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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcattatatattattgttctttactgtgatctatctggaagatggatggcttctaaccaaattattttatgcattag

Basic information

species Glycine max
transcript GLYMA04G40550.3
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40550.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os03g02960.1 (Oryza sativa), 5'ss of exon 2
GCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcattatata-ttattgt--tctttactgtgatctatctggaagatgga--tggcttctaaccaaattattttatgcattag
||||||||| || |||||||||||||| || || ||| ||||||| ||| ||||||| || || || || || ||| | || ||||||||| | || ||||| ||  | | |  |  |  ||    |  |    | ||     |||||||  ||  |    | |   |  | |    | ||  | ||
GCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGGAGTCAGCAGGATTACCATCAAGAGAGCCAAGAATgtaagaaactgtgcagctgctgcaaacaatctattcattcgaatggaagacagaattaatgttttctctgaatcccgtgtgtttcag

upper sequence: GLYMA04G40550.1 (Glycine max), 5'ss of exon 3
lower sequence: LOC_Os01g50360.1 (Oryza sativa), 5'ss of exon 3
GCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcattatata-ttattgttctttact--gtgatctatctggaagatgga--tggcttctaaccaaattattttatgcattag
||||||||| || |||||||||||||| || || ||| ||||||| ||| ||||||| || || || || || ||| | || ||| ||||| | || ||||| ||  | | || |  |  ||      | |   | ||     |||||||  ||  |    | |  |  |||     | ||  | ||
GCAGAGCAGGAGCGAGAAGAAGAGCCGCAAGGCCATGATGAAGCTCGGAATGAAACCCGTCACGGGAGTCAGCAGGATTACCATCGAGAGAGCCAAGAATgtaagaaactgtacagctgctgcaaacaatttattcattcgaatggaagacagagttaatgtttctctgaatc-ccgtgtgtttcag

upper sequence: GLYMA04G40550.1 (Glycine max), 5'ss of exon 3
lower sequence: AT3G49470.1 (Arabidopsis thaliana), 5'ss of exon 3
GCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcattatatattattgttctttactgtgatctatctggaagatggatggcttctaac--caaattatttta-tgc-attag
|||||| |||||||| ||||||||  | || || ||||||||||| ||  |||||||||| |||||||||||| | || || ||||||||||| ||||| || |  | || | | || || |   | | | |    | | |      ||  ||  ||||||    | | ||  ||| ||  || ||
GCAGAGTAGAAGTGAAAAGAAGAGTAGGAAGGCGATGTTGAAGCTCGGTATGAAACCTGTCACTGGTGTTAGTCGAGTAACCATCAAGAGAACGAAAAACgtaaacctttctctgtt-ttctcaataagtttagatttttttctgcgtgtgtga-ttctaatgatacactacattaatgttatcag

upper sequence: GLYMA04G40550.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0098g00830.t01 (Vitis vinifera), 5'ss of exon 3
GCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcattatatattattgttctttactgtgatctatctggaagatggatggcttctaaccaaattattttatgcattag---
||||||||||||||||||||||||||| || |||||||||||||| ||  ||||||| |||||||||||| | |||||||| || ||||||||||||||||| |   ||| | | | ||  |||| | ||   ||  |  || |  ||| |||   | || |||  || |  |  || || |   
GCAGAGCAGAAGTGAGAAGAAGAGCCGCAAGGCAATGTTGAAGCTCGGCATGAAACCCGTTACTGGTGTTGGAAGGGTCACCATTAAGAGAACAAAAAATgtaaa--attttgtctgat--ttctgttcttgtattcacttgtatcatgaatgttcttta-ccagtttttcctgggc-ttggcag

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|31469185|gb|CD411213.1|CD411213
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|209720038|gb|BW651107.1|BW651107
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|31459753|gb|CD401781.1|CD401781
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACTGTAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|31310248|gb|CD395451.1|CD395451
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCCAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|31462171|gb|CD404199.1|CD404199
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACCAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|8826871|gb|BE210601.1|BE210601
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|254337610|gb|GR849456.1|GR849456
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|4307759|gb|AI444093.1|AI444093
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|31309197|gb|CD394400.1|CD394400
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|120534441|gb|EH262574.1|EH262574
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|31476067|gb|CD418095.1|CD418095
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACCATAAAT                         ATTCTTTTCTTCATCTCCAAACCCGATGTCTTCAAGAGTCCCAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|31468820|gb|CD410848.1|CD410848
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|31463939|gb|CD405967.1|CD405967
EST:     GAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: GAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
EST: gi|14009231|gb|BG725835.1|BG725835
EST:     TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAAT                         ATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG
genomic: TGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcatt ... tatgcattagATTCTTTTCTTCATCTCAAAACCCGATGTCTTCAAGAGTCCAAATTCTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAGCAGAAGTGAGAAGAAGAGCCGAAAAGCAATGTTGAAGCTGGGACTGAAACCTGTTACTGGTGTTAGTAGGGTCACAATCAAGAGAACAAAAAATgtgagtcattatatattattgttctttactgtgatctatctggaagatggatggcttctaaccaaattattttatgcattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA