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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaatggtaagtagtagcttttttttagaatcgagaagctgtgggatcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG

Basic information

species Glycine max
transcript GLYMA04G01140.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g58530.2 (Oryza sativa), 3'ss of exon 3
----aaaatggtaagtagtagcttttttttagaatcg-agaagctgtgggatcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG
    ||  ||  |        || |||  ||| ||   | | |||      |   ||    |   | | || | |||| |  ||||||    |||  |||  ||||| ||| |||||||||||||| ||||| |||||| |||| ||| ||||||||||||  ||| |||||||
gacaaacttgacatacctctcctgtttgctagtatgacacatgctcaattcttcaattgcaaaaataatttatttgatct--gttgtt---gattgacataacagGTTTTGCAAATGTGAGATGCCATACAATCCTGATAACCTTATGATCCAATGTGAGGATTGCTCTGACTG

upper sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 3'ss of exon 2
-aaaatggtaagtagtagcttttttttagaatcgagaagctgtgggatct-tatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG
     | |   |     ||| | | ||| | |     |  | | | ||   ||||   ||| |   |  | |  | | |    ||||  |     ||  |||||  || || ||||||||||| ||||| ||||||||||| ||| ||||||||||||  ||| |||| ||
atgctttgctggcctatgctatctattaaattgatttatgtattgcattaatatcatcattttatttgattt--tctcatccctttactaacaatatgacagGTTCTGCAAGTGTGAGATGCCATACAATCCTGATGACCTTATGATCCAATGTGAGGAATGCTCTGATTG

upper sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g00160.t01 (Vitis vinifera), 3'ss of exon 2
----aaaatggtaagtagtagcttttttttagaatcgagaagctgtgggatcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG
      | |   ||   |||| |     ||   ||   |||  | |   ||   || |  |||  | ||| | || | ||   |   |  | ||| | | |||||||||||||||| ||||||||||||||||| |||||||||||||| || |||||||| |||||||| ||
gatttcagttccaatgggtagttgagggttgtgattttgaatttatttcattccatttt-atttgggcttttctggttta---tcactcgattttccgtggcagGTATTGTAAATGCGAGATGCCTTACAACCCCGATGACCTAATGGTGCAGTGTGAGGGGTGCACTGATTG

upper sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S298_65V6.1 (Physcomitrella patens), 3'ss of exon 2
--aaaatggtaagtagtagcttttttttagaatcgagaagctgtgggatcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG
  | |    ||  ||      | | | ||  |||   |   |||| |   || | |   ||| |  ||     |  | |    |  |      |  |||||| ||||| || || |||||||||||||| ||||||||| | ||||| ||||||||   |||||  |||||
atatatatatatatatatatatatatatatcatctt-atcatgtgtgtgtttgtgtttgttccgcattactgaacatca-ccatcgactccgctgtttgcagTTATTGCAAGTGCGAGATGCCTTACAATCCTGATGACTTGATGGTTCAATGTGAAATCTGCAAAGACTG

upper sequence: GLYMA04G01140.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S307_14V6.1 (Physcomitrella patens), 3'ss of exon 2
-----aaaatggtaagtagtagcttttttttagaatcgagaagctgtgggatcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG
      || | |   |||  |  ||   || || |  | | |    |    | | || || |  |||||   | || |||       |   | | |||  |  |||||||||||||||||||||||||| || || |||||  | ||||| |||||||||   ||||  || ||
tatcctaagtcgagtgtaaaacattgagttaagtaaggtgtattcctttcttgtgatataaaggctgacccatttggtgtt-----ctctgactgttctgtatagGTATTGTAAATGTGAGATGCCTTATAATCCAGATGATTTGATGGTTCAATGTGAGACTTGCAAAGATTG

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|298196200|gb|HO044591.1|HO044591
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|151404297|gb|EV274107.1|EV274107
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|298184224|gb|HO029437.1|HO029437
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|20811514|gb|BQ295992.1|BQ295992
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|298169727|gb|HO021087.1|HO021087
EST:     TATGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|193618792|gb|FK572118.1|FK572118
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCCGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTGCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|13562988|gb|BG551208.1|BG551208
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|27427183|gb|CA938703.1|CA938703
EST:     ACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: ACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|254327563|gb|GR837172.1|GR837172
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|254330184|gb|GR839737.1|GR839737
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|254316702|gb|GR828239.1|GR828239
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|208110150|gb|GD904900.1|GD904900
EST:     CGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: CGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|254330185|gb|GR839738.1|GR839738
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|13562907|gb|BG551127.1|BG551127
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGG                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|15285488|gb|BI469379.1|BI469379
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|298163162|gb|HO011895.1|HO011895
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
EST: gi|254316701|gb|GR828238.1|GR828238
EST:     TTTGAGTACAATTCCTCCACCGGCGCCTTCAAT-CTGATAGAGTTGCTGT                         GTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG
genomic: TTTGAGTACAATTCCTCCACCGGCGCCTTCAATCCTGATAGAGTTGCTGTgtgagtccat ... ttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG
            ttctgac  putative branch site (score: 2)
                                           ttttcatt  putative PPT
                             taagttgtttaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaatggtaagtagtagcttttttttagaatcgagaagctgtgggatcttatctagattctgacttgtgtgatgtaagttgtttaaaattttcattgcagGTATTGTAAATGTGAGATGCCTTACAACCCTGATGACCTAATGGTCCAATGTGAGGGCTGCACTGACTG

- - - - - - - - - - - - - - - - - gaagctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtga