Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGTGGTAGATCTTCTGCAAGAGAAACAATTGGAAGGGTTGCTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttacttgtctcatgagtttaggttattattcttttttgtagtagtttctttgtgtttttttgttgttgttataactggccaagaatgatttatta...

Basic information

species Glycine max
transcript GLYMA20G31980.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv06s0004g02960.t01 (Vitis vinifera), 5'ss of exon 6
GGTGGTGGTAGATCTTCTGCAAGAGAAACAATTGGAAGGGTTGCTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttacttgtctcatgagtttaggttattattcttttttgtagtagtttctttgtgtttttttgttg-ttgttataactggccaagaatgatttatta-
|| ||||| || ||||| || |||||||| |||| ||| |||||| |||| ||||| || ||||||||||| ||  |||||||||| || |||||| |||  |  |||       | |  | |||  | |||   ||  |  |    |||| |||||        | | ||  |||      |   | | || | 
GGCGGTGGAAGGTCTTCAGCGAGAGAAACCATTGCAAGAGTTGCTGCTGGAGCTGTAGCAAAGAAAATCCTCAAGAAATTTTCTGGGACGGAGgtgtgtttatgatctttgtcactgaaatcatt-ctttttaacgttatcatgaagttgtatttttacacaaactataatttctgagttctacaaaatgatcag

upper sequence: GLYMA20G31980.1 (Glycine max), 5'ss of exon 6
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 5'ss of exon 6
GGTGGTGGTAGATCTTCTGCAAGAGAAACAATTGGAAGGGTTGCTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttacttgtctcatgagtttaggttattattcttttttgtagtagtttctttgtgtttttttgttgttgttataactggccaagaatgatttatta----
||||||||||||||||| || |||||||| ||||| || |||||  |||| ||||||||||| ||||| || ||| | |||||||||||||||||  ||  | || || |   |  | | ||||| |||||| || |  |||||  |||    | || | | | | | | |  |         ||||  ||      
GGTGGTGGTAGATCTTCAGCGAGAGAAACCATTGGGAGAGTTGCAGCTGGAGCTGTTGCTAAAAAAATACTCAAAAATTTTTCTGGAACTGAGgtatgtc-catgactgactggggt-gtttatt-ttctttattcttctagttgttttaaactcttatatgggtat-agagttcttatgttttgatgcatctagtt
















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|37994824|gb|CF806413.1|CF806413
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAG
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAG
EST: gi|254322919|gb|GR835634.1|GR835634
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|23052733|gb|BU577224.1|BU577224
EST:     AAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: AAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|208117633|gb|GD916419.1|GD916419
EST:     TTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: TTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|16346555|gb|BI972150.1|BI972150
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|120533980|gb|EH262113.1|EH262113
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|19934393|gb|BQ079423.1|BQ079423
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|254316986|gb|GR828523.1|GR828523
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTC
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTC
EST: gi|192325343|gb|FK017144.1|FK017144
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAATTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|192296954|gb|FG991950.1|FG991950
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACCGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|254340228|gb|GR858353.1|GR858353
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|9900006|gb|BE608974.1|BE608974
EST:     CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: CTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
EST: gi|208044536|gb|GD837936.1|GD837936
EST:     TGGTGCTGTTGTTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG                         ATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT
genomic: TGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttact ... tatttttcagATTCTGGCCTATGTCTCTCAAGTTCATAAGATTGTTCTTCCAGAGGACCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGTGGTAGATCTTCTGCAAGAGAAACAATTGGAAGGGTTGCTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAGgtgggttacttgtctcatgagtttaggttattattcttttttgtagtagtttctttgtgtttttttgttgttgttataactggccaagaatgatttatta

- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA