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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatgttttggactttttgattatttttctgccagttcatgagtcctctttttatatcgtcaagtcttaaactgtatttatttaatttcaatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA

Basic information

species Glycine max
transcript GLYMA11G20840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 3'ss of exon 3
-ttgatgttttggactttttgattatttttctgccagttcatgagtcctctttttatatcgtcaagtcttaaact--gtatttatttaatttcaatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA
  |  |||||      | || |  | || |       |   |   |  ||    ||||| |||| || || |  |   || | |   | ||||  ||   |||||||||| || |||||||| ||||| ||||| || ||||| || || || |||||||| || || ||||||||||| || || |||||| |  |  ||||
agttctgtttgaagactgtttacaagttatagttttttctctctctgttcaaggtatat-gtcatgttttgagattaataataacccactttctgttc--cagGAATGGTTGCAGCTTTAACTAATGAGAGTGCAACAAGCAAGTCGGTGTATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTCACAGA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 3'ss of exon 3
ttgatgttttggactttttgattatttttctgccagttcatgagtcctctttttatatcgtcaagtcttaaactgtatttatttaatttca--atttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA
   ||| |||        |  | || ||   |   | ||||  | | | |||||   | ||  |  |||    |   ||| |  |||||    ||    |||| ||||| || ||| |||||||||| ||||| ||||||||||| || ||||||||||  || || || || |||||||  || || || || |||| |||
gctatgctttacgtcgcgttttaatcttgtcgt--ggtcatctgcctttttttttcttggtttatgcttctgttaattttctgaaattttgttatcctgcagGTATGGTGGCAGCTCTAACAAATGAGAGTGCAACCAGCAAATCCGTTTACTTTGCTCTTTGCACATCTGAAATGATTTACATAACCCACCTTTTGGAAGA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G155348_T01 (Zea mays), 3'ss of exon 3
ttgatgttttggactttttgattatttttctgccagttca-tgagtcctctttttatatcgtcaagtcttaaactgtatttatttaatt---tcaatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA
  ||  |   |     |      |        |||  |||   ||    | |||        | ||| |||     ||||| | |||||   |  || |  |||||||||| || ||||||||||| || ||||| || |||||||||||||| |||||||| || || ||||||||||| || || |||||| |  || ||||
--gacctgaggagtgctactcagaccacctaaccaactcagctagaggccctttcgcgagtaccagtttta--tcatatttctctaattctctttatgtttcagGAATGGTGGCAGCTTTAACAAACGAGAGTGCAACAAGCAAATCTGTATATTTTGCTCATTGCACGTCAGAGATGATATTCATTACTCATTTGCTGACAGA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G090747_T02 (Zea mays), 3'ss of exon 3
--ttgatgttttggactttttgattatttttctgccagttcatgagtcctctttttatatcgtcaagtcttaaactgtatttatttaatttcaatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA
      ||   |  | | | ||   ||   | || |  |   |||  || |    ||     | |  || | || | |  | |      |   || |  |||| |||||||||||  |||| || || ||||| |||||||||||||| |||||||| |  || || || |||||||| |  ||||| || ||  ||| |||
gtgcagtgaactttattctatgcacatagct-tggcgctcagtgacacccccaagtagcctatgatttcatcaatt-tgctgaacattctgatatcttgcagGTATGGTAGCTGCACTAACCAACGAGAGTGCAACCAGCAAATCTGTTTACTTTGCACTTTGCACATCTGAGATGATCTACATCACACACCTTCTGGAAGA

upper sequence: GLYMA11G20840.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0158g00340.t01 (Vitis vinifera), 3'ss of exon 2
ttgatgttttggactttttgattatttttctgccagttcatgagtcctcttt-------ttatatcgtcaagtcttaaactgtatttatttaatttcaattt----aacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA
           |  || |||  |  |  | | | | || ||   |||| ||        ||   |      ||   ||  ||||  |  ||| ||| |||||    ||||||||||||||| ||| |||| ||||| ||||||||||||||||| || |||||||| || ||||| ||||||||||||||||| || ||||| ||  ||||
-----------gcattcttgtgtgatcctgttctaatttatatttccttttgaagaatattgagtttctgggttggaatttgtaagttcttactttgaatttgcataacagGAATGGTAGCAGCTCTAACCAATGAGAGTGCCACCAGCAAATCAGTGTACTTTGCACATTGTACATCAGAGATGATTTTTATTACCCATCTTTTATCAGA

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|207773438|gb|GD744506.1|GD744506
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|193658134|gb|FK602567.1|FK602567
EST:     AAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: AAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|193330428|gb|FK292742.1|FK292742
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTG
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTG
EST: gi|193468338|gb|FK434459.1|FK434459
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|193346146|gb|FK310548.1|FK310548
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|207760790|gb|GD734113.1|GD734113
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|207845242|gb|GD814839.1|GD814839
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|15812784|gb|BI785059.1|BI785059
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|193701567|gb|FK639503.1|FK639503
EST:     ACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATAC
genomic: ACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTA-TTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATAC
EST: gi|207732396|gb|GD709003.1|GD709003
EST:     CTCATGAAATCATGGGTGGATTAAAGAATGGTATATGCTATTGGAGCGAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATAC
genomic: CTCATGAAATCATGGGTGGATTAAAGAAT-GTATATGCTATTGGAGC-AGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATAC
EST: gi|208190300|gb|GD990094.1|GD990094
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|193395920|gb|FK364909.1|FK364909
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|193557888|gb|FK513685.1|FK513685
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|207783963|gb|GD755487.1|GD755487
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|18734350|gb|BM528131.1|BM528131
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|207792315|gb|GD764221.1|GD764221
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
EST: gi|207774479|gb|GD746317.1|GD746317
EST:     CTATTGGAGCAG                         GAATTGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATAC
genomic: CTATTGGAGCAGgtaatttctc ... aatttaacagGAA-TGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATAC
EST: gi|208321772|gb|GE119965.1|GE119965
EST:     TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAG                         GAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT
genomic: TACTCATGAAATCATGGGTGGATTAAAGAATGTATATGCTATTGGAGCAGgtaatttctc ... aatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctctttttatatcgtcaagtcttaaactgtatttatttaatttcaatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA
                                   atttaat  putative branch site (score: 4)
                 aagtcttaaactgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatgttttggactttttgattatttttctgccagttcatgagtcctctttttatatcgtcaagtcttaaactgtatttatttaatttcaatttaacagGAATGGTAGCTGCTTTAACAAATGAAAGTGCCACCAGCAAATCTGTATACTTTGCTCACTGTACTTCAGAGATGATTTTTATCACTCATCTATTGGCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - tgttttg
- - - - - - - - - - - - - - tctgcca
- - - - - - - - - - - - - - - - - - -tcatgag