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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggggcttttaattcaaaatgggtgaatcttttataagacatgctttgatataataagacattccttacaagaattttttgcatttgtttgtgccaagcagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAATGAGCTGGGTGTGTGATGAGTCAAACCGCCAACATGAGAAGGTAAGGCTG

Basic information

species Glycine max
transcript GLYMA05G14330.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G14330.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv08s0040g00410.t01 (Vitis vinifera), 3'ss of exon 8
ggggcttttaattcaaaatgggtgaatcttttataagacatgctttgatata-ataagacattccttacaagaattttttgcattt---gtttgtgccaagcagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAATGAGCTGGGTGTGTGATGAGTCAAACCGCCAACATGAGAAGGTAAGGCTG
      |||  ||   |     |||| |||  ||||   ||  |   || |  ||   |  || || ||     |  |    ||||    ||  ||  |||||| || ||||| || || |||||||| |||||||| |  |||||| | |||||||||||||| ||||| |||||||||||||| ||| |||||         
----tatttgttttccatgttctgaaacttacataatggatcttcaaattttcattttatttttctgacccagttcatggttattttacattaatggtaagcagCATTTATGGGGTACACGATGAGGCCAAGGACAAGGCATTTGAGTTGGAAATGAGCTGGGTTTGTGAGGAGTCAAACCGCCAGCATCAGAAG---------

upper sequence: GLYMA05G14330.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S72_57V6.1 (Physcomitrella patens), 3'ss of exon 10
ggggcttttaattcaaaatgggtgaatcttttataagaca--tgctttgatataataagacattccttacaagaattttttgcatttgtttgtgccaag-cagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAATGAGCTGGGTGTGTGATGAGTCAAACCGCCAACATGAGAAGGTAAGGCTG
      |||| ||     |  | ||  || || |          ||||| |||         || |  |      | ||||  ||   ||||   ||   |||||| ||||| || ||||||||||| |||||||| |  |||||||| || ||||||||| | ||||| |||||||||||  | ||| |             
---agatttagttttgcttatgagatcctgttgtgcttttgtcactttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagTATTTATGGTGTGCATGATGAGGCCAAGGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA---------

upper sequence: GLYMA05G14330.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S72_57V6.6 (Physcomitrella patens), 3'ss of exon 10
ggggcttttaattcaaaatgggtgaatcttttataagacatgctttgatataataagacattccttacaagaattttttgcatttgtttgtgccaag-cagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAATGAGCTGGGTGTGTGATGAGTCAAACCGCCAACATGAGAAGGTAAGGCTG
                      ||   ||||| | |      ||||| |||         || |  |      | ||||  ||   ||||   ||   |||||| ||||| || ||||||||||| |||||||| |  |||||||| || ||||||||| | ||||| |||||||||||  | ||| |             
----------------------tgtg-cttttgtca------ctttgttatttatgtttgttaccaatggttgtattttttatgcatttggaacatttcagtatttatggtgtgcatgatgaggccaagGACAAGGCCTTTGAGCTGGAGATGAGCTGGATTTGTGACGAGTCAAACCGTGAGCATCAACGA---------

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|15813832|gb|BI786107.1|BI786107
EST:     AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAAT                         TATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAAT
genomic: AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAATgtaagtagcc ... tgccaagcagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAAT
EST: gi|192295112|gb|FG986831.1|FG986831
EST:     AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAAT                         TATATATGGGAGTTCATGATGAGGCAAAG-ACAAAGATTTTGAGCTAGAAA
genomic: AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAATgtaagtagcc ... tgccaagcagTATATATGG-AGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAA
EST: gi|151400518|gb|EV270332.1|EV270332
EST:     AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAA-T                         TATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTT-GAGCTAGAA-T
genomic: AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAATgtaagtagcc ... tgccaagcagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAAT
EST: gi|213590582|gb|DB973327.1|DB973327
EST:     AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAANAT                         TATATATGGAGTTCATGATGAG
genomic: AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAATgtaagtagcc ... tgccaagcagTATATATGGAGTTCATGATGAG
EST: gi|298174725|gb|HO014756.1|HO014756
EST:     AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAAT                         TATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAAT
genomic: AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAATgtaagtagcc ... tgccaagcagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAAT
EST: gi|151409026|gb|EV278834.1|EV278834
EST:     AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAAT                         TATATATGGAGTTCATGATGAGGC
genomic: AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAATgtaagtagcc ... tgccaagcagTATATATGGAGTTCATGATGAGGC
EST: gi|207713803|gb|GD696262.1|GD696262
EST:     AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAAT                         TATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAAT
genomic: AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAATgtaagtagcc ... tgccaagcagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAAT
EST: gi|151410622|gb|EV280437.1|EV280437
EST:     AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAAT                         TATATATGGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAA
genomic: AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAATgtaagtagcc ... tgccaagcagTATATATGG-AGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAA
EST: gi|192303719|gb|FG994557.1|FG994557
EST:     AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAAT                         TATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAA-T
genomic: AAGCTTGCTGATATGACATGTCGACAAGGGGTTATTGAAGTGGCTAAAATgtaagtagcc ... tgccaagcagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatataataagacattccttacaagaattttttgcatttgtttgtgccaagcagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAATGAGCTGGGTGTGTGATGAGTCAAACCGCCAACATGAGAAGGTAAGGCTG
                tccttac  putative branch site (score: 2)
                   ttacaagaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggggcttttaattcaaaatgggtgaatcttttataagacatgctttgatataataagacattccttacaagaattttttgcatttgtttgtgccaagcagTATATATGGAGTTCATGATGAGGCAAAGGACAAAGATTTTGAGCTAGAAATGAGCTGGGTGTGTGATGAGTCAAACCGCCAACATGAGAAGGTAAGGCTG

- - - - - - - - - tgggtga
- - - - - - - - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcattt