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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctacatattctcgttaaccgtctattttagttcttgtggttttttttattatatatgtttattgctttaaaataatttttatctatgttaattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTTGTCTTCCAG

Basic information

species Glycine max
transcript GLYMA20G22600.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G22600.3 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 3
ttctacat-attctcg---ttaaccgtctattttagttcttgtggttttttttattatatatgtttattgctttaaaataatttttatctatgttaattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTTGTCTTCCAG
 | ||||| | ||||    ||    |  | || ||  | |  |     |  || |   |  |||||||  || |||    | |||  | ||| |  | || ||||| ||||| |||||||| ||||| ||||| ||||||||||||||||||||||| || || 
-tatacattaatctctaatttgtttggatgttctacatttattctccatgattgtcccaattgtttat--ctctaatgccaattt-gtatatttataattccagACAATAAGTTACATGGCTGAGCGCGTTGTTGGGCATGGATCATTTGGAGTTGTTTTTCAA
















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|213591295|gb|DB959865.1|DB959865
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|5605873|gb|AI899971.1|AI899971
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|209716478|gb|BW657522.1|BW657522
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTACGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|18039891|gb|BM308185.1|BM308185
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|209721765|gb|BW666385.1|BW666385
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|7686353|gb|AW757001.1|AW757001
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|254333709|gb|GR848627.1|GR848627
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|213607101|gb|DB965071.1|DB965071
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|192296530|gb|FG991636.1|FG991636
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|213604448|gb|DB970624.1|DB970624
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|22522553|gb|BU081364.1|BU081364
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|208111645|gb|GD911911.1|GD911911
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|298175413|gb|HO015046.1|HO015046
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCATGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|209700632|gb|BW670435.1|BW670435
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|213593805|gb|DB957925.1|DB957925
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|209696848|gb|BW680470.1|BW680470
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|254327042|gb|GR836651.1|GR836651
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|8826044|gb|BE209774.1|BE209774
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|209702060|gb|BW670544.1|BW670544
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|298177763|gb|HO027316.1|HO027316
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|209720625|gb|BW654452.1|BW654452
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|8826054|gb|BE209784.1|BE209784
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|213591448|gb|DB955740.1|DB955740
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|15814184|gb|BI786459.1|BI786459
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|26058927|gb|CA801841.1|CA801841
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|209699787|gb|BW655800.1|BW655800
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|298189801|gb|HO038204.1|HO038204
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
EST: gi|8825941|gb|BE209671.1|BE209671
EST:     GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAG                         ACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT
genomic: GACATATCATTGTGACTACCATTGGGGGTAGAAATGGTCAGCCCAAGCAGgtataccttc ... taattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttattatatatgtttattgctttaaaataatttttatctatgttaattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTTGTCTTCCAG
                                          tgttaat  putative branch site (score: 3)
                                                ttttc  CT-rich tract
     ttatatatgtttattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctacatattctcgttaaccgtctattttagttcttgtggttttttttattatatatgtttattgctttaaaataatttttatctatgttaattttcagACTATAAGCTACATGGCAGAGCGTGTTGTAGGGCATGGATCATTTGGAGTTGTCTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG