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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtatgtatgcatatttctatttgtgtatatatatatatatatgtgtgtgtgtgtgtcaaaattgcctcctcaactaacctgttgatcatgcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAAAGGAATATCAGCAAGCGATGTAGTTGTTGACTTCGGTGAACAGATG

Basic information

species Glycine max
transcript GLYMA11G02340.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G02340.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv02s0025g00450.t01 (Vitis vinifera), 3'ss of exon 5
tgtatgtatgcatatttctatttgtgtatatatatatatatatgtgtgtgtgtgtgtcaaaattgcctcctcaacta----acctgttgatcatgctta---accagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAAAGGAATATCAGCAAGCGATGTAGTTGTTGACTTCGGTGAACAGATG
       |   | ||      || | | || | |     ||    |    |  || |   || | |   |||| ||        || |||  ||   ||   | |||||||||||||||||||||||| || ||||||||||||||| |||||||||| || ||| ||| ||   | || || ||| |||| | || |||||  
-------acttacatgctagcttatctttacacaatagcattgacgaagttacgtttttgaactactgtctcagctgtatggtttgctgacaataaatatttaacagGCATGAATACTACCAGAAGCCTGAGGAAGTGGTTGTGACAATATTTGCAAAGGGTATACCAGAAAATAACGTGGTCGTTCACTTTGCTGTACAGACA
















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|208294967|gb|GE091188.1|GE091188
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGT
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGT
EST: gi|207780523|gb|GD751716.1|GD751716
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|193676052|gb|FK617826.1|FK617826
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|193395648|gb|FK362215.1|FK362215
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|207704051|gb|GD684977.1|GD684977
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|193498042|gb|FK458754.1|FK458754
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|208138863|gb|GD938105.1|GD938105
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|207825580|gb|GD797291.1|GD797291
EST:     GTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: GTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAA-GACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|208316882|gb|GE112751.1|GE112751
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|208107647|gb|GD903433.1|GD903433
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         ACATGAATACTACCA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCA
EST: gi|9439962|gb|BE440474.1|BE440474
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATNTGCA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCA
EST: gi|207736936|gb|GD709511.1|GD709511
EST:     GTTTGGTATCCCAAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: GTTTGGTATCCC-AAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|192329164|gb|FK021459.1|FK021459
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|208092101|gb|GD889306.1|GD889306
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|193592990|gb|FK548826.1|FK548826
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCNCACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|208057839|gb|GD858542.1|GD858542
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAGTACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|193694983|gb|FK634355.1|FK634355
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|208028133|gb|GD822247.1|GD822247
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGG
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGG
EST: gi|193556529|gb|FK515182.1|FK515182
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|207825464|gb|GD799345.1|GD799345
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|193461286|gb|FK428825.1|FK428825
EST:     AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAG                         GCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
genomic: AGTTTGGTATCCCAAAAGAATGAAGCCACACTAAAAAGACCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAA
EST: gi|193320943|gb|FK287696.1|FK287696
EST:     CCAAAATACAG                         GCATGAATACTACCAGTAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAA
genomic: CCAAAATACAGgttctcactc ... gcttaaccagGCATGAATACTACCAG-AAGCCAGAAGAAGTGGTTGTGACACTATTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgtgtgtgtcaaaattgcctcctcaactaacctgttgatcatgcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAAAGGAATATCAGCAAGCGATGTAGTTGTTGACTTCGGTGAACAGATG
           tcaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatgtatgcatatttctatttgtgtatatatatatatatatgtgtgtgtgtgtgtcaaaattgcctcctcaactaacctgttgatcatgcttaaccagGCATGAATACTACCAGAAGCCAGAAGAAGTGGTTGTGACACTATTTGCAAAAGGAATATCAGCAAGCGATGTAGTTGTTGACTTCGGTGAACAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - -gtatgca
- - - - - - - - - - tttgtgt
- - - - - - - - - - - - - - - - - - - - - tgtgtgt
- - - - - - - - - - - - - - - - - - - - - -gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgttg