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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGGAAATAGCTGACTTAATCAGAGGATTAGGTTTAACCATCTTGAAGGGAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaagggaaataactgatcataactcagaagtataatgaacttcctatagtataattcagtatttgtagcctttaatatttgaacattttcagc...

Basic information

species Glycine max
transcript GLYMA12G09990.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G09990.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os01g64560.2 (Oryza sativa), 5'ss of exon 9
TCTGGAAATAGCTGACTTAATCAGAGGATTAGGTTTAACCATCTTGAAGGGAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaagggaaataactgatcataactcagaagta----taatgaacttcctatagtataattcagtattt-gtagcctttaatatttgaacattttcagc--------------------------------------------------------------------
  |||||||||||||   ||| ||||| ||||| || || |||||||| || || ||||||| ||| || || ||||| ||||| |||||||||||||||||| ||||           ||      |||| || |  |    | ||||   ||   |  | |     |  |    | |   |   ||  | |     ||| |                                                                      
CTTGGAAATAGCTGATCAAATTAGAGGTTTAGGGTTGACTATCTTGAAAGGTGTGATGGAAGTTCGTAAAGATAAGATTTGGGCTCGCTTTGCTGTTGAGgtattaaatctttcctcgtctctcttcaacttagtaccagttcttatgactatcaatttttctgccaaaacaccaagcaaaatcacattctagcgtgatttgattatgaagctacaagtggtgtggactgagtagtatatcaaagtttaattaaaatattgaaatttctgcag

upper sequence: GLYMA12G09990.1 (Glycine max), 5'ss of exon 4
lower sequence: LOC_Os12g06330.1 (Oryza sativa), 5'ss of exon 9
TCTGGAAATAGCTGACTTAATCAGAGGATTAGGTTTAACCATCTTGAAGGGAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaagggaaataactgatcataactcagaagtataatgaacttcctatagtataattcagtatt-tgtagcctttaatatttgaacattttca-gc--
  |||| ||||||||||| |||| |||| | || ||||| ||||||| ||| || |||||||| |||||  | || |||||||| |||||  | ||||||||||   |  |  |  ||  |||  |        |  | |  |  |||    ||   | ||     |||  |  |  || ||| ||||||  ||   || ||  
CTTGGAGATAGCTGACTTCATCAAAGGACTTGGATTAACTATCTTGAGGGGTGTGATGGAAGCACGCAAAAATAAAATCTGGGCTCGCTTCACCGTTGAGgtaa-gcagcgcaatgtatttgagaaagctctctagttttggttcactatgaatgcaagaacatcttatcctacatgctgtaacatttgattatacccatgcag

upper sequence: GLYMA12G09990.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G031656_T01 (Zea mays), 5'ss of exon 9
TCTGGAAATAGCTGACTTAATCAGAGGATTAGGTTTAACCATCTTGAAGGGAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaa--------------taaaaaggg---aaataactgatcataactcagaag--tataatgaacttcctatag----tataattcagtatttgtagcctttaatatttgaacattttcagc--------------------------------------
  |||| ||||||||||| || | |||| | || ||||||||||| | ||| ||||||||||| |||||  | || ||||||||||| ||  ||||||||||||              ||| ||||      |     | | | ||||||||||  |  |||    | ||   ||    | | ||||  |   |  |    ||    ||    || | || ||                                      
CTTGGAGATAGCTGACTTTATTAAAGGACTCGGATTAACCATCTTAAGGGGCGTCATGGAAGCACGCAAAAATAAAATCTGGGCACGGTTCACTGTTGAGgtaagcagttcaatgcattaagaaggttctctaggttggctgagaactcagaaggcttgaatagcttccccccagagcatgttattccatgactagatttcttttgcttcctccactgtctgctctatggaagttctcattttactttgtttattatgcag

upper sequence: GLYMA12G09990.1 (Glycine max), 5'ss of exon 4
lower sequence: GRMZM2G069408_T01 (Zea mays), 5'ss of exon 9
TCTGGAAATAGCTGACTTAATCAGAGGATTAGGTTTAACCATCTTGAAGGGAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaa----------agggaaat------aactgatc-ataactcagaag--tataatgaacttcc--tatag-----tataattca-gtatttgtagcctttaat-atttgaacattttcagc-----------------------------------------------------------
  |||| ||||||||||| || | |||| |||| ||||||||||| | ||| || |||||||| |||||  | || ||||||||||| ||  ||||||||||||  |            | | |  |         || |  |  |||||||||  || | |    ||||  |||||     |||| ||   || | |||   |||| || | | ||   ||||  ||                                                           
CTTGGAGATAGCTGACTTCATTAAAGGACTAGGATTAACCATCTTAAGGGGCGTTATGGAAGCACGCAAAAATAAAATCTGGGCACGGTTCACTGTTGAGgtaagcagttcagtgcattatgaaggttctctaggttggttgagtactcagaaggctagagtagttttcccttatagcatgttatagtttgtgtgtgtgttatctttcatgagtagatttttttttgcttcctcaactcaactgtctgctttatggacgttcttgttttactttgtttattatgcag

