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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggtgcctttactgaagcatagtttttgttatgcaagtttcgactaaaatttgttgattcatatttgattttcattctcattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTCTCATTAACTGATCGTCTTCGTGAAAGATTTGTGAGTGGATATTTGCTTC

Basic information

species Glycine max
transcript GLYMA15G40060.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40060.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0176g00140.t01 (Vitis vinifera), 3'ss of exon 9
--------------------gtttggtgcctttactgaagcatagtttttgttatgcaagtttcgactaaa--atttgttgattcatattt-gattttcattctca---ttctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTCTCATTAACTGATCGTCTTCGTGAAAGATTTGTGAGTGGATATTTGCTTC--
                    ||||| |   | || | |  | |    | ||| |   |  ||| |  |     |||| ||   |||| |||  ||| |      ||   || |  ||||| |||||||||||||| |||||||||||| ||||| ||||| |  |||  ||||| || ||  ||   ||  || |  || |  |||| ||||| |    
gtattttcccagtattctgagtttgtt--ttatatttagacctcagctatgtcaatgatattttgctttgtttatttatttgctcattttttaattgttgcatgcaactttttacagGGTCAGTCCTTCAAAGACACCAGTGAGGCCACGGGTCCCTCGTGCAACGTTGCATTAGCTAATTATCGGAGTATAA-ACCTGCGGATGGA-ATTTGGTGTAA
















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|254314632|gb|GR829625.1|GR829625
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|7588858|gb|AW704644.1|AW704644
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAT                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCA
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCA
EST: gi|58020690|gb|CX707432.1|CX707432
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|19053081|gb|BM731748.1|BM731748
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|151403013|gb|EV272826.1|EV272826
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|208250786|gb|GE047781.1|GE047781
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|193698363|gb|FK638986.1|FK638986
EST:     TTAATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: TT-ATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|193583619|gb|FK541087.1|FK541087
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|58020886|gb|CX707628.1|CX707628
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|58020497|gb|CX707239.1|CX707239
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|18038912|gb|BM307206.1|BM307206
EST:     CAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
genomic: CAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTC
EST: gi|298191171|gb|HO038650.1|HO038650
EST:     ATTATTACACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTCAAAGACTCC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTTCAAAGACTCC
EST: gi|8284333|gb|BE021892.1|BE021892
EST:     ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAG                         GGTGAGTCCTTTCAA-GACTCC
genomic: ATTATTGCACTAAACTGTAGTGGGATGCTCTTGGGGACCCAGCCAATAAGgtttggtgcc ... cattctgtagGGTGAGTCCTT-CAAAGACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagtttcgactaaaatttgttgattcatatttgattttcattctcattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTCTCATTAACTGATCGTCTTCGTGAAAGATTTGTGAGTGGATATTTGCTTC
                                   ttttcattctcattct  CT-rich tract
           taaaatttgttgattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggtgcctttactgaagcatagtttttgttatgcaagtttcgactaaaatttgttgattcatatttgattttcattctcattctgtagGGTGAGTCCTTCAAAGACTCCAGTGAGGCCAAGGGTCACTCGTCCGGCGTCTCATTAACTGATCGTCTTCGTGAAAGATTTGTGAGTGGATATTTGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA