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

...tttagctgatcaggtggtttatggcatatttaattacacattacgattactttgcactaccatatgtatttgatatgaagatggtattacacttgtgcagAAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCCCGTGGTCGCCATGATCCTTGTGTTGTCCCAAGAG

Basic information

species Glycine max
transcript GLYMA20G31980.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G31980.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv13s0019g04190.t01 (Vitis vinifera), 3'ss of exon 11
tttagctgatcaggtggtttatggcatatttaattacacattacgattactttgcactaccatatgtatttgatatgaagatggtattaca---cttgtgcagAAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCCCGTGGTCGCCATGATCCTTGTGTTGTCCCAAGAG
 || |  | |    |  | | | || ||| ||  |   | |  | ||   |||    |   |  | |||  ||     | ||| || | ||    |  |||||||||| ||  | ||||| ||| |||||||| |||| |||||| | ||||| ||||| ||||||||||| |||||||| ||| |||
-ttgg--gttttacttttattttgcgtatatagattgtcctggctatgtttttttcttcttaattatataggaatcatatatgttactgcaatgttcatgcagAAGAAACAGCACACTGTTACTAGAGATAAACAAGAGACAGAGCTAATAGCTCGTGGCCGCCATGATCCATGTGTTGTTCCACGAG
















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|58017502|gb|CX704244.1|CX704244
EST:     GGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGA                         AAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCC
genomic: GGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGAgtaagtctta ... acttgtgcagAAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCC
EST: gi|19052637|gb|BM731304.1|BM731304
EST:     GGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGA                         AAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCC
genomic: GGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGAgtaagtctta ... acttgtgcagAAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCC
EST: gi|120533980|gb|EH262113.1|EH262113
EST:     GGTGGTGGTAGATCTTCTGCAAGAGAAACAATTGGAAGGGTTGCTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG
genomic: GGTGGTGGTAGATCTTCTGCAAGAGAAACAATTGGAAGGGTTGCTTCTGGTGCTGTTGCTAAGAAAATCCTTAAAGAATTTTCTGGAACTGAG
EST: gi|6668053|gb|AW279504.1|AW279504
EST:     GGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGA                         AAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCC
genomic: GGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGAgtaagtctta ... acttgtgcagAAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCC
EST: gi|254340229|gb|GR858354.1|GR858354
EST:     GGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGA                         AAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCC
genomic: GGGAAATCATTAATATGAGAATAGCTTTCAAGCCAACATCAACAATTGGAgtaagtctta ... acttgtgcagAAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attactttgcactaccatatgtatttgatatgaagatggtattacacttgtgcagAAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCCCGTGGTCGCCATGATCCTTGTGTTGTCCCAAGAG
                      atttgat  putative branch site (score: 5)
                atatgtatttgatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttagctgatcaggtggtttatggcatatttaattacacattacgattactttgcactaccatatgtatttgatatgaagatggtattacacttgtgcagAAGAAGCAAAAGACTGTGACTCGAGATAAAAAAGAAACAGAGTTTATAGCCCGTGGTCGCCATGATCCTTGTGTTGTCCCAAGAG

- - gctgatc
- - - - - - ggtggtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - -actacca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gatggta