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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagtaggaaaatttttccttttcttgtatgtctgtttcaattgaatatgcctgatctaattgaacattttttttttttggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAAATGATCTTGACATTCACGGCTTATTTAATGA

Basic information

species Glycine max
transcript GLYMA11G34980.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------------------------------------------------------------------gtacgagtaggaaaatttttc-cttttcttgtatgtctgtttcaattgaatatgcctg--atctaattgaacattttttttttttggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAAATGATCTTGACATTCACGGCTTATTTAATGA
                                                                                                          |  || | | |    |  |  | |||   ||||| | | ||   || ||| ||  ||   |  || |||   || |      |   |   ||||||| |||||||| ||||||||||| |||||||| || ||||| || |||||||||||||||||| | |   |||||   ||
gtattcttactacttctttcctccaactgattaacttctttgtagttgtttggatgaagaacgcagctgcaagtttagcggtgtgttttaaccaatattttctaattttgactggtatgtctcgtaacattttgagtatggcagatttg-ttaaatctgtttgtggtaaaactgactgttgtaagacgtgtttgctcagCAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA

upper sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ23777 (Selaginella moellendorffii), 3'ss of exon 2
gtacgagtaggaaaatttttccttttcttgtatgtctgtttcaattgaatatgcctgatctaattgaacattttttttttttggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAAATGATCTTGACATTCACGGCTTATTTAATGA
                                        | | ||     ||  |  |||  |||       ||   |||  | || |||| |||||||| ||||| || ||||| ||||||||||| || || || || || ||||||||||||||||   | ||||   |
---------------------------------------gtaagttcttcgtgttttttct--ttgcttggcattacgtttgtgcttgcagCGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAA

upper sequence: GLYMA11G34980.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ21414 (Selaginella moellendorffii), 3'ss of exon 2
gtacgagtaggaaaatttttccttttcttgtatgtctgtttcaattgaatatgcctgatctaattgaacattttttttttttggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAAATGATCTTGACATTCACGGCTTATTTAATGA
                                        | | ||     ||  |  |||  |||       ||    ||  | || |||| |||||||| ||||| || ||||| ||||||||||| || || || || || ||||||||||||||||   | ||||   |
---------------------------------------gtaagttcttcgtgttttttct--ttgcttggcattacgcttgtgcttgcagCGAAGGAGCACGTTGTTGGATGGTACAGCACTGGTCCCAAACTACGTGAGAACGATCTTGACATTCACGAGCTCTTTAGGAA

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|208231458|gb|GE029433.1|GE029433
EST:     TTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|254323156|gb|GR835764.1|GR835764
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193452589|gb|FK418015.1|FK418015
EST:     AAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: AAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|6071648|gb|AW101035.1|AW101035
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193363769|gb|FK330485.1|FK330485
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193347090|gb|FK310960.1|FK310960
EST:     TTCCATGTTTAAAAGAATAAATAGA                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAA
genomic: TTCCATGTTTAAAAGAATAAAT-G-gtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAA
EST: gi|193347090|gb|FK310960.1|FK310960
EST:     TTCCATGTTTAAAAGAATAAATAGA                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAA
genomic: TTCCATGTTTAAAAGAATAAAT-G-gtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAA
EST: gi|58016090|gb|CX702832.1|CX702832
EST:     TTTCCATGTTT-AAAG-ATAAAATG                         CAANGGAGCATG-TGTGGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGA
genomic: TTTCCATGTTTAAAAGAAT-AAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGT-GGGGTGGTATAGCACTGGTCCAAAGCTGCGCGA
EST: gi|193497923|gb|FK462499.1|FK462499
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|207781762|gb|GD754439.1|GD754439
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193732371|gb|FK668361.1|FK668361
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193408977|gb|FK371609.1|FK371609
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATG-TTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|208317923|gb|GE116676.1|GE116676
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|208269553|gb|GE070351.1|GE070351
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193350354|gb|FK317442.1|FK317442
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193302125|gb|FK266960.1|FK266960
EST:     TTAAAAGAAT-AATG                         A
genomic: TTAAAAGAATAAATGgtacgagtag ... tggtttacag-
EST: gi|193302125|gb|FK266960.1|FK266960
EST:     TTAAAAGAAT-AATG                         A
genomic: TTAAAAGAATAAATGgtacgagtag ... tggtttacag-
EST: gi|6718815|gb|AW306462.1|AW306462
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAGTAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAC
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|208079786|gb|GD873748.1|GD873748
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193358044|gb|FK319672.1|FK319672
EST:     GACCACAATTACCATGAATCTATGTTTTCCATGTTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: GACCACAATTACCATGAATCTATGTTTTCCATG-TTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|58017218|gb|CX703960.1|CX703960
EST:     GACCACAATTACCATGAATCTATGTTTCCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: GACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193702807|gb|FK639197.1|FK639197
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCAATAGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGC-AT-GTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGA
EST: gi|208165655|gb|GD959443.1|GD959443
EST:     GTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: GTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|24136280|gb|BU926790.1|BU926790
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|208205725|gb|GE006136.1|GE006136
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|207840530|gb|GD812655.1|GD812655
EST:     TGACCACAATTACCATGAATCTACGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|207811079|gb|GD783000.1|GD783000
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193429218|gb|FK398016.1|FK398016
EST:     TGACCACAATTACCATGAATCTATG-TTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGTAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCG-AA
EST: gi|193645638|gb|FK588282.1|FK588282
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|193532136|gb|FK489338.1|FK489338
EST:     TGACCACAATTACCACGAATCTATGTTT-CCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|298172443|gb|HO019483.1|HO019483
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|208333750|gb|GE132031.1|GE132031
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|207824956|gb|GD797172.1|GD797172
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
EST: gi|151411180|gb|EV280991.1|EV280991
EST:     TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATG                         CAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA
genomic: TGACCACAATTACCATGAATCTATGTTTTCCATGTTTAAAAGAATAAATGgtacgagtag ... tggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttcaattgaatatgcctgatctaattgaacattttttttttttggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAAATGATCTTGACATTCACGGCTTATTTAATGA
                     atctaat  putative branch site (score: 3)
                                  ttttttttttttggtt  putative PPT
                        taattgaacatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgagtaggaaaatttttccttttcttgtatgtctgtttcaattgaatatgcctgatctaattgaacattttttttttttggtttacagCAAAGGAGCATGTTGTGGGGTGGTATAGCACTGGTCCAAAGCTGCGCGAAAATGATCTTGACATTCACGGCTTATTTAATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC