Skip to another splice site:
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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atggtggtgccataggccgccatggtgatggcggaattttggccttccgccatccatcattgataatgttgactctgaccgtgttttcaacttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCTAGGCTACAGAAGAAAAATGATGCTATGAATGATTTGGTTTCCTGTGCTG

Basic information

species Glycine max
transcript GLYMA02G06480.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G06480.3 (Glycine max), 3'ss of exon 3
lower sequence: AT2G43720.1 (Arabidopsis thaliana), 3'ss of exon 2
atggtggtgccataggccgccatggtgatggcggaattttggccttccgccatccatcattgataatgttgactctgaccgtgtttt-caacttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCTAGGCTACAGAAGA---AAAATGATGCTATGAATGATTTGGTTTCCTGTGCTG
 | ||  ||   |   | |   |    ||  |   |     ||  |  |   |   |  | |||| |   ||   ||     ||||| |   |   || ||||||||||||||||||||||  |||| |||||||| ||||  ||||  |||| || ||||||||    || ||| ||  | ||||||||||     ||||   
ttagtt-tgttgtctcctggattctctattacatgacaacagcgcttgggtttgagtactagatattcaagatggtgttttggttttactgatgaatgtagGAGAGGTTGAATAGATCTCTTGTGGTTTGTCAAGACAAGTTTGAGGTTGCTAAGCAACAGAAGACGAGAAGTGAAGCGGTAAATGATTTGGAGCATTGTG---
















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|298187975|gb|HO031932.1|HO031932
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|298165398|gb|HO011447.1|HO011447
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|298171875|gb|HO021467.1|HO021467
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|298185727|gb|HO030940.1|HO030940
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGCTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|298193579|gb|HO040227.1|HO040227
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|151413045|gb|EV282853.1|EV282853
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|9203807|gb|BE330031.1|BE330031
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|298167850|gb|HO013113.1|HO013113
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|298186773|gb|HO037406.1|HO037406
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|120528844|gb|EH256978.1|EH256978
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|23058483|gb|BU578317.1|BU578317
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|192327573|gb|FK021278.1|FK021278
EST:     CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CTCTTTCTAATGTGCAACATACATTTGATCATGAGATGGCACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
EST: gi|192327574|gb|FK021279.1|FK021279
EST:     CACAGTTTCAG                         GAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT
genomic: CACAGTTTCAGgtaacccata ... cttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccgccatccatcattgataatgttgactctgaccgtgttttcaacttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCTAGGCTACAGAAGAAAAATGATGCTATGAATGATTTGGTTTCCTGTGCTG
                           ctctgac  putative branch site (score: 3)
             attgataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atggtggtgccataggccgccatggtgatggcggaattttggccttccgccatccatcattgataatgttgactctgaccgtgttttcaacttggtgcagGAGAGGTTGAATAGATCTCTGATGGTGTGTCAAGATAAGTACGAGGCGGCTAGGCTACAGAAGAAAAATGATGCTATGAATGATTTGGTTTCCTGTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
-tggtggt
- - - - - - - -gccgcca
- - - - - - - - - - - -ggtgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - -ccatcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgtgtt