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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taacgagaaaaaaaagatattcttagagatcaaacactttaaatagtagcaccaaagtataaaagatagatgctggcattacatgctttatatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAGAGAGAGATGAGGTACTCTGATTTGAAGAAAATTGACCGTGGTGTCCGCC

Basic information

species Glycine max
transcript GLYMA02G05030.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G05030.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os06g50380.1 (Oryza sativa), 3'ss of exon 5
-----taacgagaaaaaaaagatattcttagagatcaaacactttaaatagtagcaccaaagtataaaagatagatgctggcattacatgctttatatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAGAGAGAGATGAGGTACTCTGATTTGAAGAAAATTGACCGTGGTGTCCGCC
      |  |  |   || |   ||    | | |    ||||  ||| |  |       ||||  || |    |||| |    ||     ||||  ||||| ||||||| |||| |||||||||| || || || |||||||||||||| || || ||||| ||||||||||| ||| | ||||| |||||||||||||| ||||
gccctcagtggaaggcaacatgcatgaaaacaaaatggacacgctaagtgttgattgtgaagtgaaagaatctgatgat----ttgtgctctttg-atctttcagGGAAGTGCTAGGAGGCTCATAAAGGCAGCTTTGCAAGAAGCAGCCAAGAAAAGAGAAATGAGGTACTCAGATCTCAAGAAGATTGACCGTGGTGTTCGCC

upper sequence: GLYMA02G05030.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G151254_T02 (Zea mays), 3'ss of exon 4
taacgagaaaaaaaagatattcttagagatcaaacactttaaatagtagcaccaaagtataaaagatagatgctggcattacatg-ctttat---atcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAGAGAGAGATGAGGTACTCTGATTTGAAGAAAATTGACCGTGGTGTCCGCC
     | | |||| ||| |     | | || ||| |  ||   |  |||  | || |||  ||    ||   ||     | ||   || | |   |||||||||||   |||| ||||||| || | ||| ||  ||||||| ||||| || || ||||||||||||||||| ||  | ||||| |||||||| ||||| ||||
-gtttaaacaaaataga-aggaacaaatatgaaatatcttctgtt-tagtgctaa-gtactaactgcagcgcctaatgctgcacatctctgtttgatcttgcagGGCTGTGCTAGGAGGCTGATAAGAGCGGCACTGCAAGAGGCAGCCAAGAAAAGAGAGATGAGGTACTCGGACCTCAAGAAGATTGACCGCGGTGTTCGCC
















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|58023975|gb|CX710716.1|CX710716
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|193481670|gb|FK446047.1|FK446047
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTACTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAA-G
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|193525818|gb|FK478859.1|FK478859
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCCCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|207717810|gb|GD697282.1|GD697282
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCG
EST: gi|193424789|gb|FK392052.1|FK392052
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAG
EST: gi|193433718|gb|FK400612.1|FK400612
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|208111922|gb|GD911040.1|GD911040
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCT
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCT
EST: gi|208065096|gb|GD862116.1|GD862116
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAAGAAAGCAGCAAAAA
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAA-GAA-GCAGCAAAAA
EST: gi|58024161|gb|CX710902.1|CX710902
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|193497986|gb|FK463416.1|FK463416
EST:     AAAACAACCCACACAAT                         GAAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: AAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|214006042|gb|DB990451.1|DB990451
EST:     TCAGGATGCCGTTGATATAGTTCAAAACAACCTACAAAAG                         GGAATTTTTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: TCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|208198056|gb|GD995945.1|GD995945
EST:     CCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACTACAAT                         GGAATTGCTCGGAGGCTCATCAA-GCTGCGTTGCAAGAAGCAGCAAAAA-
genomic: CCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCAC-ACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAA
EST: gi|207804949|gb|GD779088.1|GD779088
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|9205292|gb|BE331516.1|BE331516
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|193528356|gb|FK485146.1|FK485146
EST:     ACCTTAGCAATCAGGATGTCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAA
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAA
EST: gi|192309158|gb|FG999091.1|FG999091
EST:     GCCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|193484083|gb|FK451993.1|FK451993
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|193474571|gb|FK440960.1|FK440960
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|192309173|gb|FG999092.1|FG999092
EST:     GCCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|208119886|gb|GD919751.1|GD919751
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGG
EST: gi|208215722|gb|GE008532.1|GE008532
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTAGACGTTAGCAAGAAGCA
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCT-G-CGTT-GCAAGAAGCA
EST: gi|209708137|gb|BW671153.1|BW671153
EST:     GCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: GCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|9205274|gb|BE331498.1|BE331498
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|8403074|gb|BE058708.1|BE058708
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
EST: gi|208212915|gb|GE009160.1|GE009160
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGACAAAAAA
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAG-CAAAAAA
EST: gi|208153800|gb|GD953929.1|GD953929
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagcaccaaagtataaaagatagatgctggcattacatgctttatatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAGAGAGAGATGAGGTACTCTGATTTGAAGAAAATTGACCGTGGTGTCCGCC
        aaagtataaaagata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taacgagaaaaaaaagatattcttagagatcaaacactttaaatagtagcaccaaagtataaaagatagatgctggcattacatgctttatatcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAGAGAGAGATGAGGTACTCTGATTTGAAGAAAATTGACCGTGGTGTCCGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - -aaaaaaa
- - - - - -aaaagata
- - - - - - - - - - - - - - - caaacac
- - - - - - - - - - - - - - - - - - - - - - - - -caccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acatgct