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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaactttaagaaaataaacatcaattgttttcagttctatttattttttgaattaatatgatgtcataacctttgtacccattggttaagtatttgtcattttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

Basic information

species Glycine max
transcript GLYMA03G34890.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os09g39320.1 (Oryza sativa), 3'ss of exon 11
gtaaactttaagaaaataaacatcaattgttttcagttctatttat---tttttgaattaatat---gatgtcataacctttgtacccattggttaagtatttgtcattttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
    | | ||  |    | |      || || | | || | | ||     |||   || ||  |     |  || |||     | |  | |  ||||||| |      || | ||  ||||| ||||| ||||| ||||| |||||||| |  ||||| ||||||||| | ||| |||| |||||||| ||||| ||||||||||| ||||| ||||| 
--gtattgtattatctcatattctcttttttgtgacttttgtctacctgctttcacatgaacttttaactcccaaaacaagaattcatactatttaagtaatctctggttgcttg-acagGCAAAGGGAATGAACTATCTACATAAACGTAGCCCTCCTATTGTTCATCGTGATTTGAAGTCTCCAAATCTTCTAGTTGACAAGAAGTATACCGTGAAA

upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g32610.2 (Oryza sativa), 3'ss of exon 11
--------------------------------gtaaactttaagaaaataa------acatcaattgttttcagttctatttattttttgaattaatatgatgtcataacctttgtacccattggttaagtatttgtcattttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
                                 | |  | ||| | ||| |      | ||   || | |  |||     ||     | |||| || ||  |        |||| ||   ||   || | | | ||| |  ||| | | |||||||||||||||||||| ||||| || ||||||||||| || || ||  | ||||| || || ||||| ||  | ||||| || || || || ||||||
gtaaaatcatatatacttatctcaatacagaatttaggtctaacagaatgactggacatatgctttatataaagtaaaggttgaccgtagaatcaaaattgtaggtgcttctttataaaaatca-ttgattttgtgt-accttcgtatccagGCTAAGGGGATGAATTACCTTCACAAGCGCAATCCTCCTATAGTCCACCGGGATCTAAAGTCACCAAATCTGTTGGTTGATAAAAAGTACACTGTGAAG

upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaaactttaagaaaataaacatcaattgttttcagttctatttattttttgaattaat-atgatgtcataacctttgtacccattggttaagtatttgtc-----attttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
                           | | || | |||  | | ||   || ||   | || |  || | | ||| ||     ||      | | ||        ||| ||     ||||||||||| |||||||||||||| || ||||||||||| ||||| ||||||||||| |||||||||||| |  | |||||||| ||||||||||| |||
--------------------------gtatgtttaattccttatgttacatgtatgggtgattacttcctgatcttggtgtttcttcacatggaactttctttccaattctctgtcacagGCTAAGGGAATGAATTATCTTCACAATCGCAATCCTCCAATTGTGCATAGAGATCTAAAATCTCCAAACTTATTGGTTGACAAAAAATATACAGTCAAG

upper sequence: GLYMA03G34890.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 10
gtaaactttaagaaaataaacatcaattgttttcagttctatttattttttgaattaatatgatgtcataacctttgtacccattggttaagtatttgtcattttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
 ||   ||| ||    | |   | | |||  | ||   |  ||||     | || |||  || | |  || | |||     | ||       | ||| |  ||   |    ||||| ||||| ||||||||||||||||||||||||||||||||||||||| ||||| |||| |||||||||||| | |||||||| ||||| || ||||||
-tatttttttag----tgattgttatttggatgca---ccttttaccagctaaaataacttgttttattatcatttccgtgctttt------tttttttttttaaaacaaacagGCCAAGGGCATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATCGAGATTTGAAGTCTCCAAACCTTTTGGTTGACAAAAAATACACCGTGAAG

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|208169470|gb|GD969643.1|GD969643
EST:     CCACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CCACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaacttta ... tcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|193517192|gb|FK473432.1|FK473432
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CCACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaacttta ... tcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|207795547|gb|GD766852.1|GD766852
EST:     CCACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CCACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaacttta ... tcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|193597983|gb|FK552847.1|FK552847
EST:     AGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: AGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaacttta ... tcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|207735805|gb|GD713084.1|GD713084
EST:     CTACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGAATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CCACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaacttta ... tcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
EST: gi|254324292|gb|GR840609.1|GR840609
EST:     CCACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTG                         GCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA
genomic: CCACAGAGATGTTGGATGAGAGACGTAGGCTTAGTATGGCTTATGATGTGgtaaacttta ... tcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgatgtcataacctttgtacccattggttaagtatttgtcattttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG
      tcataac  putative branch site (score: 2)
                                       tcattttc  putative PPT
                            ttaagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaactttaagaaaataaacatcaattgttttcagttctatttattttttgaattaatatgatgtcataacctttgtacccattggttaagtatttgtcattttcatgtgcagGCTAAGGGGATGAATTATCTTCATAAACGCAATCCTCCCATTGTTCATAGAGATCTGAAATCTCCAAACCTTCTTGTTGACAAGAAATATACAGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA