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'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttttcttgtttcaaagtatttgtacttatgctaccatcttgataagcacgtatgtcaccaagtggactcagaaaatgttttgttctaatgtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAAGCCGCTTGTATGCTTCTGAGGATTGATGATATAGTGAGTGGGATCAAGA

Basic information

species Glycine max
transcript GLYMA09G28650.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G28650.2 (Glycine max), 3'ss of exon 13
lower sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 12
------------tttttcttgt--ttcaaagta-tttgtacttatgctaccatcttgataagcacgtatgtcaccaagtggactcagaaaatgttttgttctaatgtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAAGCCGCTTGTATGCTTCTGAGGATTGATGATATAGTGAGTGGGATCAAGA
             || || | |  | | |   | ||| || ||     || || | |||       | |||    || | |  | | |     |  ||     || |  |   |||| |||||||| || ||||||||||||||  | |||||||| ||||| || || ||||| ||||| || ||||| || || || |||||||| || || |
gttcgagattttcttctcctataatcctattcactttctaattgcttcacaatttggatttttgtttttgtttttaatttg--tgaaactggatactgcatacatatttttccagATATGGGATGCTTATAATGTGAAGGCACAGACCTTTAAGACCGCCATCGAGGCTGCTTGCATGCTGCTTAGGATCGACGACATCGTGAGTGGAATAAAAA
















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|193575184|gb|FK530743.1|FK530743
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         AATTTGGGATGCCTA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagA-TTTGGGATGCCTA
EST: gi|192309233|gb|FG999124.1|FG999124
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|58025237|gb|CX711978.1|CX711978
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|58017480|gb|CX704222.1|CX704222
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|209714673|gb|BW674236.1|BW674236
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACA-GCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|208046900|gb|GD846461.1|GD846461
EST:     TGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|22927071|gb|BU544210.1|BU544210
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|192309232|gb|FG999123.1|FG999123
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|26048688|gb|CA785141.1|CA785141
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|207708468|gb|GD691466.1|GD691466
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|209710278|gb|BW676340.1|BW676340
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|193588325|gb|FK544060.1|FK544060
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTG
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTG
EST: gi|209714674|gb|BW674237.1|BW674237
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCAC-AGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|214008281|gb|DB989823.1|DB989823
EST:     TTGGTATAGATGGAAATACTGGCAGTAACACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|193595835|gb|FK552656.1|FK552656
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|193529449|gb|FK487832.1|FK487832
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTA
EST: gi|207786727|gb|GD757958.1|GD757958
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|208095316|gb|GD892046.1|GD892046
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|208209540|gb|GE001809.1|GE001809
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|207702132|gb|GD682005.1|GD682005
EST:     TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: TTGGTATAGATGGAAATACTGGCAGTATCACTGACATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
EST: gi|209725417|gb|BW658279.1|BW658279
EST:     CATGAAAGAGCGCAAG                         ATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA
genomic: CATGAAAGAGCGCAAGgtacttcacg ... gtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcacgtatgtcaccaagtggactcagaaaatgttttgttctaatgtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAAGCCGCTTGTATGCTTCTGAGGATTGATGATATAGTGAGTGGGATCAAGA
                                      ttctaat  putative branch site (score: 2)
                           aaaatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttttcttgtttcaaagtatttgtacttatgctaccatcttgataagcacgtatgtcaccaagtggactcagaaaatgttttgttctaatgtgatgttagATTTGGGATGCCTACAATGTGAAGGCACAAGCATTTAAGACTGCCATTGAAGCCGCTTGTATGCTTCTGAGGATTGATGATATAGTGAGTGGGATCAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - -tgctacc
- - - - - - - - - - - - - - - - - - - - - - - gcacgta
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtcacc