||   ||||||||||| |  ||||| ||||||||  | || |||||| |          || |||  | | |||   |   | |||| || | ||  |      ||| |||  || | || ||| |||   |  |   | | |    |
TACAACCAAGACAGAGAAGCAGAACAAGCCTGCTAGCCTCTACCACAAGTCTGTCATGCGCAAGGAGTTCCGCAAAATGGCCAAGGCTGTCAAGAACCAGgtattagcaccagaactttatggtgcttaagtcagcctgtctaattgtttttcatg----ttgatttaattggatatctaaattctcacatcaagcttataaaa
















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|13252125|gb|BG363028.1|BG363028
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|15001179|gb|BI321993.1|BI321993
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|58014630|gb|CX701372.1|CX701372
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|151412831|gb|EV282643.1|EV282643
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|7029413|gb|AW459196.1|AW459196
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|192334453|gb|FK025574.1|FK025574
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|151404253|gb|EV274063.1|EV274063
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|58023971|gb|CX710712.1|CX710712
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|209728043|gb|BW666765.1|BW666765
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAAGGCAGCTCTGGCAAGG
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|151408919|gb|EV278727.1|EV278727
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|209700447|gb|BW664434.1|BW664434
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAAGGCAGCTCTGGCAAGG
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|10252745|gb|BE820511.1|BE820511
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|193517191|gb|FK473431.1|FK473431
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGG
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGG
EST: gi|120531646|gb|EH259779.1|EH259779
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|254314518|gb|GR829511.1|GR829511
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|192313717|gb|FK008737.1|FK008737
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|254314519|gb|GR829512.1|GR829512
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|209722539|gb|BW682637.1|BW682637
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAAGGCAGCTCTGGCAAGG
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|209700448|gb|BW664435.1|BW664435
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAAGGCAGCTCTGGCAAGG
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|209702857|gb|BW675727.1|BW675727
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAAGGCAGCTCTGGCAAGG
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|298181112|gb|HO022551.1|HO022551
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|209702858|gb|BW675728.1|BW675728
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGANAACTACTACAGGCCTGATCTCAAAAAGGCAGCTCTGGCAAGG
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|298168883|gb|HO009813.1|HO009813
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|120531553|gb|EH259686.1|EH259686
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCCAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|192295037|gb|FG986756.1|FG986756
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|16280185|gb|BI943836.1|BI943836
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|192313718|gb|FK008738.1|FK008738
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
EST: gi|151411631|gb|EV281442.1|EV281442
EST:     CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCCGTACAAAATCAG                         GTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA
genomic: CTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttga ... tgtgttgcagGTAGCAGATAACTACTACAGGCCTGATCTCAAAAGGGCAGCTCTGGCAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACAACCAAGACAAAGAAGCAAAACAAGCCTGCTGCTTTGCTTCACAAATCTGTCATGAAAAAGGAGTTCCGTAGGATGGCAAAGGCTGTGCAAAATCAGgtaatcttgatgctctattattcctaaaatatgattctatttctattggacaatatttgttttcttttggtagctacatttatagttgctgttaaatcca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG