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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA

Basic information

species Glycine max
transcript GLYMA20G02490.2
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|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|209728829|gb|BW655471.1|BW655471
EST:     TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAG                         GTTTATGCTGTT
genomic: TAACTGAAGCAGACATTCGTTTGTTTGTCACTCTTATTAGATTTGATGAGgtaaagtgtg ... ataattgtagGTTTATGCTGTT
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
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaatcattatctttagctttcctattttgggactcattttgcaatatatccatttcaatgttgtgactgttgagtaattgatctttgctataattgtagGTTTATGCTGTTCACTTCAAGTGCAACAAGAAGCTGCTACGCGAATACCCGAATCTTTTCAATTACACGAAAGACATTTTCCAAATTCCTGGCATTAGTA

- - - - - - - - gctttcc
- - - - - - - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgactg