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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaatgaaagccatctttactttctcagtaacattcttaaatgcaaattggttttgtgaacatgaggttgctttccactgacattttcatccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCATTGGTGATCCTCCTGAGGAGAGATTTGACTTGGCATTCTGTGGAAGCCTT

Basic information

species Glycine max
transcript GLYMA04G36600.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G36600.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G48420.1 (Arabidopsis thaliana), 3'ss of exon 7
agaatgaaagccatctttactttctcagtaacattcttaaatgcaaattggttttgtgaacatgaggttgctttccactgacattttcatccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCATTGGTGATCCTCCTGAGGAGAGATTTGACTTGGCATTCTGTGGAAGCCTT
    |||     |  | |    ||  | |   |||| ||| | || |    |       |  |||  |     | |  |      |   |  || || || || || || ||||||||||||   || |||||||| || || ||||||||||| || ||||| || ||||||||||| ||||||||||||||||| |||
---gtgagttttag-tctgaaatcagaatcctattcataattccataacaat----cagaattgaaatgatcattcgttctttcatctttggaattgtagATACACGGCTGATGAAGATTTCGAGAACGCAGATGCGGTTTTCGACTGCATTGGAGACCCTCCAGAAGAGAGATTTGATTTGGCATTCTGTGGAAGTCTT

upper sequence: GLYMA04G36600.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv17s0000g09910.t01 (Vitis vinifera), 3'ss of exon 7
----------------agaatgaaagccatctttacttt--ctcagtaac-attcttaaatgcaaattggttttgtgaac-atgaggttgctttccactgacattttcatccaaa---tgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCATTGGTGATCCTCCTGAGGAGAGATTTGACTTGGCATTCTGTGGAAGCCTT
                   ||||| ||  | ||||||     | | | |  | || |||||    || |    |||||    ||||||  ||||| ||  |  ||   |  | |    ||||| |||||||| |||||||| ||||| ||||| ||||| || |||||||||||||| ||||| ||||||||  ||||||| |||||||| || |||||||||
gtaagttgtttctttctttatgaatgctctatttactacacttgaatgatgaatcctaaatttttatag---ctgtgagttgtgaggt--ctttcaacaaatcttcaaaatctatggttgcagATATACAGCTGATGAAGACTTCTTGAATGCGGATGCTGTTTTTGACTGCATTGGAGATCCCCCTGAGGAACGATTTGATTTGGCATTTTGCGGAAGCCTT
















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|213595680|gb|DB977962.1|DB977962
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|120495078|gb|EH223245.1|EH223245
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|151405279|gb|EV275093.1|EV275093
EST:     AGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: AGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|209704520|gb|BW680650.1|BW680650
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|8670194|gb|BE191301.1|BE191301
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|20811539|gb|BQ296017.1|BQ296017
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|9258673|gb|BE346820.1|BE346820
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|22522399|gb|BU081210.1|BU081210
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|209718041|gb|BW671874.1|BW671874
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|31311871|gb|CD397074.1|CD397074
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACCAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|31310757|gb|CD395960.1|CD395960
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACTAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|8669990|gb|BE191097.1|BE191097
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|192318370|gb|FK011026.1|FK011026
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|6718650|gb|AW306297.1|AW306297
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|31307094|gb|CD392297.1|CD392297
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|9564563|gb|BE474072.1|BE474072
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
EST: gi|11411417|gb|BF423428.1|BF423428
EST:     TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGG                         CTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT
genomic: TTAGCAGCTGCTAAAGCAGCTGGAATGACGTGTATAGTAACAAAGAGCGGgtatgtttct ... ccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattggttttgtgaacatgaggttgctttccactgacattttcatccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCATTGGTGATCCTCCTGAGGAGAGATTTGACTTGGCATTCTGTGGAAGCCTT
                              cactgac  putative branch site (score: 2)
                                      ttttcatcc  CT-rich tract
                                     attttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaatgaaagccatctttactttctcagtaacattcttaaatgcaaattggttttgtgaacatgaggttgctttccactgacattttcatccaaatgcagCTATACAGCAGATGAAGATTTCTTAAATGCAGATGCAGTCTTTGACTGCATTGGTGATCCTCCTGAGGAGAGATTTGACTTGGCATTCTGTGGAAGCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - aaagcca
- - - - - - - - - - - - - - - - - - - -aatgcaa
- - - - - - - - - - - - - - - - - - - - - - - - -ggttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - actgaca