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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgtctctattcatccggacttaagttattttgttcaatgcttatttggtatttcacacgtgaatgggatggactaaacgtttgcaatggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCCTAGAACTTTGGCTGAGAATGCTGGCCTAAATGCAATGGAGATCATATCT

Basic information

species Glycine max
transcript GLYMA02G07910.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 10
lower sequence: LOC_Os03g59020.1 (Oryza sativa), 3'ss of exon 10
ttatgtctctattcatccggacttaagttattttgttcaatgcttatttggtattt-cacacgtgaatgggatggactaaac--gtttgcaatggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCCTAGAACTTTGGCTGAGAATGCTGGCCTAAATGCAATGGAGATCATATCT
 |  |  ||| || ||     |||   ||||  |||||| ||     || |||| | ||    ||  |        ||| |    |    ||      ||||||||||| |||||||| |||||||||||||||||||||||||||||| |||| |||||  ||||||| |||||||| || | ||| |||||||| ||||||
atgagcatctgtttatgtac-cttggtttatgatgttcattgtcc--ttagtatatacattgttgctttttgcttcctatattgatagttaacaattatgcagGTTGGACCAGTATGCCATTGCAAAATTTGCTGAAAGTTTTGAAATGGTTCCAAGAACCCTGGCTGAAAATGCTGGGCTTAGTGCTATGGAGATAATATCT

upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G381744_T01 (Zea mays), 3'ss of exon 10
---------------------------------------------------------------------------ttatg-tctctattcatccggacttaagtta----ttttgttcaatgcttatttggtatttcacacgtgaatgggatggactaaacgtttgcaatggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCCTAGAACTTTGGCTGAGAATGCTGGCCTAAATGCAATGGAGATCATATCT
                                                                            |||| ||    || | ||   || ||  ||           ||||  || ||| ||| || |    | |     ||| | |    | ||   |||    | ||||||||| |||||||| ||||| |||||||||||||| ||||||||| |||| |||||  |||| || |||||||| || |  ||||||||||| ||||| 
gtaagtttgtttctatcatgattaattaataacttttcagttttcatgtacaaggtaacagtacatctgctttcaatatgatcagggttaacccttcctcaaaataaaaacaaacaacaatcatttttttgtagtttatggat-accaccatgaagtgttgggtt-tgatgattgtacagGTTGGACCAGTATGCCATTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCCAAGAACCCTGGCAGAAAATGCTGGACTTAGCGCAATGGAGATAATATCC

upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 10
-------------------------------------------------------------------------------ttatgtctct--attcatccggacttaagtt----attttgttcaatgctta-tttggtatttcacacgtgaatgggatggactaaacgtttgcaatggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCCTAGAACTTTGGCTGAGAATGCTGGCCTAAATGCAATGGAGATCATATCT
                                                                               |||   || |  |   |     | || |||     |     |  | || |   ||   ||||     |         ||  |||    | |   ||      ||||||||||| ||||||||| |||| |||||||||||||| ||||||||| |||| |||||  |||| || ||||| || || |  ||||||||  | ||||| 
gtaagtttgtttctaccatgatagttaataacttatcatgtacaaggtatgagtacatctgctttcaatatgagcagggttaaccctttgaaagaaaaaatagtttagtggccgacaccatgaagtgttgggttctatattatgttcccctcaatcattcactggttgctcttaacaattgtgcagGTTGGACCAGTATGCTGTTGCGAAATTTGCTGAAAGCTTTGAAATGGTTCCAAGAACCCTGGCAGAAAATGCCGGACTTAGCGCAATGGATGTAATATCC

upper sequence: GLYMA02G07910.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0007g07460.t01 (Vitis vinifera), 3'ss of exon 10
ttatgtctctattcatccggacttaagttattttgttcaat---gcttatttggtatttcacacgtgaatgggatggactaaacgtttgcaatggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCCTAGAACTTTGGCTGAGAATGCTGGCCTAAATGCAATGGAGATCATATCT
   |||  | | |  ||   | |||| ||  ||  || | |   |||  | |||||  |||    ||          | |||      | |||||   ||||| |||||||||||||| |||||||| ||||||||||||||||| ||| |||||| |||  | |||||||||||||| || || || |||||||| ||||||
--ctgtgccgactagtcaaaatttaactttgttgattgatttctgctgctatggtaactcatgactgc-cacatcctattaagatggaggaatggttttgcagATTGGATCAGTATGCCATTGCAAAGTTTGCTGAAAGTTTTGAGATGGTTCCTAAAACCCTAGCTGAGAATGCTGGGCTTAACGCCATGGAGATAATATCT

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|193396251|gb|FK363616.1|FK363616
EST:     GAAATTGAGTTAGCT-AAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAG-TTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|208096240|gb|GD891724.1|GD891724
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|151397877|gb|EV267750.1|EV267750
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|193514452|gb|FK467940.1|FK467940
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|193490177|gb|FK457262.1|FK457262
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|207790586|gb|GD763053.1|GD763053
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|193306260|gb|FK273283.1|FK273283
EST:     TGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: TGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|254342219|gb|GR853356.1|GR853356
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|209700024|gb|BW656205.1|BW656205
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|14011960|gb|BG726882.1|BG726882
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|209721610|gb|BW671737.1|BW671737
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|209728114|gb|BW655349.1|BW655349
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|207800954|gb|GD775133.1|GD775133
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|298187661|gb|HO034810.1|HO034810
EST:     GAAATTGAGTTAGCTAAAAGGGTGGAGGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
EST: gi|254342218|gb|GR853355.1|GR853355
EST:     GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGG                         GTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC
genomic: GAAATTGAGTTAGCTAAAAGGGTGAAAGACTTTTCCTTCAAGGAGACAGGgtacttttta ... ggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggtatttcacacgtgaatgggatggactaaacgtttgcaatggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCCTAGAACTTTGGCTGAGAATGCTGGCCTAAATGCAATGGAGATCATATCT
                            gactaaa  putative branch site (score: 2)
      tatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgtctctattcatccggacttaagttattttgttcaatgcttatttggtatttcacacgtgaatgggatggactaaacgtttgcaatggccctgcagGTTGGATCAGTATGCTATTGCAAAATTTGCTGAAAGTTTTGAAATGATTCCTAGAACTTTGGCTGAGAATGCTGGCCTAAATGCAATGGAGATCATATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - ctattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - ttcacac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttgcaa