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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacgggttggtgtgcgtgggacgtgttggtgtgcgtatgcttggcttcctttccctctggctgctttgtggggctgggtttgtatgcattggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC

Basic information

species Glycine max
transcript GLYMA16G23920.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23920.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os04g02000.1 (Oryza sativa), 3'ss of exon 1
----gacgggttggtgtgcgtgggacgtgttggtgtgcgtatgcttggcttcctt-tccctctggctgctttgtggggctgggtttgtatgc--attggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC
       ||||| ||| | |  ||  | |||||||||||| ||||| | | | || || | ||||      ||||  | | ||||| |  ||  | ||||  ||||||||||| |||||| ||||||||||| ||| |||| ||||| || || || |  || ||||||| |||||| ||||||||| |  | ||| | |||    |
tttcattgggtttgtgcgggatggctg-gttggtgtgcgtgtgcttcggtgcgttgtctccctgg------tgtgctggttggtttatgcgccaaatggatgaatagGTTGCAGTAACAATAATTATGCATCCAGAAAGAACTGCAAAAAATGTGGCCTGCCGAAGGAGGAAGCAGCAATGCCAGCATTATCAATGGCAGGAATGGC

upper sequence: GLYMA16G23920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G162353_T05 (Zea mays), 3'ss of exon 1
gacgggttggtgtgcgtgggacgtgttggtgtgcgtatgcttggcttcctttccctctggctgctttgtggggctgggtttgtatgcattggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC----------------------------
                           ||||||||| | ||| | | | |||  ||  | ||||| ||  ||   |  | ||     | ||||  ||||||||||| |||||| ||||||||||| ||| |||| ||||| ||||| || | | | ||||||| |||||| ||||||||| |    ||| | ||     |                            
--------------------------gggtgtgcgtgtccttcggtgcgttttgct--gcctgctgtgctggttggtttatgcggcaaatggatgaataggttgcagtaacaataattatgcatccagAAAGAACTGCAAAAAGTGTGGCCTATCCAAGGAGGAAGCAGCAATGCCAGCATTGCAAATGGCAGGGATGGCTATGCCAGCTTATGCAACTTATATCGCA

upper sequence: GLYMA16G23920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G162353_T01 (Zea mays), 3'ss of exon 1
-gacgggttgg-tgtgcgtgggacgtgttggtgtgcgtatgcttggcttcctttccctctggctgctttgtggggctgggtttgtatgcattggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC
   |||| ||| ||  | | |     || ||||||||| | ||| | | | |||  ||  | ||||| ||  ||   |  | ||     | ||||  ||||||||||| |||||| ||||||||||| ||| |||| ||||| ||||| || | | | ||||||| |||||| ||||||||| |    ||| | ||     |
gtccgggatggctggtcatcgtggtggtgggtgtgcgtgtccttcggtgcgttttgct--gcctgctgtgctggttggtttatgcggcaaatggatgaatagGTTGCAGTAACAATAATTATGCATCCAGAAAGAACTGCAAAAAGTGTGGCCTATCCAAGGAGGAAGCAGCAATGCCAGCATTGCAAATGGCAGGGATGGC

upper sequence: GLYMA16G23920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G149698_T04 (Zea mays), 3'ss of exon 1
-gacgggttgg-tgtgcgtgggacgtgttggtgtgcgtatgcttggcttcctttccctctggctgctttgtggggctgggtttgtatgc--attggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC
   || | ||| ||  | |||     || |||||| || ||||| | | | |||  ||  | || || ||  ||  ||||||| |  |   | ||||  ||||||||||| |||||| ||||||||||| ||| |||| ||||| ||||| ||    || ||||||| |||||| ||||||||| |    ||| | ||     |
gtgcgtgatggctggtcatggtggtggtgggtgtgggtgtgcttcggtgcgttttgct--gcctactgtgctgg--tgggtttatgcggcaaatggatgaatagGTTGCAGTAACAATAATTATGCATCCAGAAAGAACTGCAAAAAGTGTGGCTTGCCCAAGGAGGAAGCAGCAATGCCAGCATTGCAAATGGCAGGGATGAC

upper sequence: GLYMA16G23920.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G088539_T01 (Zea mays), 3'ss of exon 1
-gacgggttgg-tgtgcgtgggacgtgttggtgtgcgtatgcttggcttcctttccctctggctgctttgtggggctgggtttgtatgcattggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC
   || | ||| ||  | |||     || |||||| || ||||| | | | |||  ||  | || || ||  ||   |  | ||     | ||||  ||||||||||| |||||| ||||||||||| ||| |||| ||||| ||||| ||    || ||||||| |||||| ||||||||| |    ||| | ||     |
gtgcgtgatggctggtcatggtggtggtgggtgtgggtgtgcttcggtgcgttttgct--gcctactgtgctggttggtttatgcggcaaatggatgaatagGTTGCAGTAACAATAATTATGCATCCAGAAAGAACTGCAAAAAGTGTGGCTTGCCCAAGGAGGAAGCAGCAATGCCAGCATTGCAAATGGCAGGGATGGC

upper sequence: GLYMA16G23920.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G17975.1 (Arabidopsis thaliana), 3'ss of exon 1
---gacgggttggtgtgcgtgggacgtgttggtgtgcgtatgcttggcttcctttccctctggctgctttgtggggctgggtttgtatgcattggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC
    |   | ||||| | |||    ||| || || | |  ||  |  |||| |    ||  |  |    | ||||  || | |    ||   ||   |||||||||| ||||||||||||||||||||| |||| ||||||||||| || || ||| | ||||| ||||||||  || ||||| |||| ||  | ||||| ||
tggaatttgctggtgggtgtgt--tgtggtg-tgcgtgcgtgtgtatcttcttcgttctacgttttgcgtttgggtgtgtggtgtggtgtggtgtggcaatagGTTGTACTAACAACAATTATGCATCACGAGAAAAGTGCAAGAAATGTGGGCAATCTAAGGAAGTAGCAGCATTGTCAGCACTTGCTATCCCTGGAGCTTC

upper sequence: GLYMA16G23920.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0023g03280.t01 (Vitis vinifera), 3'ss of exon 1
gacgggttggtgtgcgtgggacgtgttggtgtgcgtatgcttggcttcctttccctctggctgctttg---tggggctgggtttgtatg-cattggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC
      ||||| || |  || |  |||||||||||||| ||||||||||||| |||||  |||  | |     ||| ||||| |||||| || |||| |||||||||||||||||||||||||||| ||| |||| |||||||| ||||||||||||||||||||| ||||||| |||||||| ||||| ||| | ||||| ||
----ttttggtctgggatgggctggttggtgtgcgtatacttggcttccttttcctctccctggctggattctgggttgggtgtgtatggcaatggatcaatagGTTGCACTAACAACAATTATGCGTCACGAGAAAAGTGCAAAAAGTGCGGACAACCAAAGGAGATAGCAGCAATGCCAGCGATTGCAATGCCTGGAGCTTC

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|151408697|gb|EV278505.1|EV278505
EST:     CCCCGCTGATTCCAAGTGGCTCCCCCGTATCGGCGATCGGATCTGCACCG                         GTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGAC
genomic: CCCCGCTGATTCCAAGTGGCTCCCCCGTATCGGCGATTGGATCTGCACCGgttagttttg ... ggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGAC
EST: gi|298191616|gb|HO039095.1|HO039095
EST:     CCCCGCTGATTCCAAGTGGCTCCCCCGTATCGGCGATTGGATCTGCACCG                         GTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGAC
genomic: CCCCGCTGATTCCAAGTGGCTCCCCCGTATCGGCGATTGGATCTGCACCGgttagttttg ... ggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGAC
EST: gi|192295986|gb|FG993379.1|FG993379
EST:     CCCCGCTGATTCCAAGTGGCTCCCCCGTATCGGCGATTGGATCTGCACCG                         GTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGAC
genomic: CCCCGCTGATTCCAAGTGGCTCCCCCGTATCGGCGATTGGATCTGCACCGgttagttttg ... ggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGAC
EST: gi|298192757|gb|HO033191.1|HO033191
EST:     CCCCGCTGATTCCAAGTGGCTCCCCCGTATCGGCGATTGGATCTGCACCG                         GTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGAC
genomic: CCCCGCTGATTCCAAGTGGCTCCCCCGTATCGGCGATTGGATCTGCACCGgttagttttg ... ggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctttccctctggctgctttgtggggctgggtttgtatgcattggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC
                                 tttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacgggttggtgtgcgtgggacgtgttggtgtgcgtatgcttggcttcctttccctctggctgctttgtggggctgggtttgtatgcattggaacaatagGTTGCACTAACAACAATTATGCATCAAGAGAGAAGTGCAAGAAGTGCGGACAACCAAAGGAGGTAGCAGCCATGCCAGCAATTGCGATGACCGGAGCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- -gggttgg
- - - -tggtgtg
- - - - - - -gcgtggg
- - - - - - - - - - - - - - - - - gtatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggctggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtatgca