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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtaaatagattatgtgacaatgcaggtaatatttgtacatttgcagaatatttagtcagtggaacttaacataatcttgcatatcatctaatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATTTCCTTCACGTACCGAAGCATCTATTC

Basic information

species Glycine max
transcript GLYMA13G24360.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G24360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G083344_T03 (Zea mays), 3'ss of exon 6
--ttgtaaatagattatgtgacaatgcaggtaatatttgtacatttgcagaatatttagtcagtggaacttaacataatcttgcatatcatctaatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATTTCCTTCACGTACCGAAGCATCTATTC
   |  ||| | | | | |   | || |  |  ||     | || |    | || |  ||   || | ||||   |   |     |||  || |||   ||||||| ||  | |||||  | || || |||||||| || |||   |||||||| | ||| ||||| ||||| ||||| ||||| |||||||||||||||||
ggattaaaacacactgtttctgactg-attttttaaaataagatctcacaactactgtgtttttgta-cttatattttgccaatctattttcaaatgatcagGTGTCTCGGTAGCATCCCTCACTGAACTCTCATTTAATTGGACTGGCTTCATTAATGCCATGATCTCAAATATTTCTTTCACCTACCGAAGCATCTATTC

upper sequence: GLYMA13G24360.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G070605_T01 (Zea mays), 3'ss of exon 6
ttgtaaatagattatgtgacaatgcaggtaatatttgtacatttgcagaatatttagtcagtggaacttaacataatcttgcatatcatctaatatac-agGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATTTCCTTCACGTACCGAAGCATCTATTC
                     ||| |      | ||  |   |      ||| ||| ||  |    ||  |  ||| |   || || |  | |  | | |||||| || ||||||||  | || ||||||||||||||||||   |||||||| | ||| ||||| |||||||| || ||||| ||| | ||||| |||||
-------------------gtatgtaatcctcagttcgatcatcatctcataattaatcc-taatgctctagctaagcgatcacatgaaattacctgccagGTGTTTCAATGGCATCCCTTACTGAGCTCTCATTCAACTGGACTGGCTTCATCAATGCCATGATATCAAACATCTCATTCACCTACAGGAGCATTTATTC

upper sequence: GLYMA13G24360.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 6
ttgtaaatagattatgtgacaatgcaggtaatattt---gtacatttgcagaatatttagtcagtggaacttaacataatcttgcatatcatctaatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATTTCCTTCACGTACCGAAGCATCTATTC
   | ||    | |  |   | |  | |   | ||      | | |||   |  |    ||       | || |  | || ||   |   |  ||| || |||||||||| |||||||| ||||| ||||| |||||||||||| | |||||||| |||||||||||||| || || |||||||| ||| | || ||||||||
---tgaacttgtgaattcttattcaaagctgttttccagaaatacttgattatgacagtgtttccaccatttcatgtgattttaacttcaaaataaaatgcagGTGTGTCAATGGCATCATTGACTGAGCTATCATTCAACTGGATTGGCTTCATTAGTGCTATGATTTCTAATATCTCCTTCACTTACAGGAGTATCTATTC

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|7588731|gb|AW704520.1|AW704520
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTT-A
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|15287940|gb|BI471831.1|BI471831
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|26269191|gb|CA820254.1|CA820254
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|26056377|gb|CA799291.1|CA799291
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|20498046|gb|BQ272976.1|BQ272976
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|22524479|gb|BU083290.1|BU083290
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|16995981|gb|BM085353.1|BM085353
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|10845918|gb|BF068938.1|BF068938
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCAGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|120530166|gb|EH258300.1|EH258300
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|22524864|gb|BU083675.1|BU083675
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|22524883|gb|BU083694.1|BU083694
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|9564410|gb|BE473919.1|BE473919
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         -TGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTG
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTG
EST: gi|22540054|gb|BU089897.1|BU089897
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|17964192|gb|BM270931.1|BM270931
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|13481992|gb|BG511335.1|BG511335
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|193465757|gb|FK433362.1|FK433362
EST:     CCAATCAGTCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|7690833|gb|AW758970.1|AW758970
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|207810509|gb|GD781618.1|GD781618
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|9819687|gb|BE555200.1|BE555200
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACC
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACC
EST: gi|7926336|gb|AW832362.1|AW832362
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|20448949|gb|BQ253073.1|BQ253073
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|9900710|gb|BE609678.1|BE609678
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|23053059|gb|BU577550.1|BU577550
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|208277399|gb|GE081210.1|GE081210
EST:     TCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACTGAGCTCTCGTTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|26048112|gb|CA784701.1|CA784701
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|151395328|gb|EV265199.1|EV265199
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
EST: gi|7285024|gb|AW597511.1|AW597511
EST:     CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTG                         GTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA
genomic: CCAATCAATCCCCATCACTTTGTGGCTGTCACTGGCTCCTGTTGTTATTGgtaacatccc ... taatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaatatttagtcagtggaacttaacataatcttgcatatcatctaatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATTTCCTTCACGTACCGAAGCATCTATTC
                                          atctaat  putative branch site (score: 3)
                                     atatcatctaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtaaatagattatgtgacaatgcaggtaatatttgtacatttgcagaatatttagtcagtggaacttaacataatcttgcatatcatctaatatacagGTGTGTCCATGGCATCTTTGACCGAGCTCTCATTCAACTGGGTCGGCTTCATAAGTGCTATGATTTCAAACATTTCCTTCACGTACCGAAGCATCTATTC

- - - - - - - - - - - tgcaggt
- - - - - - - - - - - - - - - - - - - -catttgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatat