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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtccttctttgtacttatattgtcctctgctattttaatagtttagtctactatgatgctttgaagagaccacttatattctggtgatatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGATG

Basic information

species Glycine max
transcript GLYMA11G07910.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G07910.1 (Glycine max), 3'ss of exon 13
lower sequence: GRMZM2G116434_T01 (Zea mays), 3'ss of exon 13
gtgtgtccttctttgtacttatattgtcctctgctattttaatagtttagtctactatgatgctttgaagagaccacttat-attctggtgatatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGATG
                     | || |    |   | |  ||   | |   |  || ||    |  || | |||  | | | ||| |  ||   |    |||||||||| || ||||||||||||||  | || |||||||||||||||     
----------------gtgggtgttattagatcacactccaaatctgtgtccccctgtgtatatcagatgtgacatcgtgttatttttatgg-gtcaatagGTGATGAAAAACGGATATATTGCAACTGTCACCCTCTTCCAATCATGAG----

upper sequence: GLYMA11G07910.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv04s0023g02970.t01 (Vitis vinifera), 3'ss of exon 13
---------------------------------------------------------------------------gtgtgtccttctttgtacttatattgtcctctgctattttaatagtttagtctactatgatgctt--tgaagagaccacttata----ttctggtgatatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGATG---------
                                                                            |||     |   | ||  ||| | ||    ||  |   | |   || | | |  |  | |  |   ||| ||||    | | |    |  || ||||| | |||||| |||||||||||||||||||||||  ||||||||||||| || |||| |           
gtgggttattgatgaatactcaatccatgtgttttgctttggaaacttctttatctattcaaagcaaccaccaccatgttctgattgctttatgtatttcgttaaatggcacaatcaattttcaatttcttcagtttatgggtgaggagattcttaacaaagatcttgctgatact-gcagGTAATGAAGAATGGATATATTGCAACTGTAACTCTCTTCCAGTCGTGATTAAACATTGAATG
















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|11687754|gb|BF595430.1|BF595430
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|51343377|gb|CO984110.1|CO984110
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|18039193|gb|BM307487.1|BM307487
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|192324841|gb|FK015352.1|FK015352
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|254331134|gb|GR843253.1|GR843253
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|21257365|gb|BQ454253.1|BQ454253
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|213597190|gb|DB981582.1|DB981582
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|5666923|gb|AI930959.1|AI930959
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|9984165|gb|BE658273.1|BE658273
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|18720306|gb|BM523249.1|BM523249
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|120533133|gb|EH261266.1|EH261266
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|254331133|gb|GR843252.1|GR843252
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|120533498|gb|EH261631.1|EH261631
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
EST: gi|11689775|gb|BF597451.1|BF597451
EST:     ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAG                         GTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA
genomic: ACCCCTTTGGTTCTACTCTTGTATATGGTTATCAAAATATTGCCTTTGAGgtgtgtcctt ... atatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagtctactatgatgctttgaagagaccacttatattctggtgatatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGATG
                              acttatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtccttctttgtacttatattgtcctctgctattttaatagtttagtctactatgatgctttgaagagaccacttatattctggtgatatttgcagGTGATGAAGAATGGATATATTGCAACAATAACTCTCTTCCAATCATGATGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA