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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtatcattgctgcaattgaagtttagttttgtaacctattctgagatactaggttaagtgtaatgtttctttattttaacaaatcaagtcgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATTTTGTCTAAGAGCAAGCCTGGTGATCAGTATG

Basic information

species Glycine max
transcript GLYMA10G38590.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 17
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 17
gtaggtatcattgctgcaattgaagtttagttttgtaacctatt-ctgagatactaggttaagtgt-aatgtttctttattttaacaaatcaagtcgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATTTTGTCTAAGAGCAAGCCTGGTGATCAGTATG
              |   ||||    | | |||||| ||  ||  ||  |  ||||  || | ||| ||     | | | |||   |   | | |   |    ||||||||||||||||||| |||||||| ||||| || || ||  |||| || ||||||||||||||| | |||||    ||||
-------------gtaagattgtgtatgaattttgttacagatcgcttgggaactaattttaatgtgaaaaccccctcaatttttta---cgactgtgtgatcagGAATGTGAATCTGAAGGAGCCAATAAAATGATCGAGTATCTTAGAGAAATCTTGTCTAAGAGCAAGGCCGGTGACGTTTATG

upper sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 17
lower sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 17
---------------------------------gtaggtatcattgctgcaattgaagtttagttttgt--aacctattc-------tgagatac-taggttaagtgtaatg-tttctttattttaacaaat-caagtcgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATTTTGTCTAAGAGCAAGCCTGGTGATCAGTATG
                                    ||    | |  |||  |  |  ||  ||||| |  ||| ||  |       | ||||   |||  | || |||    ||| ||| |||| || ||| ||| || ||||  |||||||||||||||||||||||||||| ||||||||||| ||  ||||| |  | |||||||||||| | |||||  ||||||
gtgagcatgtacatctaatttgtattgaattatactggctcaacttttgctgtcaattttgtgttttctggaacatacacactagaattagatgtatagtcttagagtagcaattttttttttttgactaattcaaatccttattcagGAATGTGAATCTGAAGGTGCCAATAAAATGATAGAATATCTTAGAGATTTGGTCTCTAAGAGCAAGGCAGGTGAAAAGTATG
















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|120494406|gb|EH222573.1|EH222573
EST:     AGCACTGGGCAACTTATGGAAGGAATGTCTTCTCTAGATATGACTACGAG                         GAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACTAGATATT
genomic: AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAGgtaggtatca ... cgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
EST: gi|57574855|gb|CX547830.1|CX547830
EST:     AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAG                         GAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
genomic: AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAGgtaggtatca ... cgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
EST: gi|58020248|gb|CX706990.1|CX706990
EST:     AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAG                         GAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
genomic: AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAGgtaggtatca ... cgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
EST: gi|22541844|gb|BU091687.1|BU091687
EST:     AGCACTGNGCAACTTATGGAAGGAATNTCTTCTCTAGATATGACTACGAN                         GAATGTGAATCTGAAGGTGCCCATAAGATGATAGAATACCTACGAGATATT
genomic: AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAGgtaggtatca ... cgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
EST: gi|192333011|gb|FK024660.1|FK024660
EST:     TTTCTTCTCTAGATATGACTACGAG                         GAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTCCGAGATATT
genomic: TTTCTTCTCTAGATATGACTACGAGgtaggtatca ... cgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
EST: gi|120494776|gb|EH222943.1|EH222943
EST:     AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAG                         GAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
genomic: AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAGgtaggtatca ... cgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
EST: gi|58015952|gb|CX702694.1|CX702694
EST:     ACCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAG                         GAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
genomic: AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAGgtaggtatca ... cgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
EST: gi|15203242|gb|BI426010.1|BI426010
EST:     AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAG                         GAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
genomic: AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAGgtaggtatca ... cgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
EST: gi|120494261|gb|EH222428.1|EH222428
EST:     AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAG                         GAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT
genomic: AGCACTGGGCAACTTATGGAAGGAATTTCTTCTCTAGATATGACTACGAGgtaggtatca ... cgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatactaggttaagtgtaatgtttctttattttaacaaatcaagtcgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATTTTGTCTAAGAGCAAGCCTGGTGATCAGTATG
                             ttttaac  putative branch site (score: 2)
                taatgtttctttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtatcattgctgcaattgaagtttagttttgtaacctattctgagatactaggttaagtgtaatgtttctttattttaacaaatcaagtcgttatatagGAATGTGAATCTGAAGGTGCCAATAAGATGATAGAATACCTACGAGATATTTTGTCTAAGAGCAAGCCTGGTGATCAGTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG