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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattcttcctacattttccttgccaaaatatttagtgccttttatggttaacttgatcgatatggatgttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGAGAACCAAAGGTTGCTTCTGCGAAACAG

Basic information

species Glycine max
transcript GLYMA17G07380.1
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 20
gtaaaat----tcttcctacattttccttgccaaaata-tttagtgccttttatggttaact--tgatcgatatgga----tgttgcc-----atagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGAGAACCAAAGGTTGCTTCTGCGAAACAG
|||| ||    |  |  |   |||   ||||    |||  ||  || |||  || |     |  ||  |  |||| |    ||   ||     | |||||||||||||||| |||||| |||| |||||||| | || |||||||||||| ||||||||| |||||||||| |||
gtaatatatcattgttttctttttcttttgcttttatagctttatgtcttccattggaggataatgcccagtatgcacttatgcaacctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAG
















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|6725436|gb|AW309835.1|AW309835
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|207821964|gb|GD796881.1|GD796881
EST:     TTGGGGCTC-AATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|151410382|gb|EV280197.1|EV280197
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|208160487|gb|GD960435.1|GD960435
EST:     GGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: GGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|298173204|gb|HO020188.1|HO020188
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|18693005|gb|BM521853.1|BM521853
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|18733023|gb|BM527382.1|BM527382
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|21887322|gb|BQ740535.1|BQ740535
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|151407803|gb|EV277618.1|EV277618
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|5175496|gb|AI759829.1|AI759829
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|10234449|gb|BE803337.1|BE803337
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|51335738|gb|CO979604.1|CO979604
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|208192569|gb|GD994169.1|GD994169
EST:     AATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: AATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|22525640|gb|BU084451.1|BU084451
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|20814470|gb|BQ298948.1|BQ298948
EST:     CGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: CGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|19934808|gb|BQ079838.1|BQ079838
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|13252690|gb|BG363593.1|BG363593
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|7030028|gb|AW459811.1|AW459811
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|9903061|gb|BE612029.1|BE612029
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAAGAAGGTCAAGGAATGGGG
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAG-AAGAAGGTCAAGGAATGGGG
EST: gi|163921552|gb|EH039311.1|EH039311
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|192327522|gb|FK018198.1|FK018198
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGG
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTT-GAACTGCTTGAGAAGAAGGTCAAGGAATGGGG
EST: gi|208062973|gb|GD860875.1|GD860875
EST:     ATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: ATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|22524847|gb|BU083658.1|BU083658
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
EST: gi|22932991|gb|BU550130.1|BU550130
EST:     TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAG                         GCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA
genomic: TTCGTAAGCGTTATCAGAGTTTTGACACTGAAATTGGGGCTCAAATAGAGgtaaaattct ... gttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaaaatatttagtgccttttatggttaacttgatcgatatggatgttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGAGAACCAAAGGTTGCTTCTGCGAAACAG
     atatttagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattcttcctacattttccttgccaaaatatttagtgccttttatggttaacttgatcgatatggatgttgccatagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGAGAACCAAAGGTTGCTTCTGCGAAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA