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

caagctgagtctttaatttttcattcagcttctcaggactctgtggcttgatttatggtgtgacgctgtctgtcaacgtgaataagttttggtgtggtatggtgtgcttgattaagtaattctgcagttgtggtttgataaatttgatggctataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCTAATCGAAGGCCTTGAAGGAAATGATTTATTGTTCTATACTCACTTGCTA

Basic information

species Glycine max
transcript GLYMA18G04360.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G04360.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G37850.3 (Arabidopsis thaliana), 3'ss of exon 3
caagctgagtctttaatttttcattcagcttctcaggactctgtggcttgatttatggtgtgacgctgtctgtcaacgtgaataagttttggtgtggtatggtgtgcttgattaagtaattctgcagttgtggtttgataaatttgatggctataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCTAATCGAAGGCCTTGAAGGAAATGATTTATTGTTCTATACTCACTTGCTA
                                   | | | | |||    |    |  |||   ||    |||    |  ||| | | |||  ||    | || |  | |  ||  | | ||| | | | |||  | |  ||        || |  | |||| ||||| || ||||| || |||||||||||||| |||||| | || ||| | || ||||| ||||||| ||| ||||| |||||||| |||||  |  | 
-----------------------------------gtaatatttggtcaca---gtaatgtagagcctaatgttcctg-aaattactgttgtcgtatcttcgt-tattggtgtatctgaatctactgatttggcattactaa------aacttttttccagGGTATCCTACATTTAAAGGACAGGTTTTGAATGGTCAGCAATTGTGTGATTTGATTGAAGGTCTTGAAGCAAACGATTTGTTGTTCTACACTCATGTATT-

upper sequence: GLYMA18G04360.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0006g01660.t01 (Vitis vinifera), 3'ss of exon 3
caagctgagtctttaatttttcattcagct--tctcaggactctgtggcttgatttatggtgtgacgctgtctgtcaacgtgaataagttttggtgtggtatggtgtgcttgattaagtaattctgcagttgtggtttgataaatttgatggctataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCTAATCGAAGGCCTTGAAGGAAATGATTTATTGTTCTATACTCACTTGCTA
       ||    | ||  |||| |||     |||||| ||||||  || |||  ||||||| || |    ||| |||  |  || ||||  ||  ||  ||  |       ||| ||      |  | || ||||| |  || ||  ||  ||    ||||||||| || || |||||||| || ||||||||||||||||||||  | ||| |||| | |||||| ||||  ||| | ||||| | |||||| || ||| | 
----gcaagctgcttatacttcactcaaacagtctcagaactctgaagcctgaaatatggtgcgaggtcaactgccaatctatatgagttcaggcatgagatcctagtagcaattgagg-----ttaaattatggttagtcaacttgaatatct----tgcagGATACCCAACTTTTAAGGGCCAAGTTTTGAATGGACAGCAACTAGGAGATTTAATAGCAGGCCTGGAAGAGAATAACTTATTATACTATACCCATTTGTT-
















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|151401899|gb|EV271712.1|EV271712
EST:     GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG                         ATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
genomic: GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGGcaagctgagt ... ataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
EST: gi|192332257|gb|FK023906.1|FK023906
EST:     GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG                         ATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
genomic: GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGGcaagctgagt ... ataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
EST: gi|298186757|gb|HO037390.1|HO037390
EST:     GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG                         ATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
genomic: GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGGcaagctgagt ... ataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
EST: gi|213600856|gb|DB958434.1|DB958434
EST:     GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG                         ATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
genomic: GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGGcaagctgagt ... ataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
EST: gi|7684914|gb|AW755562.1|AW755562
EST:     GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG                         ATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
genomic: GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGGcaagctgagt ... ataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
EST: gi|27423806|gb|CA935326.1|CA935326
EST:     GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG                         ATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
genomic: GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGGcaagctgagt ... ataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
EST: gi|298188142|gb|HO032099.1|HO032099
EST:     GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG                         ATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
genomic: GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGGcaagctgagt ... ataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
EST: gi|213588703|gb|DB957697.1|DB957697
EST:     GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGG                         ATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT
genomic: GGATATGATGTCGATCCAATTAATTCCGTGCAGTTTTCGAATCATACAGGcaagctgagt ... ataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattaagtaattctgcagttgtggtttgataaatttgatggctataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCTAATCGAAGGCCTTGAAGGAAATGATTTATTGTTCTATACTCACTTGCTA
                                  atttgat  putative branch site (score: 5)
                          tttgataaatttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caagctgagtctttaatttttcattcagcttctcaggactctgtggcttgatttatggtgtgacgctgtctgtcaacgtgaataagttttggtgtggtatggtgtgcttgattaagtaattctgcagttgtggtttgataaatttgatggctataatgcaggATATCCGACGTTTAAGGGTCAGGTTTTGAATGGACAGCAACTCTGGGATCTAATCGAAGGCCTTGAAGGAAATGATTTATTGTTCTATACTCACTTGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA