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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatagaacatattatataaaatgaaaatgtttattgatgatatctttatattgtgtgaagctttgtatatgataattttaacctcttttatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCTGATTCCTGAAATATTAGACCTATTGGGAGCCTTTCACTTTGTAGAACCA

Basic information

species Glycine max
transcript GLYMA17G38220.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G38220.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv18s0122g00430.t01 (Vitis vinifera), 3'ss of exon 3
ttgatagaacatattatataaaatgaaaatgtttattgatgatatcttta----tattgtgtgaagctttgtata-tgata--attttaacctcttttatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCTGATTCCTGAAATATTAGACCTATTGGGAGCCTTTCACTTTGTAGAACCA
       |   ||||        |       || |        | |||||    | |||  | ||  |||   |  | |||  | |||||  ||| ||||   | || ||||||||| ||||||| || ||||||||||||||| || | ||||||||  |||| ||| ||||||||||||||||||||||||||||||| ||||| 
-------agtctatttccattcctatcccctttcaccagcctcacctttagttcttttgacttaaattttaactgctaatatcagtttaatttctgttatttttcagTTTTGAGATACTGCATGCGCGCTGGGCTATGCTTGCAGCCCTTGGTGCTCTACTTCCAGAATTATTAGACCTATTGGGAGCCTTTCACTTTGTTGAACCT

upper sequence: GLYMA17G38220.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S215_109V6.3 (Physcomitrella patens), 3'ss of exon 4
ttgatagaacatattatataaaatgaaaatgtttattgatgatatctttatattgtgtgaagctttgtatatgataatt-ttaacctcttttatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCTGATTCCTGAAATATTAGACCTATTGGGAGCCTTTCACTTTGTAGAACCA
 |  |         |   |    ||| | |  || |  ||   |   |||         || ||      || |   |  |||   | |  |    || ||||||||||| ||||||||||| ||||| ||||||||  |  | ||||   | || || ||  |  | ||||  || || |   | || |||   || || 
-tactgttttccggttgtttgtgtgagattccttttccatcgcaagcttactcgtaacaaaactaatggaattaccttcattattgtttcatcgtgatcagCTTTGAGATCTTGCATGCTCGCTGGGCAATGCTTGCTGCTTTGGGTGTAGTAATCCCGGAGCTTCTGGACCGCTTTGGTGGAGTCCAATTTTCGGAGCCT
















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|120491971|gb|EH220138.1|EH220138
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|151404020|gb|EV273830.1|EV273830
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|209716259|gb|BW657562.1|BW657562
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|10846954|gb|BF069679.1|BF069679
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCC
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCC
EST: gi|120491987|gb|EH220154.1|EH220154
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|15285088|gb|BI468979.1|BI468979
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|151395535|gb|EV265412.1|EV265412
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|22539788|gb|BU089631.1|BU089631
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|120533754|gb|EH261887.1|EH261887
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|209703879|gb|BW667920.1|BW667920
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|193642044|gb|FK593654.1|FK593654
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCGGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|20075945|gb|BQ094728.1|BQ094728
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|24136537|gb|BU927047.1|BU927047
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|6727137|gb|AW311491.1|AW311491
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTATGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCAGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|51337747|gb|CO981613.1|CO981613
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|22524231|gb|BU083042.1|BU083042
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|22540334|gb|BU090177.1|BU090177
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTNTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCNGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|209714192|gb|BW679521.1|BW679521
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|193379221|gb|FK345227.1|FK345227
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|151404614|gb|EV274428.1|EV274428
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|193623783|gb|FK578241.1|FK578241
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCNCTGCGGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|192297292|gb|FG990626.1|FG990626
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|209718155|gb|BW677426.1|BW677426
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
EST: gi|13481342|gb|BG510685.1|BG510685
EST:     GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAA                         CTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT
genomic: GACATTGCTGGGCTTGGCCAGGATCCTGTGGCACTGCAGAAATACTTCAAgtatgtcatt ... tatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttatattgtgtgaagctttgtatatgataattttaacctcttttatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCTGATTCCTGAAATATTAGACCTATTGGGAGCCTTTCACTTTGTAGAACCA
                                ttttaac  putative branch site (score: 2)
                                ttttaacctctttt  CT-rich tract
                  tttgtatatgataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatagaacatattatataaaatgaaaatgtttattgatgatatctttatattgtgtgaagctttgtatatgataattttaacctcttttatcaataagCTTTGAGATATTGCATGCTCGGTGGGCTATGCTTGCATCCGTCGGTGCTCTGATTCCTGAAATATTAGACCTATTGGGAGCCTTTCACTTTGTAGAACCA

- - - - - - - - - - aaatgaaa
- - - - - - - - - - - - - - - - - - tgatgat
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtga