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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcctttattatcctttttccaccagatcaataaagaaattctttattttctaaggacattgctaccatatgcag

Basic information

species Glycine max
transcript GLYMA19G22530.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os01g70960.1 (Oryza sativa), 5'ss of exon 7
ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcctttattatcctttttccaccagatcaataaagaaattctttattttctaaggacat--tgctaccat-atgcag-
||||| |||||| |||| || ||| || | ||||| ||||| ||||||||||||||||||||||||||     || |  |   ||| | |   |   |  |  ||     | | || ||| |||||   | |  | ||   ||  |||   
ATGGGAAAAGATGTTGTCTCGTTCTTGTCATGGGCGGCGGAGCCTGAGATGGAAGAGAGAAAACTGgtaaccctcttggaacctccctgtagaatt-gtcctctatttctactgttaattgtctaatttcttcatactggaattgtgctag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 7
lower sequence: LOC_Os05g23620.1 (Oryza sativa), 5'ss of exon 8
ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgt--ttgtttcctttattatcc-tttttccaccagatcaataaagaaattctttattttctaaggacattgctaccatatgcag
||||| || ||| | || || ||| || | ||||| || |||||||||||||||||||| ||||||||  |    ||   | || ||| ||| |  |  |  |  |    | |||  ||  |  |   |    | |   |    ||| ||
ATGGGCAAGGATGTCGTTTCGTTCTTGTCATGGGCAGCTGAACCTGAGATGGAAGAGAGGAAACTGgtaatcagctcaacttttgtccatttatatattactttcaattcgcaatatttcctaataccaacctactctaatttgatgtag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G032367_T04 (Zea mays), 5'ss of exon 6
ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgt--ttgtttcctttattatcctttttccaccagatcaataaagaaattctttattttctaaggacattgctaccatatgcag-----------------
|||||||| ||| |||||||||||||  | ||||| || || |||||||||||||||||||| |||||       ||     |||  |  ||  |  ||| |       |    | || | |||   |  | | |  | |      ||                  
ATGGGTAAGGATGTTGTATCATTCCTTTCATGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacctcgcgacttaatcaattaactgcagtttg-cgctgttgcttttcaatttgctataatacttatcctgatcacaactcaaatttcatggtag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G158479_T01 (Zea mays), 5'ss of exon 6
----------------------------------ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtt-tgtttcctttattatcctttttccaccagatcaataaagaaattctttattttctaaggacattgctaccatatgcag---------------
                                  |||||||| ||| | |||||||||||  | ||||| || || |||||||||||||||||||| |||||        ||| | |    |   ||     | || ||    |     |||  |     |   | |    || ||   |                 
CAGGACTAAAGTTTGATCACTCATATTCCCTCAGATGGGTAAGGATGTCGTATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacctcttgacttaaatcgctcagattgctctattgctattcaatttgctactccatatcctgatcacaatccactcaaaaatccattgtag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 7
lower sequence: GRMZM2G158479_T04 (Zea mays), 5'ss of exon 7
ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtt-tgtttcctttattatcctttttccaccagatcaataaagaaattctttattttctaaggacattgctaccatatgcag---------------
|||||||| ||| | |||||||||||  | ||||| || || |||||||||||||||||||| |||||        ||| | |    |   ||     | || ||    |     |||  |     |   | |    || ||   |                 
ATGGGTAAGGATGTCGTATCATTCCTTTCGTGGGCAGCTGAGCCTGAGATGGAAGAGAGAAAGCTGgtaacaacctcttgacttaaatcgctcagattgctctattgctattcaatttgctactccatatcctgatcacaatccactcaaaaatccattgtag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 7
lower sequence: AT3G27240.1 (Arabidopsis thaliana), 5'ss of exon 7
ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcctttattatcctttttccaccagatcaataaagaaattctttattttctaaggacattgctaccatatgcag-------------------------
|||||||||||||||||||||||| || | ||||| || ||||| || ||||||||||| ||||||||  ||||     ||  | || | | | |  | | || |  | | ||  |   |     | |  |||  ||| | ||  ||                         
ATGGGTAAAGATATTGTATCATTCTTGGCCTGGGCAGCTGAACCAGAAATGGAAGAGAGGAAACTGgtaggttt-----atctttctctgttcgct-ggtgaacattgtattttctccctagactatgcaattaatactagatttagtttatgatcgatcaagttgacttag

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 7
lower sequence: AT5G40810.2 (Arabidopsis thaliana), 5'ss of exon 6
ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcctttattatcctttttccaccagatcaataaagaaattctttattttctaagg-acattgctaccat--atgcag------------------
|||||||||||| ||||||| ||| || | ||||| || ||||| |||||||||||||| ||| ||||  |||||  ||| | || | | | |      | ||        |||  ||| | | |     || |   |  ||  ||   |                  
ATGGGTAAAGATGTTGTATCCTTCTTGTCCTGGGCAGCTGAACCAGAGATGGAAGAGAGGAAATTGgtaagtttc--ttagtttcatatattccatgttttaagctgtcgtttccatatgtacgagattgcaataggaatatcaatctggattctgattatttgattt

upper sequence: GLYMA19G22530.2 (Glycine max), 5'ss of exon 7
lower sequence: Vv14s0171g00330.t01 (Vitis vinifera), 5'ss of exon 7
ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcctttattatcctttttccacca-gatcaataaag---aaattctttattttctaaggacattgctaccatatgcag
||||| |||||| ||||||||||  |||| ||||| |||||||| ||||||||||| || ||||||||   ||  |||    || |  | ||||  | ||| | ||||    |  || |||||    | ||   ||  || | | ||||||
ATGGGGAAAGATGTTGTATCATTTTTGACATGGGCAGCGGAACCAGAGATGGAAGAAAGGAAACTGgtaatttggcttctgaattccctgtccattatgatgagtaaaatttagtttgtttatgactttag---atctcttcaaaatgcag

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|151407875|gb|EV277690.1|EV277690
EST:     TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|6951794|gb|AW423862.1|AW423862
EST:     TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|9984923|gb|BE659031.1|BE659031
EST:     TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|21595027|gb|BQ610344.1|BQ610344
EST:     TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|13479755|gb|BG509098.1|BG509098
EST:     TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|17401890|gb|BM178672.1|BM178672
EST:     TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|151405084|gb|EV274898.1|EV274898
EST:     GGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: GGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|5760158|gb|AI965521.1|AI965521
EST:     GGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: GGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|192306981|gb|FG999986.1|FG999986
EST:     TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|14008807|gb|BG725411.1|BG725411
EST:     TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
EST: gi|9203731|gb|BE329955.1|BE329955
EST:     TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTG                         ATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC
genomic: TATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcc ... ccatatgcagATGGGATTCAAATGGATATTTGTTCTATCACTGGCATTACTTCAAGCTGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGGGTAAAGATATTGTATCATTCCTGACTTGGGCTGCGGAACCTGAGATGGAAGAGAGAAAACTGgtttgtttcctttattatcctttttccaccagatcaataaagaaattctttattttctaaggacattgctaccatatgcag

- - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA