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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgacttctatatttaatacctgattacaataatgatcattttatttggatgtttcaaggtaaaggtaattaaattggacctattattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTTTTCTTTAGGAATCCTGAGGGTATGTGGATCCCATGTGGGCCAAAGCAAC

Basic information

species Glycine max
transcript GLYMA11G19120.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g04814.3 (Oryza sativa), 3'ss of exon 6
gtaagtttgacttctatatttaatacctgattacaataatgatcattttatttggatgtttcaaggtaaaggtaattaaattggacctattattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTTTTCTTTAGGAATCCTGAGGGTATGTGGATCCCATGTGGGCCAAAGCAAC
||||||| |  ||||  |    | |      |  |   ||| ||    | || | || |    |  |   | |  |    ||       |  ||| |||||| |||||||| |||||||||||||| |||||||| || ||||||||||| ||||||| |  |  ||  | ||||||||| || ||||| ||||||||| 
gtaagtt-gttttctgca----acattctcatgtatccatgctc----tgttagcatatactgaaatctcgttgctcttttt-------tctttcaacagGTAAAGGATGTGTTATTTGAACCTGTCCGCAAAACACAGGATGCCATGTTCTTCTTTAAGGCTGATGGTGATATGTGGATGCCTTGTGGACCAAAGCAAT

upper sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 6
gtaagtttgacttctatatttaatacctgattacaataatgatcattttatttggatgtttcaaggtaaaggtaattaaattgg--acctatta-ttctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTTTTCTTTAGGAATCCTGAGGGTATGTGGATCCCATGTGGGCCAAAGCAAC
|||||      |    | || |||   | ||||| ||  |   || || | |   || | ||    ||   | |||| |||  |  || | ||  ||| |||||| |||||||| |||||||||||||| |||||||| || ||||||||||| ||||| | |      |  |  |||||||| |||||||| ||||| ||||
gtaagcaattttggactcttgaatctgtcattactatgctccacagttcagtctcatctatcttactat--gcaatttaatctgatacttgtttcttcaacagGTTAAGGATGTCTTATTTGAACCTGTGCGCAAAACACAGGATGCCATGTTCTTCTTCAAGGCAGACGGTGACATGTGGATGCCATGTGGACCAAAACAAC

upper sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 6
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaagtttgacttctatatttaatacctgattacaataatgatcattttatttggatgtttcaaggtaaaggtaattaaattggacctatta---ttctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTTTTCTTTAGGAATCCTGAGGGTATGTGGATCCCATGTGGGCCAAAGCAAC
||| ||       |   | ||| | | |  |  |  ||||  ||    ||| | | | |    || |||   |   |     | | || ||    |  | ||||| || |||||| | |||||||||||||| ||||| |||||||| ||||| || || | |  |||||| ||||  ||||| ||||||||||| | ||| |
gtacgtaacttggcctgagttatttcttattgtccttaatt-tccccctatgttgctatagatagataagcctttgtcttgagaatctttttggctcttgcagGTAAAAGATGTTCTGTTTGAACCTGTTCGTAAAACACAAGATGCAATGTTCTTTTTCAAGTCTCCTGATGGTACATGGATGCCATGTGGGCCTAGGCACC

upper sequence: GLYMA11G19120.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 6
gtaagtttgacttctatatttaatacctgattacaataa-----tgatcatt--ttatttggatgtttcaaggta----aaggtaattaaattggacctattat---------------------tctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTTTTCTTTAGGAATCCTGAGGGTATGTGGATCCCATGTGGGCCAAAGCAAC
||||||  || | ||||||   || |   | || | |       ||| | ||  | | | | ||| || |||||     |   || |  ||     | ||| ||                     | | ||||| || |||||  | |||||||||||||| |||||||||||||| ||||||||| |||  | |||  | | ||||||| | || ||||| ||||||||||
gtaagtgcgagtgctatatcagatgctcaactaaattctccctttgagctttcctcagtagtatggtttaaggtgggacagaatagtagaaaatagcttatcatcttgctttttttggtgtaccctttgcagGTTAAAGATGTACTGTTTGAACCTGTTCGTAAAACCCAAGATGCAATGTTTTTCATTAATACTCCAAATGATATGTGGGTACCGTGTGGACCAAAGCAAC

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|254326206|gb|GR840798.1|GR840798
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|207759130|gb|GD731697.1|GD731697
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCAT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCAT
EST: gi|208138195|gb|GD933371.1|GD933371
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTCCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAAGATGCCATGTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAA-GATGCCATGTT
EST: gi|193375619|gb|FK340458.1|FK340458
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGGTATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATG
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATG
EST: gi|193715723|gb|FK655886.1|FK655886
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|308098773|gb|HO760514.1|HO760514
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|193489979|gb|FK453662.1|FK453662
EST:     GGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTTTTCGCAAAACCCAAGATGCCATGTTT
genomic: GGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|193518520|gb|FK475699.1|FK475699
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTG
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTG
EST: gi|193572413|gb|FK531404.1|FK531404
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTAGAAAGGAATAGTTTTATTTGAACCTG
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGT-GAA-GGA-T-GTTTTATTTGAACCTG
EST: gi|193594868|gb|FK546335.1|FK546335
EST:     AGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: AGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|208327695|gb|GE124583.1|GE124583
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|193512438|gb|FK469034.1|FK469034
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAA
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAA
EST: gi|22525915|gb|BU084726.1|BU084726
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|12489948|gb|BG043469.1|BG043469
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCATGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTCTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|193702900|gb|FK638772.1|FK638772
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAA
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAA
EST: gi|9565843|gb|BE475352.1|BE475352
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCATAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|193703290|gb|FK640044.1|FK640044
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTAATTTAGAACCTGTTCGCAAA
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTA-TTT-GAACCTGTTCGCAAA
EST: gi|193665062|gb|FK612072.1|FK612072
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|207842912|gb|GD815506.1|GD815506
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|23730472|gb|BU763325.1|BU763325
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|193718861|gb|FK655239.1|FK655239
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|207691497|gb|GD675774.1|GD675774
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGAT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGAT
EST: gi|193488655|gb|FK454476.1|FK454476
EST:     GGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTACTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: GGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|24137035|gb|BU927545.1|BU927545
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|208222151|gb|GE017789.1|GE017789
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|193404005|gb|FK367375.1|FK367375
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|23730696|gb|BU763444.1|BU763444
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|22928118|gb|BU545257.1|BU545257
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|13312394|gb|BG406045.1|BG406045
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
EST: gi|17023275|gb|BM094309.1|BM094309
EST:     ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGT                         GTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT
genomic: ATTTGGCTCGCAAGACAGAGGGGTTTTCAGGTTCAGATATATCTGTCTGTgtaagtttga ... tattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatttggatgtttcaaggtaaaggtaattaaattggacctattattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTTTTCTTTAGGAATCCTGAGGGTATGTGGATCCCATGTGGGCCAAAGCAAC
                                            ttattct  CT-rich tract
                     taaaggtaattaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgacttctatatttaatacctgattacaataatgatcattttatttggatgtttcaaggtaaaggtaattaaattggacctattattctacagGTGAAGGATGTTTTATTTGAACCTGTTCGCAAAACCCAAGATGCCATGTTTTTCTTTAGGAATCCTGAGGGTATGTGGATCCCATGTGGGCCAAAGCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA