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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatattatcttcatgattctactctttggtatccctgttatatagtagtcagcatgttataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA

Basic information

species Glycine max
transcript GLYMA17G10640.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 5
-----ttatatattat--cttcatgat-tctactctttggtatccctgttatatagtagtcagcatgttataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA
       |||| | ||    ||| ||  |  ||   ||     |  | | ||  | |   | |     ||    ||||| |||     |   ||||| |      |||||  ||||||| ||||| ||||||||||| ||||| ||||| ||||| || ||  | || ||||||||||||||||| ||||| |||| |||| | || |
acaatgcatatttcatggactcaagacattgacatattacaggcaatttcattgatttaactgttcagtacttctatttcctgc----tttgtattatttc----cagTCGCTGCTTTGCGATCCAAACCCAAATTCACCTGCCAACTCTGAAGCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGA

upper sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 5
ttatatattatcttcatgattctactctttggtatccctgttatatagtagtcagcatgttataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA----------------------------------------------
                                      | | ||  | |   | |     ||    ||||| |||     |   ||||| |      |||||  ||||||| ||||| ||||||||||| ||||| ||||| ||||| || ||  | || ||||||||||||||||| ||||| |||| |||| | || |                                              
--------------------------------------tttcattgatttaactgttcagtacttctatttcctgc----tttgtattatttc----cagtcgctgctttgcgatccaaacccaaattcacctgccaactctgaagCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGATAGTGGAGCAGAGCTGGACCGCGGACTGATCCACTCCATCTAACCA

upper sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
------------ttatatattatcttcatgattctactctttggtatccctgttatatagtagtcagcatgt-tataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA
            ||||  |||||  | ||| |  ||  |      |||  || |      ||    || ||| | | | ||   |     || |   |   | |     |||||||||| | || ||||| ||||| ||||| || || ||||| ||||| || || ||||| || ||||||||||| |||||||| || | |||| | ||  
tgccatcgctgtttatgaattattatgatgttcttaaacc-----atctgtgctgatggctacagtgcgtgtgtgtgactaacct----gaggtttgtgccattt----gcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG

upper sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g05820.t01 (Vitis vinifera), 3'ss of exon 5
-ttatatattatcttca--tgattctactctttggta--tccctgttatatagtagtcagcatgttataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA
  | |  |||   | ||  | |      |||||| ||  | |  ||||  |  | |  |  |   || | | || |||| |    |    ||     ||  ||||||| |||| |||||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||| ||||| ||||||||  ||||||| || ||||
actctggattgcttacaagtaagatggatctttgttaaattcaagttacctcat-gcaaatactctaca-tgatgttctaac---ttttcatcctcttgttgcagTCACTGCTCTGTGATCCCAACCCCAATTCTCCTGCAAATTCAGAAGCTGCTCGGATGTTTAGTGAGAATAAGCGTGAGTACAACAGAAGAGTGAGGGAAA

upper sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ16328 (Selaginella moellendorffii), 3'ss of exon 4
ttatatattatcttcatgattctactctttggtatccctgttatatagtagtcagcatgttataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA
                           |||||| |   || |      | ||  | ||         | ||||| | |  |||  ||         ||||||| ||||||||||||| |||||||| || || || ||||| |||||||| || |||| ||||||||||   || |||||||| || |||||  | || |
--------------------------gtttggtttttttgct-cgcctttgttggaatag-------actttcttacacttacccatc--------gcagTCACTGCTTTGTGATCCTAACCCAAACTCGCCGGCGAACTCCGAAGCAGCGCGGATGTATAGTGAGAACCGTCGAGAGTACAACCGGAGAGTCCGCGACA

upper sequence: GLYMA17G10640.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ17802 (Selaginella moellendorffii), 3'ss of exon 4
ttatatattatcttcatgattctactctttggtatccctgttatatagtagtcagcatgttataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA
                           |||||| |   | |       | ||  | ||         | |||||         | | |  ||    ||||||| ||||||||||||| |||||||| || || |||||||| |||||||| || |||| ||| ||||||   || |||||||| || |||||  | || |
--------------------------gtttggt-tttttttctcgcctttgttggaatag-------actttct--------tacacttatccatcgcagTCACTGCTTTGTGATCCTAACCCAAACTCGCCGGCAAACTCCGAAGCAGCACGGATGTATAGCGAGAACCGTCGAGAGTACAACCGGAGAGTCCGCGACA

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|6846800|gb|AW349090.1|AW349090
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|15001308|gb|BI322122.1|BI322122
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|151412180|gb|EV281992.1|EV281992
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|254317222|gb|GR826167.1|GR826167
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|8284603|gb|BE022162.1|BE022162
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
EST: gi|10235145|gb|BE804033.1|BE804033
EST:     ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAG                         TCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT
genomic: ACCAGTGGAGTCCTATATATGATGTAGCTGCTATACTCACTTCTATCCAGgtattatctt ... tctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtagtcagcatgttataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA
                                         ttactct  CT-rich tract
              ttataattattttctg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatattatcttcatgattctactctttggtatccctgttatatagtagtcagcatgttataattattttctgaaagatacatattactctgcggcagTCATTGCTTTGTGATCCCAACCCAAATTCTCCTGCAAACTCAGAAGCAGCTCGAATGTTTAGTGAGAACAAGCGGGAGTACAATCGAAGAGTTAGAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA