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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgcatgtgctgctctgtttgtgtaattatttgtttatattactataacccttcaggttatccgggacaataaatgagtttttttgcctccttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTAGAGGCTGTTGTTGTGCC

Basic information

species Glycine max
transcript GLYMA11G20020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G20020.2 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0007g05050.t01 (Vitis vinifera), 3'ss of exon 4
tgcatgtgctgctctgtt-tgtgtaattat--ttgtttatattactataacccttcaggttatccgggacaataa-atgagtttttttgcctccttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTAGAGGCTGTTGTTGTGCC
    | |||| || ||   ||| || | ||  |  | ||| | | |  |       | | | | |     | |   |||  | | |||| ||| || |   ||||| |||||||| || ||||||||||| ||  ||||||||||||||||| ||||  |||||||  | ||
-ttgtttgcttctttgaaatgtatactcatcatcctctatttgaattcattttaatatgctgtgcattcaagttctatgtatctatttgactcttttt---tagGTAGCACCAGCTGAGCTTGAAGGGCTGCTGCTTTCTCACCCTGAAATATTAGATTCTGTTGTCATCCC
















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|192312246|gb|FK003939.1|FK003939
EST:     TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|17153148|gb|BM143081.1|BM143081
EST:     TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|254345794|gb|GR859441.1|GR859441
EST:     TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|254317801|gb|GR826785.1|GR826785
EST:     GTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: GTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|151406633|gb|EV276448.1|EV276448
EST:     TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|6134407|gb|AW132800.1|AW132800
EST:     TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|13479882|gb|BG509225.1|BG509225
EST:     AAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: AAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|192306688|gb|FG998086.1|FG998086
EST:     CGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: CGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|254318430|gb|GR832598.1|GR832598
EST:     TTATGTGGTTGACCGTTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCA-CCTGAAATACTA
genomic: TTATGTGGTTGACCG-TATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|37994920|gb|CF806509.1|CF806509
EST:     TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|21994574|gb|BQ786102.1|BQ786102
EST:     TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
EST: gi|192312245|gb|FK003938.1|FK003938
EST:     TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAG                         GTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA
genomic: TTTATGTGGTTGACCGTATCAAAGAACTGATCAAGTACAAAGGTTTCCAGgtatgtagtg ... ttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacccttcaggttatccgggacaataaatgagtttttttgcctccttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTAGAGGCTGTTGTTGTGCC
 ctataac  putative branch site (score: 3)
                                tttttttgcctccttg  putative PPT
                      aataaatgagtttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgcatgtgctgctctgtttgtgtaattatttgtttatattactataacccttcaggttatccgggacaataaatgagtttttttgcctccttgtaactagGTTGCACCAGCAGAACTTGAAGGGCTTCTCGTTTCTCACCCTGAAATACTAGAGGCTGTTGTTGTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
tgcatgt
- - - - ctgctct
- - - - - - - -gtttgtg
- - - - - - - - - - - - - - - - - - - - - - - -cccttca