Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATGAGAGAATATTTATTGATGAAGATTTTGCAAAAGTGACTGTTCGCCATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacctattgctgaaaatactcagtgaatattgaacttgtaaccctgaactgattagtgcatgcataaaaaattgctgatcctgtaggttctctga...

Basic information

species Glycine max
transcript GLYMA04G39340.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G39340.1 (Glycine max), 5'ss of exon 5
lower sequence: AT5G39590.1 (Arabidopsis thaliana), 5'ss of exon 5
AAATGAGAGAATATTTATTGATGAAGATTTTGCAAAAGTGACTGTTCGCCATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacctattgc--tgaaaatactcagtgaatattgaacttgtaaccctgaactgat--tagtgcatgcataaaaaattgctgatcctgtaggttctctga--
|||||||||||| || ||||||||||| ||||| ||| | || || || ||||||||  |||| |||||||||| |   || ||||| || ||| | |||||| |  |  |   |  | ||   ||  | ||| |||  | | || |   |  |  |  |  |  || ||    | || ||  ||       || | | |||    
AAATGAGAGAATTTTCATTGATGAAGACTTTGCTAAAATCACAGTCCGTCATCATGCAGTTGATAAAACTTACCAGTCAGGCTCTCTTTTCCCAAACCAGgtaaagccacaacaccataaaggaacaaaatgagtat--atcatgcatgtcaaattttgtgctcttggatcttaataacatctcttgctaaatatgatttctacag

upper sequence: GLYMA04G39340.1 (Glycine max), 5'ss of exon 5
lower sequence: Vv18s0001g13900.t01 (Vitis vinifera), 5'ss of exon 5
AAATGAGAGAATATTTATTGATGAAGATTTTGCAAAAGTGACTGTTCGCCATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacctattgctgaaaatactcagtgaatattgaacttgtaaccctgaactgattagtgcatgcataaaaaattgctgatcctgtaggttctctga--------
 |||||||||||||||||||| || |||||||| | ||| |||||||||||||||||  ||||||||||||| |    ||| || ||| | || ||||||||| |  |  |    | |||||  ||| |    || |    |        ||||| ||  ||       | || |  || | ||  | | | |||  |||        
GAATGAGAGAATATTTATTGACGAGGATTTTGCTAGAGTTACTGTTCGCCATCATGCAGTTGACAAAACTTATCAACCTGGTTCCCTCATCCCTGATCAGgtagatgcagagacattaaaatggtca-tactcatagttgatactgatgggaactcatgggt-------tgaacatgtgatcattttctggtttccatgaaaagaaat
















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|213605159|gb|DB982227.1|DB982227
EST:     CATGCTATTGACAAAACTTACCGGAGT-CA-ATCTCTTGCCTGAGATCAG                         GGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACT
genomic: CATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCC--AGATCAGgtataaacct ... tatgtttcagGGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACT
EST: gi|254319085|gb|GR828813.1|GR828813
EST:     ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAG                         GGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
genomic: ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacct ... tatgtttcagGGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
EST: gi|12688334|gb|BG154670.1|BG154670
EST:     ATCATGCTATTGACAAAACT-ACCGGAGTGGATCTCTCTTACCAGATCAG                         GGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGAGGACTT
genomic: ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacct ... tatgtttcagGGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
EST: gi|58023713|gb|CX710454.1|CX710454
EST:     ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAG                         GGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
genomic: ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacct ... tatgtttcagGGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
EST: gi|51341487|gb|CO982804.1|CO982804
EST:     ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAG                         GGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
genomic: ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacct ... tatgtttcagGGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
EST: gi|9440130|gb|BE440641.1|BE440641
EST:     ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAG                         GGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
genomic: ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacct ... tatgtttcagGGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
EST: gi|58020079|gb|CX706821.1|CX706821
EST:     ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAG                         GGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
genomic: ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacct ... tatgtttcagGGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
EST: gi|15204819|gb|BI427587.1|BI427587
EST:     ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAG                         GGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
genomic: ATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacct ... tatgtttcagGGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
EST: gi|9901717|gb|BE610685.1|BE610685
EST:     CAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAG                         GGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT
genomic: CAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacct ... tatgtttcagGGTTTCCTTCCTGTCGAGGGTCTGATTTCTGAAGTTGAAGTTTGGGGACTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATGAGAGAATATTTATTGATGAAGATTTTGCAAAAGTGACTGTTCGCCATCATGCTATTGACAAAACTTACCGGAGTGGATCTCTCTTTCCAGATCAGgtataaacctattgctgaaaatactcagtgaatattgaacttgtaaccctgaactgattagtgcatgcataaaaaattgctgatcctgtaggttctctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaaaa