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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaggaagtaattgttagcttcattatatatatattgggtaattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT

Basic information

species Glycine max
transcript GLYMA15G41550.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g45710.1 (Oryza sativa), 3'ss of exon 4
-----gtttgtaggaagtaattgttagcttcattatatatatattgggt-aattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT
      | | |  | | | | |   ||||   ||   |  | |||   | || ||||||||   |  |     |||   | |  | |  | |    | | |||| ||||| ||||| ||||| |||||  | |||||||| | |||||||||||| ||||| |||||||| ||||||||  | |||||||| || |||||  
ttaaattgtatccgcaatgaattcaagctgtttttccttgagattttttgaaatatgtaatccttttaaaattttgtagtaac-tgtcctcaccaatct-agGAACTTGACTATCTTGTTGGAGCTGTTGCCAACCCCAAAAAACCATTTGCTGCCATTGTTGGTGGATCCAAGGTGTCAACAAAGATTGGGGTGATTGAGA

upper sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G79550.1 (Arabidopsis thaliana), 3'ss of exon 3
gtttgtaggaagtaattgttagcttcattatatatatattgggtaattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT
        | | | |   || ||  ||| |    ||| ||     || |     |||||     ||||    ||  |   | ||| ||||| |||||| |||||||| || || || |||||| ||||||||||||  || |||||||| ||||| || || || ||||| ||  | |||||||| || ||||| |
--------gtatttaaaatttgcagcataaagagtatcttcttagatgagtctctttattttactgatcagactattacttgttttattgtgtcagGAACTTGATTACCTTGTCGGAGCTGTGGCAAACCCCAAGAAGCCTTTTGCTGCCATTGTTGGAGGCTCAAAGGTTTCAACAAAGATTGGTGTCATTGAGT

upper sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0085g00370.t01 (Vitis vinifera), 3'ss of exon 3
--gtttgtaggaagt--aattgttagcttcat-tatatatatattgggtaattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT
     |||| |||||  || |  | ||| ||  ||  | |   || | | |  ||    | | |    ||  ||||  | |  | | |||  | |||| |||| ||||| || || ||||| |||||||||||||||||||| ||||||||||| ||||| ||||| ||||||||||| || || |||||||| |||||||
cttaatgtatgaagtccaaatagtggctacacctaggttttcttttgtttagaatact-tctttgagtttacttgacataacatttgttttctggttttagGAACTTGACTACCTTGTTGGAGCTGTGTCAAACCCCAAGAGGCCATTTGCTGCAATTGTTGGTGGCTCGAAGGTGTCATCGAAAATTGGAGTGATTGAAT

upper sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ26731 (Selaginella moellendorffii), 3'ss of exon 5
gtttgtaggaagtaattgttagcttcattatatatatattgggtaattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT
                                      | |  |   | | |  ||| | |   || ||   ||||  |       | | |  ||||| || || || || | ||| || ||||| || || || |||||||||||||| || || || || || |||||||| |||||||||||||| |||||||
-------------------------------------gtagattttcttttttctttttcccaatgcttc-cctgagttgacgacgaatttgccagGAACTCGACTACCTCGATGGAGCCGTGTCGAATCCTAAAAGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT

upper sequence: GLYMA15G41550.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ26420 (Selaginella moellendorffii), 3'ss of exon 3
gtttgtaggaagtaattgttagcttcattatatatatattgggtaattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT
                                       | | |  |  | |  ||| | |   || ||   ||||  |       | | |  |||||||| || || || | ||| |||||||| || || ||  ||||||||||||| || || || || || |||||||| |||||||||||||| |||||||
--------------------------------------gtagattttcttttcctttttcccaatgcttc-cctgagttgacgacgaatttgccagGAGCTCGACTACCTTGATGGAGCTGTGTCGAATCCTAAACGACCATTTGCTGCCATCGTTGGAGGCTCCAAGGTGTCGTCCAAGATTGGAGTGATTGAAT

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|15815937|gb|BI788212.1|BI788212
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAA                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|254319185|gb|GR830533.1|GR830533
EST:     AGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGC
genomic: AGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAA-Ggtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGC
EST: gi|213618073|gb|DB963706.1|DB963706
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|208147825|gb|GD948040.1|GD948040
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|254333427|gb|GR841289.1|GR841289
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|209726275|gb|BW659601.1|BW659601
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|18040418|gb|BM308712.1|BM308712
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|14259501|gb|BG882409.1|BG882409
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|19347371|gb|BM892251.1|BM892251
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|254340232|gb|GR858357.1|GR858357
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|298192401|gb|HO036483.1|HO036483
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTG
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTG
EST: gi|254333389|gb|GR841251.1|GR841251
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         -AGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|151408797|gb|EV278605.1|EV278605
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|207704296|gb|GD685054.1|GD685054
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGG
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGG
EST: gi|254343942|gb|GR857698.1|GR857698
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|120531954|gb|EH260087.1|EH260087
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|151410791|gb|EV280606.1|EV280606
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGGCTGTGTCAAACCCCAAGAGACCATTTGC
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGG-CTGTGTCAAACCCCAAGAGACCATTTGC
EST: gi|192329504|gb|FK021874.1|FK021874
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|209709214|gb|BW657183.1|BW657183
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|193353995|gb|FK320715.1|FK320715
EST:     AGTTGCCAAATACTTGAAGACCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTT-GGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: AGTTGCCAAATACTTGAAG-CCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|213606522|gb|DB971318.1|DB971318
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTT
EST: gi|209700685|gb|BW670461.1|BW670461
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAC                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAA
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAA
EST: gi|254335643|gb|GR847171.1|GR847171
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
EST: gi|208291437|gb|GE094603.1|GE094603
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGG
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGG
EST: gi|209717628|gb|BW653990.1|BW653990
EST:     GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAG                         GAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT
genomic: GAGTTGCCAAATACTTGAAGCCCTCTGTTGCAGGATTCCTAATGCAGAAGgtttgtagga ... attgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtaattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT
                                        ttttaat  putative branch site (score: 3)
                                              ttgtttc  CT-rich tract
                                  atgtatttttaattgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaggaagtaattgttagcttcattatatatatattgggtaattatgtaatttatacagttgattgatctgatgtatttttaattgtttcagGAGCTTGATTATCTAGTTGGGGCTGTGTCAAACCCCAAGAGACCATTTGCTGCTATTGTCGGTGGATCGAAGGTGTCTTCCAAGATTGGAGTTATTGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG