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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacttttatattctttcatttattgattaccttctagctttgtcatatgtcgaagcaaagttggagtatagctttattattatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTGCATAGGGTAGAGCCTTATGTTACCTATGG

Basic information

species Glycine max
transcript GLYMA09G06860.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0054g00140.t01 (Vitis vinifera), 3'ss of exon 2
gacttttat-attctttcatttattgattaccttctagctttgtcatatgtcgaagcaaagttgga--gtatagctttattattatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTGCATAGGGTAGAGCCTTATGTTACCTATGG
  || |||| ||    | | | ||  |   |   ||| |    |   |    | ||     || ||    |||   |  |     |   |  ||||  | ||||| || ||||| || |||||||||||||||||||| ||  |||| ||| |||| ||||| ||||||||||| || |||||
--ctcttatcatgagcttactaatctaa-gcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv11s0052g00290.t01 (Vitis vinifera), 3'ss of exon 4
gacttttatattctttcatttattgattacctt----ctagctttgtcatatgtcgaagcaaagttggagtatagctttattattatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTGCATAGGGTAGAGCCTTATGTTACCTATGG
  | | |   ||   |  | | ||  ||   |      ||  |||  | | |  |    || | | | |||     ||||  |  || | | || ||| | ||||| |||||||| |||||||| ||||| ||||| || ||  ||||||||||||| ||||| ||||||||||| || || ||
--catgtggttttccttgtgttttagttgtgtcaaagttattttttccttgttaccttacagattcgtagt-cgtatttaaaagaat-tcttttatggtttcagATATTTAATGGTGTCTTTCTGAAAGTAAACAAGGCAACAATGAATATGCTGCACAGGGTTGAGCCTTATGTGACATACGG

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0054g00030.t01 (Vitis vinifera), 3'ss of exon 3
gacttttat-attctttcatttattgattaccttctagctttgtcatatgtcgaagcaaagttgga--gtatagctttattattatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTGCATAGGGTAGAGCCTTATGTTACCTATGG
  || |||| ||    | | | ||  |   |   ||| |    |   |    | ||     || ||    |||   |  |     |   |  ||||  | ||||| || ||||| || ||||||||||||||| |||| ||  |||| ||| |||| ||||| ||||||||||| || |||||
--ctcttatcatgagcttactaatctaa-gcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACGAAGCAACAATGAACATGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0054g00060.t01 (Vitis vinifera), 3'ss of exon 3
gacttttat-attctttcatttattgattaccttctagctttgtcatatgtcgaagcaaagttgga--gtatagctttattattatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTGCATAGGGTAGAGCCTTATGTTACCTATGG
  || |||| ||    | | | ||  |   |   ||| |    |   |    | ||     || ||    |||   |  |     |   |  ||||  | ||||| || ||||| || |||||||||||||||||||| ||  |||| | | |||| ||||| ||||||||||| || |||||
--ctcttatcatgagcttactaatctaa-gcaagctatcccattagaaaaatggagtgttctttgatgacataagatcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACAAGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

upper sequence: GLYMA09G06860.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0054g00010.t01 (Vitis vinifera), 3'ss of exon 3
gacttttat-attctttcatttattgattaccttctagctttgtcatatgtcgaagcaaagttgga--gtatagctttattattatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTGCATAGGGTAGAGCCTTATGTTACCTATGG
  || |||| ||    | | | ||  |   |   ||| |    |   |    | ||     || ||   ||||   |  |     |   |  ||||  | ||||| || ||||| || |||||||||||||||||||| ||  |||| ||| |||| ||||| ||||||||||| || |||||
--ctcttatcatgagcttactaatctaa-gcaagctatcccattagaaaaatggagtgttctttgatgatataaggtcttctcattcacttctttgaatacagATATTCAATGGGGTGTTTCTTAAAGTGAACAAAGCAACAATGAACATGTTGCACAGGGTTGAGCCTTATGTGACTTATGG

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|193462755|gb|FK427310.1|FK427310
EST:     GGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAAGCTACCGTGAATATGCT
genomic: GGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAAC-AAAGCTACCGTGAATATGCT
EST: gi|192302637|gb|FG994889.1|FG994889
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|193691684|gb|FK628905.1|FK628905
EST:     GGAAGATTCTTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: GGAAGATTC-TGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|7285803|gb|AW598290.1|AW598290
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|19345954|gb|BM890834.1|BM890834
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|298188869|gb|HO035562.1|HO035562
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|298175439|gb|HO015072.1|HO015072
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCATAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|192302636|gb|FG994888.1|FG994888
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|209706672|gb|BW676168.1|BW676168
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|6072110|gb|AW101429.1|AW101429
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|192307307|gb|FK001265.1|FK001265
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAGGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|24205580|gb|BU964833.1|BU964833
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
EST: gi|151401089|gb|EV270903.1|EV270903
EST:     CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAG                         ATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG
genomic: CCATGGATCCTAAAACAAGGAAGATTCTGCAGCTTCTGCGTTTGAGACAGgtaaactact ... ttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtcgaagcaaagttggagtatagctttattattatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTGCATAGGGTAGAGCCTTATGTTACCTATGG
                                       tttatttt  CT-rich tract
                   agtatagctttattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacttttatattctttcatttattgattaccttctagctttgtcatatgtcgaagcaaagttggagtatagctttattattatgtttattttggctgcagATTTTTAATGGCGTCTTTCTTAAAGTGAACAAAGCTACCGTGAATATGCTGCATAGGGTAGAGCCTTATGTTACCTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - -ccttcta
- - - - - - - - - - - - - - - - - - - - - -catatgt
- - - - - - - - - - - - - - - - - - - - - - - - - -gaagcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttggag