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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtctattttaatcagctctgtattaatattattattcataatttcatatacataaatggccttattttaattagtgtttttttttcttttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGTAAAATCGTTGAGGGTGTTCTTAGCCACCAAATGAAGCAGTTTGTTATTG

Basic information

species Glycine max
transcript GLYMA07G18500.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G18500.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0217g00020.t01 (Vitis vinifera), 3'ss of exon 4
ttgtctattttaatcagctctgtattaatattattattcataatttcatatacataaatggccttattt-taattag------tgtttttttttcttttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGTAAAATCGTTGAGGGTGTTCTTAGCCACCAAATGAAGCAGTTTGTTATTG
      ||| |  | |  ||| ||||| |||| ||  |  |  ||| || | |     |    | |||  |||  ||      ||   | | |  || ||    ||||| ||||||||||  || |||||||| ||||||||||||||||||||||| ||||| || || ||||| || ||||||||  | ||||||||||| || |
------attgtggttaa-tctttattattattgttggtgttgtttttatgtgccctgttcatttgattggtaaaaagctgagttgcagtctctctttataatggcagAATAAGGATGTAACAGAAGCAATTCAGAAGGTTGCTGCTGCCTATGACTGCAAAATTGTCGAAGGTGTACTCAGCCACCAGCTAAAGCAGTTTGTGATAG

upper sequence: GLYMA07G18500.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g06870.t01 (Vitis vinifera), 3'ss of exon 5
--ttgt-ctatt-ttaatcagctctgtattaatattattattcataatttcatataca-taaatggccttattttaattagtgtttttttttcttttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGTAAAATCGTTGAGGGTGTTCTTAGCCACCAAATGAAGCAGTTTGTTATTG
  ||   | ||| | ||   | |    ||||  |||  ||| |||   || |  | || |   |  | |||||||  | | |   |||| |  || |     ||||||||||| ||||  ||||| ||||| ||||| ||||||||||||||||| || || ||||| |||||||| || |||||| | || |||||||| ||||
ttttacacgattatcaaatggttggtcattagaatt--tatgcatgtgtttactttcaatttttctctttattttgttcactaagttttgtggttgtg---gcagAACAAGGAAGTAACAGATGCTATTCAGAAGGTGGCTGCTGCCTATGACTGCAAGATTGTTGAAGGTGTTCTCAGTCACCAACTAAAACAGTTTGTGATTG
















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|193454485|gb|FK420338.1|FK420338
EST:     TTGAGGCTTGTCAGGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: TTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|208268333|gb|GE072030.1|GE072030
EST:     TTGAGGCTTGTCAGGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: TTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193307502|gb|FK269242.1|FK269242
EST:     CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAA-GGTTGCTGCTGCCTATGACTGT
genomic: CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|208049996|gb|GD846283.1|GD846283
EST:     TTGAGGCTTGTCAGGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: TTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193421106|gb|FK391351.1|FK391351
EST:     CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAA-GGTTGCTGCTGCCTATGA
genomic: CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGA
EST: gi|193640235|gb|FK589316.1|FK589316
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|208109931|gb|GD904457.1|GD904457
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193476068|gb|FK441365.1|FK441365
EST:     CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAG                         AACAAGGATGTAAG
genomic: CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAG
EST: gi|193575075|gb|FK530242.1|FK530242
EST:     GGCTTGTCAGGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193501140|gb|FK465077.1|FK465077
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|208262708|gb|GE058852.1|GE058852
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193510114|gb|FK472100.1|FK472100
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193556807|gb|FK516076.1|FK516076
EST:     AAATACTGCTGCTGAGGTGGCCTTGAGGCTTG-CAGGCCAAGGAAAGAAG                         AACAAGGATGTAAG
genomic: AAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCA-GGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAG
EST: gi|207704224|gb|GD685472.1|GD685472
EST:     TTGAGGCTTGTCAGGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: TTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193371757|gb|FK336444.1|FK336444
EST:     TTGAGGCTTGTCAGGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: TTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|208037154|gb|GD836567.1|GD836567
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193393489|gb|FK359747.1|FK359747
EST:     TTGAGGCTTGTCAGGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: TTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|192298267|gb|FG991729.1|FG991729
EST:     CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193383713|gb|FK346848.1|FK346848
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|208188269|gb|GD982757.1|GD982757
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193417359|gb|FK383835.1|FK383835
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGA
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGA
EST: gi|192303104|gb|FG994222.1|FG994222
EST:     CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCA
genomic: CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCA
EST: gi|254325005|gb|GR834430.1|GR834430
EST:     CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193594978|gb|FK546361.1|FK546361
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|13562960|gb|BG551180.1|BG551180
EST:     AAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGTAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTG
genomic: AAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGG-AAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTG
EST: gi|208340150|gb|GE133192.1|GE133192
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|7147473|gb|AW509395.1|AW509395
EST:     CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: CAAATACTGCTGCTGAGGTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|207695827|gb|GD677672.1|GD677672
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCT
EST: gi|193713291|gb|FK654444.1|FK654444
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193557273|gb|FK511586.1|FK511586
EST:     GTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GTGGCCTTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|208166419|gb|GD962517.1|GD962517
EST:     TTGAGGCTTGTCAGGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: TTGAGGCTTGTCAGGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|193684480|gb|FK624346.1|FK624346
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|207702017|gb|GD683891.1|GD683891
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
EST: gi|207694906|gb|GD676653.1|GD676653
EST:     GGCCGGGAAAGAAG                         AACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT
genomic: GGCCAGGAAAGAAGgtaatcaact ... ttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatatacataaatggccttattttaattagtgtttttttttcttttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGTAAAATCGTTGAGGGTGTTCTTAGCCACCAAATGAAGCAGTTTGTTATTG
                     ttttaat  putative branch site (score: 3)
                               tgtttttttttctttt  putative PPT
                  ttattttaattagtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtctattttaatcagctctgtattaatattattattcataatttcatatacataaatggccttattttaattagtgtttttttttcttttatccacagAACAAGGATGTAAGTGATGCAATTCAAAAGGTTGCTGCTGCCTATGACTGTAAAATCGTTGAGGGTGTTCTTAGCCACCAAATGAAGCAGTTTGTTATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - -ctctgta
- - - - - - - - - - - - - - - - - - - - - - - catatac