upper sequence: GLYMA12G09990.1 (Glycine max), 5'ss of exon 4
lower sequence: AT2G27230.2 (Arabidopsis thaliana), 5'ss of exon 8
TCTGGAAATAGCTGACTTAATCAGAGGATTAGGTTTAACCATCTTGAAGGGAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgta-ataaaaagggaaataactgatcat--aactcagaagtataatgaacttcctatagtataattcagt--atttgtagcct--ttaatatttgaacattttcagc
||| ||||| || || |  |||||| | ||||| ||||| ||||||||||||||||| ||| ||||    |||||||| ||||| |||||  ||||||||||| || | |   |  | |   | |  |  ||||  |||  || | ||   |  || | | ||  | | |  |  || | ||   |  ||||| ||   |       
TCTAGAAATCGCAGATTGGATCAGAAGCTTAGGGTTAACGATCTTGAAGGGAGTCATCGAAACTCGAGTAGACAAGATTTGGGCTCGCTTCACTGTTGAGgtatattatataagttacacaaggttgtttaacttggaaagatga-gattgtgttagaatgtatcttatttaaactgaaaccgggtcgatattggattgtag-----

upper sequence: GLYMA12G09990.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv06s0009g00440.t01 (Vitis vinifera), 5'ss of exon 9
TCTGGAAATAGCTGACTTAATCAGAGGATTAGGTTTAACCATCTTGAAGGGAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaagggaa-ataactgatcataactcagaagtataatgaacttcctatagtataattcagtatttgtagcctttaatatttgaacattttcagc
||| |||||||||||  |||| |||||  | || || |||||| |||| || || |||||| |||| |||||||||||||||||||||||| |||| |||||||   |    ||  ||   || || |  |       |||  |  |  |  | || |    |  | ||    ||   || |   |   |   | ||  | 
TCTAGAAATAGCTGATATAATTAGAGGGATGGGATTGACCATCCTGAAAGGGGTGATGGAAACTCGGAATGACAAGATCTGGGCACGCTTTACTGTAGAGgtaaactacccagagtattcttgctcttgccaagtggctattttttatcttgt-taattgcttctaataggaataaagttcatgctgatagtttatttgga

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|254315695|gb|GR825504.1|GR825504
EST:     GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAG                         GCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
genomic: GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaa ... tgctttgcagGCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
EST: gi|6667338|gb|AW278789.1|AW278789
EST:     GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAG                         GCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
genomic: GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaa ... tgctttgcagGCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
EST: gi|13791477|gb|BG654068.1|BG654068
EST:     GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAG                         GCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
genomic: GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaa ... tgctttgcagGCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
EST: gi|254335547|gb|GR847075.1|GR847075
EST:     CGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAG                         GCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
genomic: CGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaa ... tgctttgcagGCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
EST: gi|19269654|gb|BM885910.1|BM885910
EST:     GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAG                         GCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
genomic: GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaa ... tgctttgcagGCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
EST: gi|298190070|gb|HO032191.1|HO032191
EST:     GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAG                         GCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
genomic: GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaa ... tgctttgcagGCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
EST: gi|207760262|gb|GD732689.1|GD732689
EST:     GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAG                         GCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCA
genomic: GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaa ... tgctttgcagGCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCA
EST: gi|21677028|gb|BQ629379.1|BQ629379
EST:     GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAG                         GCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
genomic: GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaa ... tgctttgcagGCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
EST: gi|4436966|gb|AI522831.1|AI522831
EST:     GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAG                         GCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT
genomic: GAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaa ... tgctttgcagGCAAACAGGGATGTAACCAGGATGGAAATATTTATGTCACTGGTTCGTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGGAAATAGCTGACTTAATCAGAGGATTAGGTTTAACCATCTTGAAGGGAGTCATGGAAGCTCGCAATGACAAGATCTGGGCACGCTTTGCTGTTGAGgtaataaaaagggaaataactgatcataactcagaagtataatgaacttcctatagtataattcagtatttgtagcctttaatatttgaacattttcagc

- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggaaataa