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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctatttgaattaaaaaatgtagataaaaaatttctctcaattactatatataaatagtaatatactgatttgtaatgtggcatatggttggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCATGCATTAGGCCACGTGACCAGCAATGTCTCATTTGCTGCAGTTGCTGTTT

Basic information

species Glycine max
transcript GLYMA13G24360.1
intron # 4
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 4
lower sequence: Vv10s0003g00300.t01 (Vitis vinifera), 3'ss of exon 4
tctatttgaattaaaaaatgtagataaaaaatttc-tctcaattactatatataaatagtaatatactgatttgtaatgtggcatatggttggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCATGCATTAGGCCACGTGACCAGCAATGTCTCATTTGCTGCAGTTGCTGTTT
||| |   ||   || | |||   |   | || |  |    || ||| | ||    |  |    |   |   ||  ||| ||| | |||||     |||||||||||||||| ||||| |||||  ||||||| || || ||||| || |||||  ||||||| ||||| ||||||||||| ||||| |||||||| || |
tctgtagaaagccaatattgtttcttctatatatgatgatgatgact-tgtagcccttattgattttgggaatgacatgcggcttgtggttttccttgtagCCTATAGACTCAAACCTCCTGAAACTGCTCATCCCCGTTGCTGTATGTCATGCTCTAGGCCATGTGACTAGCAATGTCTCCTTTGCAGCAGTTGCCGTCT
















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|209715702|gb|BW674363.1|BW674363
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|7326908|gb|AW620706.1|AW620706
EST:     GTGTGGCGTACTGTCTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTGCAACCTACTGAAGTTGCTCATTTCCGG-GGCTGTGTGCCA
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATT-CCGGTGGCTGTGTGCCA
EST: gi|15287940|gb|BI471831.1|BI471831
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|15664239|gb|BI701610.1|BI701610
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTG
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTG
EST: gi|26269191|gb|CA820254.1|CA820254
EST:     GGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|26056377|gb|CA799291.1|CA799291
EST:     TTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|213594399|gb|DB973640.1|DB973640
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCG
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCG
EST: gi|20498046|gb|BQ272976.1|BQ272976
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|22524479|gb|BU083290.1|BU083290
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|20076102|gb|BQ094885.1|BQ094885
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|31561929|gb|CD487767.1|CD487767
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|10845918|gb|BF068938.1|BF068938
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|120530166|gb|EH258300.1|EH258300
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|209725000|gb|BW659746.1|BW659746
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|22524883|gb|BU083694.1|BU083694
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|15338168|gb|BI498832.1|BI498832
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|9564410|gb|BE473919.1|BE473919
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|8404364|gb|BE059998.1|BE059998
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|17964192|gb|BM270931.1|BM270931
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|13481992|gb|BG511335.1|BG511335
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|209707100|gb|BW683287.1|BW683287
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|23057815|gb|BU578270.1|BU578270
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|209721962|gb|BW669348.1|BW669348
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|7690833|gb|AW758970.1|AW758970
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|9819687|gb|BE555200.1|BE555200
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|7926336|gb|AW832362.1|AW832362
EST:     CTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: CTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|31560884|gb|CD486722.1|CD486722
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTC
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTC
EST: gi|20448949|gb|BQ253073.1|BQ253073
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|9900710|gb|BE609678.1|BE609678
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|23053059|gb|BU577550.1|BU577550
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|20449432|gb|BQ253556.1|BQ253556
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|213615016|gb|DB957054.1|DB957054
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|26048112|gb|CA784701.1|CA784701
EST:     GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GTGTGGCGTACTGTTTGGTGAGCTGGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
EST: gi|151395328|gb|EV265199.1|EV265199
EST:     GGGCCGTGGGACTTCCTAAACGTGCT                         CCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT
genomic: GGGCCGTGGGACTTCCTAAACGTGCTgtaagtcaag ... ggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatataaatagtaatatactgatttgtaatgtggcatatggttggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCATGCATTAGGCCACGTGACCAGCAATGTCTCATTTGCTGCAGTTGCTGTTT
                  tactgat  putative branch site (score: 2)
     ataaatagtaatatac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctatttgaattaaaaaatgtagataaaaaatttctctcaattactatatataaatagtaatatactgatttgtaatgtggcatatggttggttctgtagCCTATAGACTCCAACCTACTGAAGTTGCTCATTCCGGTGGCTGTGTGCCATGCATTAGGCCACGTGACCAGCAATGTCTCATTTGCTGCAGTTGCTGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - aaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatatg