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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA

Basic information

species Glycine max
transcript GLYMA20G02490.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g21460.1 (Oryza sativa), 3'ss of exon 5
--taaatcattatctttagctttcctattttgg-gactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
   ||||  | ||| ||| |   | ||       || |  |  |   ||  ||  |        || |  |  |  |   | | | |  |  | |   || ||||||||||||| |||||||| |||||||| | ||| ||  | |||||||| ||||| ||||||||||| || ||||| | ||| ||||||||||| || |
taaaaattgtaatcattatcacacataaaccattgatttgtactaatatgcatataacaagtcattttccccttatacagactaagcaatttttt---tgcagGTTTATGCTGTCCACTTCAAATGCAACAAAAGGCTCCTCAGGGAATACCCCAATCTGTTCAATTACACCAAGGACATCTACCAGATTCCTGGCATCAGCA

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G105005_T02 (Zea mays), 3'ss of exon 5
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
        ||   ||| ||  |  |  |    || ||     |   ||| |||||  |   |  || ||||   ||         || |   |||   |||| || || |||||||||||||||||||||||||||||  | || ||||| || || ||||| ||||| || ||||| | ||| || || ||||| || |
-------gtaaacttaactaccgcagatcaaaacacaaaactctgcata-ccattcgagcttactgtctgtcccgt---------ttccatcaatcacagGTCTACGCCGTTCACTTCAAGTGCAACAAGAAGCTGCTGAGGGAGTACCCAAACCTGTTCAACTACACCAAGGACATATACCAGATCCCCGGCATCAGCA

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G19880.3 (Arabidopsis thaliana), 3'ss of exon 5
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
            || |   || | |     | |       | ||  ||||       ||| |    | ||||||    ||||||              |||||||||| || |||||||| ||||||||||| ||  || | || || |||||| | ||||| |||||||||||||||||||| || || || || ||||
-----------gttcatactttcaaagcaagaaaaagaagtacaccatatgtgaacgaatctc--taatgttgaaacgttgatcc-------------agGTTTATGCAGTCCACTTCAAATGCAACAAGAAACTCATAAGGGAGTATCCGAATTTGTTCAACTACACGAAAGACATTTTCCAGATCCCCGGTATGAGTA

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: AT4G19880.1 (Arabidopsis thaliana), 3'ss of exon 5
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
        ||  || |   || | |     | |       | ||  ||||       ||| |    | ||||||    ||||||              |||||||||| || |||||||| ||||||||||| ||  || | || || |||||| | ||||| |||||||||||||||||||| || || || || ||||
-------gtaagttcatactttcaaagcaagaaaaagaagtacaccatatgtgaacgaatctc--taatgttgaaacgttgatcc-------------agGTTTATGCAGTCCACTTCAAATGCAACAAGAAACTCATAAGGGAGTATCCGAATTTGTTCAACTACACGAAAGACATTTTCCAGATCCCCGGTATGAGTA

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: AT5G45020.2 (Arabidopsis thaliana), 3'ss of exon 5
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattga-----tctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
                          | |  || |||  |||   | | |   |   |||       |  |   ||  ||||     |||||       ||  |||||||||| ||||||||||| ||||||||||  ||  |||| || ||||||||| | ||||| ||||  |||||||||| |||||| |  ||||| ||||
-------------------------gtatatgagtcaacttgtcttctttgtttccaaatagaaaatccatcaggttcttgacatcatctttttctgcgttccagGTTTATGCAGTTCACTTCAAATGCAACAAGAGACTCTTACGGGAGTACCCGAATATCTTCAACTACATAAAAGACATTTACCAAATACACGGCATGAGTA

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g01900.t01 (Vitis vinifera), 3'ss of exon 6
taaatcattatctttagctttcctattttgggactcattttgca-atatatccatttcaat------gttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
    | |   ||   |   | | ||      |  |||||| |   || | ||  |||||||      |||  |  | ||    |  |||  | |||||||||   |||||||||| ||||| ||||| ||||||||||| || || ||||| ||||| ||||| ||||||||||||||||| |||||||| || || || || || |
---gtaaagctccaaaaaatccttacaa-aagtttcatttagtttatttctctctttcaatcaaacagttcaggatcttagaaacctgaa-tctgctataatctcagGTTTATGCAGTTCATTTCAAATGCAACAAGAAACTTCTCCGCGAGTACCCAAATCTGTTCAATTACACGAAAGAAATTTTCCAGATCCCAGGTATGAGCA

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g01890.t01 (Vitis vinifera), 3'ss of exon 6
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaa-tgttgtgactgttgagtaattgatctttgctata-at--tgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
    |   |  |  ||     |||    |     | | | |||  | ||    |   || |||| | |   |  |||   | | | |||||||| ||  || |||||||||| ||||||||||| ||||||||||| ||| |||| |||||||||||||| || |||||||  ||||||||||||||||| || ||||| || |
---gtgcatgcccatatgccccctgaaatttctttaaatatgctttttaaatttaaaaagtgttttcaaaatc-agttgctaaccgttgctatacatcatgcagGTTTATGCGGTTCACTTCAAATGCAACAAGAAACTGATACGGGAATACCCGAATCTGTTGAATTACAGCAAAGACATTTTCCAAATCCCAGGCATGAGCA

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: EFJ35587 (Selaginella moellendorffii), 3'ss of exon 4
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgt-agGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
                                      | ||   | | |   ||||    ||      |  |  | ||| |  ||   ||    ||  ||||||||| |||||| ||||||||||||||||||||| | || || ||||| || || ||||| | |   || ||| | | ||| ||   ||| ||     
--------------------------------gtaagctctggggtgtttttttttcttgctttctctcgaagttttattcaaattcattacctatgccagGTTTATGTTGTTCATTTCAAGTGCAACAAGAAGCTGATCCGTGAGTACCCAAACCTCTTCAACTTCGTCAAGGACGTGTACCAGATGGATGGGATCTCGG

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: EFJ35588 (Selaginella moellendorffii), 3'ss of exon 4
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgt-agGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
                                      | ||   | | |   ||      || |  | |  |  | ||| |  ||   ||    ||  ||||||||| |||||| ||||||||||||||||||||| | || || ||||| || || ||||| | |   || ||| | | ||| ||   | | ||     
--------------------------------gtaagctctggggtgttttttttcttgctttctctc-gaagttttattcaaattcattacctatgccagGTTTATGTTGTTCATTTCAAGTGCAACAAGAAGCTGATCCGTGAGTACCCAAACCTCTTCAACTTCGTCAAGGACGTGTACCAGATGGATCGGATCTCGG

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: EFJ11475 (Selaginella moellendorffii), 3'ss of exon 2
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
                          | ||||     ||||    |   | | | || | ||| |   |   || | ||| | || ||| |        |||||||| ||||||  |||||||||||||||||||| | || || ||||| || || ||||| | |   || ||| | | ||| ||   ||| ||     
--------------------gtaagctctggggtgttttttttcttgctttc-tctcgaagtttta--ttcagattcatt-acctatgcca--------gGTTTATGTTGTTCATGTCAAGTGCAACAAGAAGCTGATCCGTGAGTACCCAAACCTCTTCAACTTCGTCAAGGACGTGTACCAGATGGATGGGATCTCGG

upper sequence: GLYMA20G02490.3 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24322 (Selaginella moellendorffii), 3'ss of exon 4
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgact-gttgagtaattgatctttgctataattgt-agGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
                                             | | |   |||   || | |  || |  |  | ||| |  ||    |    ||  ||||||||| |||||| ||||||||||||||||||||| | || || ||||| || || ||||| | |   || ||| | | ||| ||   ||| ||     
--------------------------------------------gtgttttttttttcttgctttctctcgaagttttattcaaattcatcacctatgccagGTTTATGTTGTTCATTTCAAGTGCAACAAGAAGCTGATCCGTGAGTACCCAAACCTCTTCAACTTCGTCAAGGACGTGTACCAGATGGATGGGATCTCGG

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|120490909|gb|EH219076.1|EH219076
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|209728830|gb|BW655472.1|BW655472
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|9204775|gb|BE330999.1|BE330999
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|192313119|gb|FK004695.1|FK004695
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|13791339|gb|BG653930.1|BG653930
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|21888923|gb|BQ742136.1|BQ742136
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|120490911|gb|EH219078.1|EH219078
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|209728829|gb|BW655471.1|BW655471
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTT
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTT
EST: gi|192307449|gb|FK000777.1|FK000777
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|120491356|gb|EH219523.1|EH219523
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|213596103|gb|DB975866.1|DB975866
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|192313120|gb|FK004696.1|FK004696
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
EST: gi|15201916|gb|BI425126.1|BI425126
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA
                               aattgat  putative branch site (score: 4)
                                            tataattgta  TA-rich tract