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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatgactatggcttgtatgtttactctagagaccttgaattcattttgattatttgtaccattcagttgaaagtgttctgattattactttcaatattaaaaaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACAAATCCTGAAGCAGATGTTCTACTAGCTTATGAAATGAATGGTGAA

Basic information

species Glycine max
transcript GLYMA19G18330.5
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G18330.3 (Glycine max), 3'ss of exon 6
lower sequence: AT3G01910.3 (Arabidopsis thaliana), 3'ss of exon 2
gtgatgactatggcttgtatgtttactctagagaccttgaattcattttgattatttgtaccattcagttgaaagtgttctgattattactttcaatattaaaaaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACAAATCCTGAAGCAGATGTTCTACTAGCTTATGAAATGAATGGTGAA
 ||||  || |    |  || | ||   ||   |  |  |  |  || || ||  || |   ||||   |||||    | || |     ||||| ||||       ||| |||||||||||||| ||||| || ||||| |||||  | || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||||| || 
ttgatcgctgtaaggtagatatatat--taataaattccacctttttatgctttgttatga-attcccatgaaaagtctatgct-----ctttctatat-------ctc-taggagGAAAATGGGGGCCCTTATAAGGCGTCAATCACTCTAAGTCAAGCCACAAATCCTGAAGCGGATGTTCTACTCGCTTATGAGATGAATGGAGAG

upper sequence: GLYMA19G18330.3 (Glycine max), 3'ss of exon 6
lower sequence: AT3G01910.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgatgactatggcttgtatgtttactctagagaccttgaattcattttgattatttgtaccattcagttgaaagtgttctgattattactttcaatattaaaaaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACAAATCCTGAAGCAGATGTTCTACTAGCTTATGAAATGAATGGTGAA
                |||  | ||   ||   |  |  |  |  || || ||  || |   ||||   |||||    | || |     ||||| ||||       ||| |||||||||||||| ||||| || ||||| |||||  | || ||||| ||||||||||||||||| ||||||||||| |||||||| |||||||| || 
----------------gtagatatatattaataaattccacctttttatgctttgttatga-attcccatgaaaagtctatgct-----ctttctatat-------ctc-tagGAGGAAAATGGGGGCCCTTATAAGGCGTCAATCACTCTAAGTCAAGCCACAAATCCTGAAGCGGATGTTCTACTCGCTTATGAGATGAATGGAGAG

upper sequence: GLYMA19G18330.3 (Glycine max), 3'ss of exon 6
lower sequence: PP1S190_72V6.1 (Physcomitrella patens), 3'ss of exon 6
gtgatgactatggcttgtatgtttactctagagaccttgaattcattttgattatttgtaccattcagttgaaagtgttctgattattactttcaatattaaaaaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACAAATCCTGAAGCAGATGTTCTACTAGCTTATGAAATGAATGGTGAA
    |  || ||| || || |   | |         | ||         | |  |   |  |||    || | |||||  |||| |    ||||  |  |         | |||||||||||||||| || || ||||||||||||||  |    || || || | ||| || ||||||||| || | || ||||| ||||||||  | 
--ttttcctttggattttaagggcaattgcagcgaatggagggtgcaaaggtattggcttgcatgagcttaagagtgt--tgataacctttttctcttct---------gcagGAGGAAAATGGAGGACCTTATAAGGCTTCAATACCCTTACTGCATGCAACGACTCCAGAGGCAGATGTTTTATTGGCGTATGAGATGAATGGAAAG

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|208054138|gb|GD855367.1|GD855367
EST:     AATTTGGTGGAAGACATGNGGAATTCGTAAGCATTGATAAGTGCAAG                         GAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
genomic: AATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAGgtgatgacta ... aaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
EST: gi|208074830|gb|GD869573.1|GD869573
EST:     CTGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAG                         GAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
genomic: CTGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAGgtgatgacta ... aaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
EST: gi|193468004|gb|FK433999.1|FK433999
EST:     CTGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAG                         GAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
genomic: CTGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAGgtgatgacta ... aaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
EST: gi|193517834|gb|FK473053.1|FK473053
EST:     CTGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAG                         GAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
genomic: CTGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAGgtgatgacta ... aaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
EST: gi|208296656|gb|GE091296.1|GE091296
EST:     TGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAG                         GAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
genomic: TGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAGgtgatgacta ... aaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
EST: gi|207780471|gb|GD751692.1|GD751692
EST:     CTGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAG                         GAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA
genomic: CTGAATTTGGTGGAAGACATGTGGAATTCGTAAGCATTGATAAGTGCAAGgtgatgacta ... aaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccattcagttgaaagtgttctgattattactttcaatattaaaaaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACAAATCCTGAAGCAGATGTTCTACTAGCTTATGAAATGAATGGTGAA
                   ttctgat  putative branch site (score: 3)
                   ttctgattattacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatgactatggcttgtatgtttactctagagaccttgaattcattttgattatttgtaccattcagttgaaagtgttctgattattactttcaatattaaaaaactcgtagGAGGAAAATGGAGGCCCATACAAGGCTTCAATACCACTCAGTCAGGCCACAAATCCTGAAGCAGATGTTCTACTAGCTTATGAAATGAATGGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG