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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agagtatacatcaagatcaaacagaatctgtacctcactacctcataattttgtggaacatgtctaaaaaatattgatgaaaatgtggtctgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGTGATATTTACCAAAATGCAGATGAGGACATGAGGAGAGCAATGAGCAAGT

Basic information

species Glycine max
transcript GLYMA11G02340.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G02340.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 8
agagtatacatcaagatcaaacagaatctgtacctcactacctcataattttgt----ggaacatg--tctaaaaaatattgatgaaaat--gtggtctgccttt----cagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGTGATATTTACCAAAATGCAGATGAGGACATGAGGAGAGCAATGAGCAAGT
              | |  |  |  |||   || |   ||  |    || || |     |||| ||  | ||   |||||  |||    |   || | ||  | |    |||||||| |||||||| ||||||||||||||||| ||||  ||||| |||||||| || ||| |  |||| ||||| || ||| |||| || ||||  ||||
--------------gtttgatgaagatcctcacttatatatgtatcgatcttattgctagaacttgggtttatcgaatatgaatggggtttcatgatttgtgtctgcatcagGAGAAGGAAGAAAAACTTGATGGTGATGCTGCATTGAACAAATTCTTCCGTGACATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGATGAAGT

upper sequence: GLYMA11G02340.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 8
agagtatacatcaagatcaaacagaatctgtacctcactacctcataattttgtggaacatgtctaaaaaatattgatgaaaatgtggtctgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGTGATATTTACCAAAATGCAGATGAGGACATGAGGAGAGCAATGAGCAAGT
   || |  ||||||||    |    | |   | |||||      || ||  |        || |   ||||||  | |    |   ||| ||    |||||||| |||||||| ||||| ||||||||||| ||||  || || ||||||||||| ||| |  |||| ||||| || ||| |||| || |||  |||||
---gtttg-atcaagat--gcccacttttaggcatcacttt----tacttcagcaacttgggtttctcaaatatgaacggtgtttgtgtcggcaa--cagGAGAAGGAAGAAAAACTTGAAGGTGATGCTGCATTGAACAAGTTCTTCCGTGATATCTACAAGGATGCTGATGAAGATATGCGGAGGGCCATGGACAAGT

upper sequence: GLYMA11G02340.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv12s0035g01560.t01 (Vitis vinifera), 3'ss of exon 3
agagtatacatcaagatcaaacagaatctgtacctcactacctcataattttgtggaacatgtctaaaaaat-attgatgaaaatgtggtctgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGTGATATTTACCAAAATGCAGATGAGGACATGAGGAGAGCAATGAGCAAGT
              | |       | |||  |      ||| |     ||   |     |  | || |     ||  |       ||||| ||  ||||||||||||||||||||||| ||||| ||||| ||| |||  | ||| ||||| || ||||||| | |||||||||| ||||  || |  || |||   || |
--------------gtttgcctgcagtctagatgctgttactttggttttcattatcggaattttatatggcgatcaactctttggtggtttgaatttcagGAGAAAGAAGAAAAGCTGGATGGAGATGCAGCTCTGAACAGATTTTTCCGGGACATTTACCCAGATGCAGATGAAGACACAAGAATGGCCATGCAAAAAT

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|193335866|gb|FK299796.1|FK299796
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTT
EST: gi|208285774|gb|GE087372.1|GE087372
EST:     AAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAATAAATTGTTCCGT
genomic: AAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|193721610|gb|FK661650.1|FK661650
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|193593242|gb|FK548896.1|FK548896
EST:     GGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAATAAATTGTTCCGT
genomic: GGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|208092434|gb|GD887511.1|GD887511
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|193605125|gb|FK559869.1|FK559869
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|193600872|gb|FK551193.1|FK551193
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|208053186|gb|GD853519.1|GD853519
EST:     CCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: CCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|208303217|gb|GE101038.1|GE101038
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|208106192|gb|GD905133.1|GD905133
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|208271348|gb|GE068326.1|GE068326
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAA
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAA
EST: gi|193382871|gb|FK347734.1|FK347734
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAA-GAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCC
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCC
EST: gi|193485581|gb|FK448758.1|FK448758
EST:     GGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: GGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|193544466|gb|FK500677.1|FK500677
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|208333590|gb|GE131983.1|GE131983
EST:     AACCAAGGACAAAAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAATAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|193574245|gb|FK527882.1|FK527882
EST:     AGGACAAAAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAG
genomic: AGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAG
EST: gi|207845112|gb|GD817565.1|GD817565
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|208314468|gb|GE111816.1|GE111816
EST:     AGGACAAAAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAATAAATTGTTCCGT
genomic: AGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|208232523|gb|GE032276.1|GE032276
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|193423809|gb|FK387698.1|FK387698
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAA-GCTTGATGGTGA
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGA
EST: gi|193694906|gb|FK632976.1|FK632976
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|193388140|gb|FK353865.1|FK353865
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTT
EST: gi|208108188|gb|GD902504.1|GD902504
EST:     AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: AACCGAGGACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
EST: gi|208339388|gb|GE134432.1|GE134432
EST:     ACCGAGGTACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAG                         GAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT
genomic: ACCGAGG-ACAAGAGATTGGGATAAGTTGGAAGCTCAAGTGAAAAAAGAGgtttgccagc ... tgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taattttgtggaacatgtctaaaaaatattgatgaaaatgtggtctgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGTGATATTTACCAAAATGCAGATGAGGACATGAGGAGAGCAATGAGCAAGT
                          tattgat  putative branch site (score: 3)
                                           tctgcctttc  putative PPT
                 tctaaaaaatattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agagtatacatcaagatcaaacagaatctgtacctcactacctcataattttgtggaacatgtctaaaaaatattgatgaaaatgtggtctgcctttcagGAGAAAGAAGAAAAGCTTGATGGTGATGCTGCTTTGAGTAAATTGTTCCGTGATATTTACCAAAATGCAGATGAGGACATGAGGAGAGCAATGAGCAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - tcaaaca
- - - - - - - - - - - - - - - - cctcact
- - - - - - - - - - - - - - - - - - - - - - - - ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat