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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTAAGTGTATCCAATCCAGATACAAGGGTTGATGATGCAGAGTTTGAGGAGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagttttattaatatatttaccgatatgatgcatcttcctatcctttgcttagtaaactaccaatctcttgcag

Basic information

species Glycine max
transcript GLYMA03G07420.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv06s0004g06870.t01 (Vitis vinifera), 5'ss of exon 6
GGTAAGTGTATCCAATCCAGATACAAGGGTTGATGATGCAGAGTTTGAGGAGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaa-------tatagttttattaatatatttaccgatatgat---gcatcttcctatcctttgcttagtaaactaccaatctcttgcag----------------------
  | |||||  ||| |   || ||  | |||||||||||||| ||||| |||||||||||||||||| ||||||| ||    ||  |||| ||||| || ||||        ||   |  || |   | |   ||  ||||||   | |  |  || || ||    |  |   |     ||     |  |                      
ATTGAGTGTGCCCAGTGGTGAAACCCGAGTTGATGATGCAGAATTTGAAGAGAATGAAGTTTATGCAGTTGATATAGTCATCAGCTCTGGTGATGGAAAAgtaagtttggacatgaatgcatgatgttttagcccagtatgattttgtaattgactgtcgttaatcttatggccattgtataatccgtggaaaaaaaaaaaaactattgcag

upper sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv08s0217g00020.t01 (Vitis vinifera), 5'ss of exon 5
GGTAAGTGTATCCAATCCAGATACAAGGGTTGATGATGCAGAGTTTGAGGAGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaat-atagtttta---ttaatatatttaccgatatgatgcatct--tcctatcctttgcttagtaaactaccaatctc---ttgcag
  | |||||  ||| |||||| || || ||||| ||||||||||||||||||||||||||||||||| | ||||| ||  |||| || || ||||| |||||||| || | | |    ||||   |  ||    | | ||  | |   || ||   ||||       || | |     ||   ||||||
ACTGAGTGTTCCCAGTCCAGAGACCAGAGTTGAGGATGCAGAGTTTGAGGAGAATGAAGTTTATGCAGTAGATATAGTCACAAGCACAGGTGATGGGAAGgtaattatgggtctgattttaacccaaatattattcttattgaccacatcttactttttgtgctcataatttctggaatcaaattgcag

upper sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S119_137V6.1 (Physcomitrella patens), 5'ss of exon 5
GGTAAGTGTATCCAATCCAGATACAAGGGTTGATGATGCAGAGTTTGAGGAGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagttt-tattaatatatttac-cgatatgatgcatcttcctatcctttgcttagtaaactaccaatctcttgcag--------------------
  | ||||     ||| | || ||| | || |||||||| || |||||||| || |||||||| ||||||||||| ||| |||| ||||| || || ||||| | ||  | | | ||  | | | ||| |    ||    |  ||  | | | ||||| | ||       ||| ||||   |                    
TTTGAGTGCTGGTAATGCGGAGACACGCGTAGATGATGCTGAATTTGAGGAAAACGAAGTTTACGCAATTGATATTGTAACAAGCACTGGTGAAGGAAAGgtgaaattttctattttgttctgtatactctgggtgcaagagtttgttgtacattgctgattacgtag--aatgtcttagtgacctgaatcgaggtttttta

upper sequence: GLYMA03G07420.1 (Glycine max), 5'ss of exon 6
lower sequence: PP1S80_199V6.1 (Physcomitrella patens), 5'ss of exon 5
GGTAAGTGTATCCAATCCAGATACAAGGGTTGATGATGCAGAGTTTGAGGAGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagttttattaatatatttaccgatatgatgcatcttcctatcct-ttgcttagtaaactaccaatctcttgcag---------------------
  | || || ||||| ||||| ||  | || |||||||| ||||||||||| || ||||| || ||||| ||||||||  | || ||||| ||||| |||||||| |  | | |  | | | || | |||||| |        | ||| |  || ||  |   | |  |||    |    |                     
TCTGAGCGTGTCCAACCCAGAGACGCGTGTAGATGATGCTGAGTTTGAGGAAAACGAAGTGTACGCAATAGATATCGTGACCAGCACTGGTGATGGAAAGgtaattt--tctaaacattcttttcagcgatatcaacttctaccatatacggttactaggagcattttcaactgttgtttgaacagaatgaggttttgcttc

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|208308619|gb|GE104511.1|GE104511
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|208258591|gb|GE056368.1|GE056368
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGGTGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|193567991|gb|FK524328.1|FK524328
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|193424103|gb|FK391590.1|FK391590
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|193639633|gb|FK590074.1|FK590074
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAG
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAG
EST: gi|207847082|gb|GD819553.1|GD819553
EST:     AGAATGAAG-TTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|14009221|gb|BG725825.1|BG725825
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|208186117|gb|GD986774.1|GD986774
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|193589741|gb|FK544657.1|FK544657
EST:     TGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: TGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|208300711|gb|GE100630.1|GE100630
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|193656848|gb|FK606288.1|FK606288
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|193536766|gb|FK491826.1|FK491826
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGA
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGA
EST: gi|193474294|gb|FK441999.1|FK441999
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGA
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGA
EST: gi|13479974|gb|BG509317.1|BG509317
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|208058230|gb|GD859801.1|GD859801
EST:     AGAGTGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|208315932|gb|GE114400.1|GE114400
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|207707572|gb|GD689058.1|GD689058
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|18039999|gb|BM308293.1|BM308293
EST:     AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: AGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
EST: gi|208236030|gb|GE033394.1|GE033394
EST:     TATCGTAGCAAGTACTGGAGATGGCAAG                         CCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC
genomic: TATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagt ... tctcttgcagCCTAAGCTTTTGGATGAAAAGCAGACAACTATTTATAAGAGAGCTGTTGAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAAGTGTATCCAATCCAGATACAAGGGTTGATGATGCAGAGTTTGAGGAGAATGAAGTTTATGCAATTGATATCGTAGCAAGTACTGGAGATGGCAAGgtaatatagttttattaatatatttaccgatatgatgcatcttcctatcctttgcttagtaaactaccaatctcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG