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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcgtagttttactgaaccagtagcagtagctgtactacttttgatggattctagttctatctcttgtcgggagtagcagtttacactgaattcttacttaagattgttgttgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCTCAAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAG

Basic information

species Glycine max
transcript GLYMA09G28650.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 11
------------------------------------------------------------------------gtgagcgta-gttttactgaaccagtagcagtagctgtactacttttgatggattctagttctatctcttgtcgggagtagcagtttacactgaattcttacttaagattgttgttgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCTCAAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAG
                                                                         |    ||| ||||  || |  || |       || | | |    ||  |   ||  |   |||  |  |||   | | |  |  ||| |    |||  || ||  | ||||| | ||    |||||||| ||||||||||||||  |||| |||||||| || ||| ||||||||||||||||||||||  | ||||||||| |||  |||||    || || |
gtactttttcagcatatttttatgttagtgatttaaaaggttagcaaagtgttctcataaagaggtgcttgcctatttgtatgtttgtctaagtcattcatcaatgcagcatt--cattagtttttttaatggctactttctgttttgtg-actatgttatatcttatttatatttt-gtttgtt-tggat---cagTGGCCCTATGAAGCTGCTGCTTTAGCATTTGAAGCAATTCCAAGAACTTTGGCTCAAAATTGTGGGTTGAATGTCATCAGGATAATGACACAACTCCAGG

upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G175510_T01 (Zea mays), 3'ss of exon 11
gtgagcgtagttttactgaaccagtagcagtagctgtactacttttgatggattctagttctatctcttgtcgggagtagcagtttacactgaattcttacttaagattgttgttgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCTCAAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAG
           |  |   |    | | | ||     || |    |   |||||| | |  ||||   |||  | |     || ||    ||||    ||  ||  | |||||  ||  || |||||||| |||||||||||||| ||||| ||||| || || ||| | |||||||| |||||||||||  | ||||| ||  |||  |||||    || || |
--------gactacatatacgttgcaactgtgatgttattgtgctgagtggattattgcactattctttgatgtg-----caattc---ctga----ttgtttttgtttgtt--tg--tgtcagTGGCCCTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTGGCCCAAAATTGTGGTTTGAATGTTATTAGGATAATGACACAACTTCAGG

upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G069765_T05 (Zea mays), 3'ss of exon 11
gtgagcgtagttttactgaaccagtagcagtagctgtactacttttgatggattctagttctatctcttgtcgggagtagcagtttacactgaattcttacttaagattgttgttgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCTCAAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAG
              |   |    |||   ||     || |    |   |||||| | |  | ||   |||  | |     || |||   ||||    ||  ||  | ||  |||| | || |||||||| |||||||||||||| ||||| ||||| || || ||| | |||||||| |||||||| ||  | ||||| ||  |||  |||||    || ||||
-----------cacatatactttgtaaatgtgatgttattgtgctcagtggatttttgcaccattctttgatgtg-----caattt---ctga----ttggttttgttttctgttta-tgtcagTGGCCCTATGAAGCTGCTGCTCTAGCATTTGAGGCAATTCCAAGGACTTTGGCCCAAAATTGCGGTTTGAATGTTATTAGGATAATGACACAACTTCAAG

upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------------------------------------gtgagcgtagttttactgaaccagtagcagtagct-gtactacttttgatggattctagttctatctcttgtcgggagtagcagtttacactgaattcttacttaagattgttgttgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCTCAAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAG
                                                             ||   | | ||  |  |  |  | ||     |  |   | | || |   |||  | | |  | |  ||  |      ||| ||| | ||   |      ||  | | |||  |||   ||||||||||||||||||||||||  |||||||||| || || ||||| |||||||| || |||||||| || ||||| ||  |||||||||||||| | || |
gtaaattttgcttctttctcatgtatcaaatttgatgtggtttttccatttgaatttttcaagataaatattggttgataatcaccaaggttttatgaaattgtttagttattgcactgcagttttctgatgctttatgcaattttccctatttgtaattttctgctcgtttgtga--aacagTGGCCTTATGAAGCTGCTGCTATAGCTTTTGAGGCTATTCCACGTACTTTGGCACAGAATTGTGGTGTGAATGTGATTAGGACTATGACTGCTTTGCAGG

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|208278764|gb|GE077983.1|GE077983
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|193547528|gb|FK501465.1|FK501465
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|192309233|gb|FG999124.1|FG999124
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|58017480|gb|CX704222.1|CX704222
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|209714673|gb|BW674236.1|BW674236
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|193639863|gb|FK592320.1|FK592320
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|22927071|gb|BU544210.1|BU544210
EST:     TGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATNNCACGAACTTTG
genomic: TGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|192309232|gb|FG999123.1|FG999123
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|26048688|gb|CA785141.1|CA785141
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|193619682|gb|FK572642.1|FK572642
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|193521393|gb|FK481638.1|FK481638
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|207803832|gb|GD772791.1|GD772791
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|193529449|gb|FK487832.1|FK487832
EST:     TGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|208325439|gb|GE124105.1|GE124105
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|15199729|gb|BI423980.1|BI423980
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|208270977|gb|GE067801.1|GE067801
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTG
EST: gi|208192695|gb|GD989774.1|GD989774
EST:     TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAG                         TGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCAATACCACGAACTTT
genomic: TGTCGGCTGCCTTGAAACAAAAGAGTTCATCTATTGAGGGCATAGAGAAGgtgagcgtag ... tgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCA-TACCACGAACTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcgggagtagcagtttacactgaattcttacttaagattgttgttgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCTCAAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAG
                       aattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcgtagttttactgaaccagtagcagtagctgtactacttttgatggattctagttctatctcttgtcgggagtagcagtttacactgaattcttacttaagattgttgttgactgacagTGGCCTTATGAAGCTGCTGCCCTAGCTTTTGAAGCCATACCACGAACTTTGGCTCAAAATTGTGGAGTAAATGTCATCCGGACTATGACTGCTCTACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG