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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgttgcccttaatttgtggtgaatttaaatattctccaactttttgtgtgtaatatctgtgtatcccctgtttgttagGTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGTTGAAGCTATACCATACTTTTCTGCTGGTTTAAAGGGTGTTGCCAG

Basic information

species Glycine max
transcript GLYMA05G34790.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 11
gtagtgttgcccttaatttgtggtgaatttaaatattctccaactttttgtgtgtaatatctgtgtatcccctgtttgttagGTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGTTGAAGCTATACCATACTTTTCTGCTGGTTTAAAGGGTGTTGCCAG
|||||  ||| ||| |||| |||  |   ||  |||| |   || |      |  |  | |||  |  ||      ||| ||||||||||| ||||| |||||||| || || || || ||||||||||| ||||| || ||||| || || ||||||||||||||||| ||||||||
gtagtactgcacttcatttctggaaagaatacttattatttgacataagtcttaaatcacctgatttaccttgcaatgtcagGTTTTTTGTTACTCCATCAGATTCTGTTGCTATCATTGCTGCAAATGCAGTTGACGCAATACCCTATTTCTCTGCTGGTTTAAAGGGAGTTGCCAG

upper sequence: GLYMA05G34790.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 9
gtagtgttgcccttaatttgtggtgaatttaaatattctccaactttttgtgtgtaatatctgtgtatcccctgtttgttagGTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGTTGAAGCTATACCATACTTTTCTGCTGGTTTAAAGGGTGTTGCCAG
||||| ||   |||   ||| |     ||  | |   ||  | |||||      |||       | |  |  ||      |||||||| || ||||| |||||||| ||||| |||||||||||||||||||| ||  | ||||| || |||  | | ||| | || |||||||| ||
gtagtatttatcttt-cttgcgc----ttccagtccgctttagcttttctaagctaac------ggaatcaatgc-----agGTTTTTCGTAACTCCATCAGATTCAGTGGCTATTATCGCTGCAAATGCCGTGGATTCGATACCGTATTTTCGTTCCGGTCTGAAAGGTGTTGCGAG
















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|17154046|gb|BM143979.1|BM143979
EST:     GGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGGTTCTTGGTAAAAG                         GTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCTGT
genomic: GGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAGgtagtgttgc ... tgtttgttagGTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGT
EST: gi|16349332|gb|BI974927.1|BI974927
EST:     GGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAG                         GTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGT
genomic: GGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAGgtagtgttgc ... tgtttgttagGTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGT
EST: gi|27426004|gb|CA937524.1|CA937524
EST:     GGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAG                         GTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGT
genomic: GGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAGgtagtgttgc ... tgtttgttagGTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGT
EST: gi|7684631|gb|AW755279.1|AW755279
EST:     GGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAG                         GTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGT
genomic: GGTGCTGCTTCTGATGGTGATGCAGATCGCAACATGATACTTGGTAAAAGgtagtgttgc ... tgtttgttagGTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaatattctccaactttttgtgtgtaatatctgtgtatcccctgtttgttagGTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGTTGAAGCTATACCATACTTTTCTGCTGGTTTAAAGGGTGTTGCCAG
                                        tcccctgttt  CT-rich tract
              aacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgttgcccttaatttgtggtgaatttaaatattctccaactttttgtgtgtaatatctgtgtatcccctgtttgttagGTTTTTTGTCACTCCTTCAGATTCCGTGGCCATTATCGCTGCAAATGCCGTTGAAGCTATACCATACTTTTCTGCTGGTTTAAAGGGTGTTGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC