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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaacttgtgagcagtattaaatatgtatagccaagtcctgtaaattctgtttgttgcaaaattgctttgtggcaactctcataggctgtgaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATTATTGAAGATGTTAGGGTGCAACGAGACAAAGGTTTTGGGTTTGTGAGAT

Basic information

species Glycine max
transcript GLYMA13G17200.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G17200.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 10
---gcaacttgtgagcagtattaaatatgtatagccaagtcctgtaaattctgtttgttgcaaaattgctttgtggcaac-----tctcataggctgtgaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATTATTGAAGATGTTAGGGTGCAACGAGACAAAGGTTTTGGGTTTGTGAGAT
      | || |    |  |  | | |  ||| | ||  ||     |||  |     |||||||||| |||| || ||       ||| ||   || |  |||||||||||||||| ||||| ||||| | |||||||||| | |||   || |||  ||||||||||||| ||||||||||||| ||||| ||||| ||||||||||
attattatttttata-atcagaacacaactatgggcagctctgaagaatgtt-----ttgcaaaatt-ctttctgccattagctttcttattaact-tataattgcagGTTACTTCAGTTGACCTCCACCGACATTTTCATGCACTTGGCGCTGGAGCTATTGAAGATGTTCGGGTGCAACGAGATAAAGGCTTTGGTTTTGTGAGAT
















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|207813078|gb|GD785012.1|GD785012
EST:     GTTGGCAATCTTGCTCCGGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
genomic: GTTGGCAATCTTGCTCCGGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
EST: gi|13562965|gb|BG551185.1|BG551185
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
EST: gi|208052461|gb|GD851758.1|GD851758
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
EST: gi|10252718|gb|BE820484.1|BE820484
EST:     NGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
EST: gi|208254159|gb|GE051629.1|GE051629
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
EST: gi|193542811|gb|FK504132.1|FK504132
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
EST: gi|193429123|gb|FK393217.1|FK393217
EST:     TTGGCAATCTTGCTCCGGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
genomic: TTGGCAATCTTGCTCCGGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
EST: gi|151407111|gb|EV276926.1|EV276926
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCGGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtttgttgcaaaattgctttgtggcaactctcataggctgtgaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATTATTGAAGATGTTAGGGTGCAACGAGACAAAGGTTTTGGGTTTGTGAGAT
             aaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaacttgtgagcagtattaaatatgtatagccaagtcctgtaaattctgtttgttgcaaaattgctttgtggcaactctcataggctgtgaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAATTATTGAAGATGTTAGGGTGCAACGAGACAAAGGTTTTGGGTTTGTGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG