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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctcatgaactactgtctactgcacttgaatgtggccacagaatgaccaagattaactttttttttcttccaaattatgacatctgtatacatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG

Basic information

species Glycine max
transcript GLYMA16G28310.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g36270.1 (Oryza sativa), 3'ss of exon 8
ttctcatgaactactgtctactgcacttgaatgtggc------cacagaatgaccaagattaactttttttttcttccaa-attat--gacatctgtata-catgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG
           ||| ||    || | |||||||          ||| |||| ||  |  | ||| |||||||  ||      ||      | |||| ||       |||| ||||| |||||||| || ||||| ||||| ||||||||||| |||||||||||||| ||  | || || ||||| |||||||||||
---------cttacagttatttgaatttgaatgctctttcttacactgaat-actgaactgaacatttttttggttatgttgttgctctgcttctggatggtccacacagTATGGTTGCTGATGTCCACCGTACTTTGCTATATGGAGGCATATTTTTGTACCCTGCGGATCAGAAGAGCCCAAACGGAAAACTTCG

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 8
ttctcatgaactactgtctactgcacttgaatgtggc------cacagaatgaccaagattaactttttttttcttccaa-attat--gacatctgtata-catgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG-------------
           ||| ||    || | |||||||          ||| |||| ||  |  | ||| |||||||  ||      ||      | |||| ||       |||| ||||| |||||||| || ||||| ||||| ||||||||||| |||||||||||||| ||  | || || ||||| |||||||||||             
---------cttacagttatttgaatttgaatgctctttcttacactgaat-actgaactgaacatttttttggttatgttgttgctctgcttctggatggtccacacagTATGGTTGCTGATGTCCACCGTACTTTGCTATATGGAGGCATATTTTTGTACCCTGCGGATCAGAAGAGCCCAAACGGAAAACTTCGGTATGCTGATGCA

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------------ttctcatgaactactgtctactgcacttgaatgtggcca-cagaatg--accaagattaactttttttttcttccaaattatgacatctgtatacatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG-------------
                                                          | |  ||| |  |||| |      | | || ||  | |  || |||  | ||  |  || |    || |  |  | | |||  | ||   ||  ||   ||| ||||| |||||||| || ||||||||||| ||||||||  | |||||||||||||| ||||| || || |||||||||||||| ||             
gtgatcattttttttgggtgacaatgtatataacctagctgtagttattaataggagcttttttgaccctctgt-tgtgattcataaaagtttctaataggatgtaatcaccaccaattaacattgtagtg-acagtattgcttcctgatg-atttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCGGTACACATTAAGC

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os01g64660.4 (Oryza sativa), 3'ss of exon 7
---------------------------------------------------------ttctcatgaactactgtctactgcacttgaatgtggcca-cagaatg--accaagattaactttttttttcttccaaattatgacatctgtatacatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG
                                                          | |  ||| |  |||| |      | | || ||  | |  || |||  | ||  |  || |    || |  |  | | |||  | ||   ||  ||   ||| ||||| |||||||| || ||||||||||| ||||||||  | |||||||||||||| ||||| || || |||||||||||||| ||
gtgatcattttttttgggtgacaatgtatataacctagctgtagttattaataggagcttttttgaccctctgt-tgtgattcataaaagtttctaataggatgtaatcaccaccaattaacattgtagtg-acagtattgcttcctgatg-atttgcagTATGGTTGCTGATGTCCACCGTACGTTGCTATATGGAGGAGTATTTTTGTACCCTGCAGACAAGAAGAGCCCAAATGGAAAACTCCG

upper sequence: GLYMA16G28310.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv18s0072g00770.t01 (Vitis vinifera), 3'ss of exon 9
--ttctcatgaactactgtctactgcacttgaatgtggc----cacagaatgaccaagattaactttttttttcttccaaattatgacatctgtatacatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG
  |  |  |  |  |   | ||   |  |||||||||        |       ||||||   | |||| |  | |   | | ||  | |    | ||||      |||||||||||||||| || || || || ||||| || || |||||||||||||||||||| || || || || || |||||||| ||
gctctttgttgagcatgatgtatatcttttgaatgtgatgtggttcctttcttccaagaaggatttttctaatttctaataatacaagaatgatttaca------gCATGGTAGCTGATGTCCACCGCACATTACTTTACGGTGGTATCTTTTTGTACCCTGCTGATAAGAAGAGCCCCAACGGAAAACTGCG

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|31474714|gb|CD416742.1|CD416742
EST:     AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAG                         CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
genomic: AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAGgtatcattag ... acatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
EST: gi|26269057|gb|CA820120.1|CA820120
EST:     AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAG                         CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
genomic: AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAGgtatcattag ... acatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
EST: gi|15204366|gb|BI427134.1|BI427134
EST:     GTTCATCACCAAAGTCTCTAAGATATATTGGAAG                         CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
genomic: GTTCATCACCAAAGTCTCTAAGATATATTGGAAGgtatcattag ... acatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
EST: gi|31457542|gb|CD399570.1|CD399570
EST:     AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAG                         CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
genomic: AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAGgtatcattag ... acatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
EST: gi|31473114|gb|CD415142.1|CD415142
EST:     AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAG                         CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
genomic: AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAGgtatcattag ... acatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
EST: gi|31469604|gb|CD411632.1|CD411632
EST:     AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAG                         CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
genomic: AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAGgtatcattag ... acatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
EST: gi|151398810|gb|EV268681.1|EV268681
EST:     AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAG                         CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
genomic: AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAGgtatcattag ... acatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
EST: gi|7692550|gb|AW760653.1|AW760653
EST:     AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAG                         CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
genomic: AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAGgtatcattag ... acatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
EST: gi|192304054|gb|FG993884.1|FG993884
EST:     AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAG                         CATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA
genomic: AAGTTTCCTGAAGATGGTTCATCACCAAAGTCTCTAAGATATATTGGAAGgtatcattag ... acatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaccaagattaactttttttttcttccaaattatgacatctgtatacatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG
      gattaac  putative branch site (score: 2)
       attaactttttttttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctcatgaactactgtctactgcacttgaatgtggccacagaatgaccaagattaactttttttttcttccaaattatgacatctgtatacatgaacagCATGGTAGCTGATGTTCATCGTACGTTGCTTTATGGAGGCATCTTTTTGTACCCTGCTGACAAAAAAAGTCCAAATGGAAAACTTCG

- - catgaac
- - - - - -tactgtc
- - - - - - - - - - -tgcactt
- - - - - - - - - - - - - - gaatgtg
- - - - - - - - - - - - - - - - - - ccacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catctgt