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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccacatcttgttaaggacacttaacaaatataggttggttgctatttctactcccctaaagaaagtgattcggttttctcactgttctcctttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGATATTGTTGCTAATCGGGGAGCCCGCCTTTCTGCTGCTGGTATTTTTGGCA

Basic information

species Glycine max
transcript GLYMA01G01060.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G01060.3 (Glycine max), 3'ss of exon 8
lower sequence: Vv11s0016g03070.t01 (Vitis vinifera), 3'ss of exon 8
-ccacatcttgttaaggacacttaacaaatataggttggttgctatttctactcccctaaagaaagtgattcggttttctcactgttctcctttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGATATTGTTGCTAATCGGGGAGCCCGCCTTTCTGCTGCTGGTATTTTTGGCA
  | ||   |   |   |||  |  ||    |   |||  |||| |  ||  |       |     |  ||   | | || ||| || |  ||  ||||||||    || || ||||||||||  || ||  ||||  | || || |||||||||||||||| ||| || ||||| ||||||||||| || ||  | ||||
atcccacaatagcagaaacaagtg-catggtttatttgtctgctttaactcttttttcttatgggtttcttgcatgtcctaactttttttattcatgtcagATACCCAATACTTCCCTGAAAACAAGAAAAGTTGTCATTGAGCTGTGTGATATTGTTGCTACTCGTGGGGCCCGTCTTTCTGCTGCAGGGATCCTAGGCA
















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|58024783|gb|CX711524.1|CX711524
EST:     CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAG                         ATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
genomic: CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAGgtatggatgc ... tttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
EST: gi|58023160|gb|CX709901.1|CX709901
EST:     CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAG                         ATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
genomic: CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAGgtatggatgc ... tttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
EST: gi|192321335|gb|FK012096.1|FK012096
EST:     CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAG                         ATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
genomic: CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAGgtatggatgc ... tttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
EST: gi|16348134|gb|BI973729.1|BI973729
EST:     CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAG                         ATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
genomic: CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAGgtatggatgc ... tttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
EST: gi|58021445|gb|CX708186.1|CX708186
EST:     CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAG                         ATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
genomic: CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAGgtatggatgc ... tttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
EST: gi|58017593|gb|CX704335.1|CX704335
EST:     CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAG                         ATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
genomic: CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAGgtatggatgc ... tttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
EST: gi|58015190|gb|CX701932.1|CX701932
EST:     CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAG                         ATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT
genomic: CATCTTCAGATCTGAAGGTGGTTGGAAACAAATTGAAGGATATATTAGAGgtatggatgc ... tttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctactcccctaaagaaagtgattcggttttctcactgttctcctttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGATATTGTTGCTAATCGGGGAGCCCGCCTTTCTGCTGCTGGTATTTTTGGCA
                              ttctcac  putative branch site (score: 2)
                       ttcggttttctcactg  CT-rich tract
           taaagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccacatcttgttaaggacacttaacaaatataggttggttgctatttctactcccctaaagaaagtgattcggttttctcactgttctcctttctgtcagATCAATAACACATCCCTGAAAATGAGGAAGATTGTTGTGGAACTCTGTGATATTGTTGCTAATCGGGGAGCCCGCCTTTCTGCTGCTGGTATTTTTGGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT