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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaataaacctgatataatttcagttgtcagtttatggtagttagctgtaacactgaccagagattatgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATCGA

Basic information

species Glycine max
transcript GLYMA06G15680.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G64650.1 (Arabidopsis thaliana), 3'ss of exon 4
------gtaagtaataaacctgatataatttcagttgtcagtttatggtagttag-ctgtaacactgaccagagattatgt-tatg----cagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATCGA
          |||       |  |    |||   |||  |  || |  ||   |  ||||   ||   |  ||  ||| || | ||    ||| ||||||||||| |||||||| ||| ||||||| || || ||||| || ||||||||||| || ||||||||||||||
gtgaattctcgtatctcgttttttccttttttttttgggatcttttcctatgcactctgttttaccagctggatgttacgtatgtgttaacagAGATAGAGCTGGTGGATACACAAGAATGCTTCGTACTCGCATTCGTGTTGGTGATGCTGCCCCAATGGCCTATATCGA

upper sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G09770.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaagtaataaacctgatataatttcagtt-gtcagtttatggt---agttagctgtaaca-ctgaccagagattatgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATCGA
|| |||  | ||  |  | |    ||| ||   ||||  || |    ||     || |  | |||   | | ||||| |  | ||| ||||||||||| |||||||| ||| |||| || || || || ||||| ||||||||||| || ||||||||||||||
gtgagtcttcaaattcttttggcatcattttaacagtccattgcctaagcgctttgcattatctggatatatattatttgttacagAGATAGAGCTGGTGGATACACAAGACTGCTACGTACTCGCATACGAGTTGGTGATGCTGCTCCTATGGCCTATATCGA

upper sequence: GLYMA06G15680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0044g00980.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtaataaacctgatataatttcagttgtcagtttatggtagttagctgtaacactgaccagagattatgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATCGA
|| | |  |||||||| |  | |||||||| ||    | | |||  | | ||||| | ||    |  ||| | |  | ||| ||||||||||| ||||| || ||||| ||||| || || || ||||| |||||||||||||| ||||||||||| ||
gtgaatcttaaacctgttgcattttcagttttc----ttttgta--tggttgtaatattggatgggcattctctgtttcagAGATAGAGCTGGTGGATATACAAGATTACTTCGAACTCGCATACGAGTTGGTGATGCTGCACCAATGGCCTATATTGA

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|298180743|gb|HO022182.1|HO022182
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|298170767|gb|HO015743.1|HO015743
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192322981|gb|FK016712.1|FK016712
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192306136|gb|FG993698.1|FG993698
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|22927036|gb|BU544175.1|BU544175
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|151396812|gb|EV266685.1|EV266685
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCGGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192306137|gb|FG993699.1|FG993699
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192317271|gb|FK010502.1|FK010502
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|298174884|gb|HO014801.1|HO014801
EST:     GGAGATGATGTCATTCACAAGTT-TT-ACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|151407106|gb|EV276921.1|EV276921
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|151395463|gb|EV265340.1|EV265340
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192317270|gb|FK010501.1|FK010501
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|192299353|gb|FG990749.1|FG990749
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|7588869|gb|AW704655.1|AW704655
EST:     GGAGATGATGTCATTCACAAGTTGTGTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCNGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
EST: gi|58020226|gb|CX706968.1|CX706968
EST:     GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAA                         GGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG
genomic: GGAGATGATGTCATTCACAAGTTGTTTACAGAACTAGCTTATCGGTACAAgtaagtaata ... tgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttgtcagtttatggtagttagctgtaacactgaccagagattatgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATCGA
                             cactgac  putative branch site (score: 2)
                                         attatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaataaacctgatataatttcagttgtcagtttatggtagttagctgtaacactgaccagagattatgttatgcagGGATAGAGCTGGGGGATACACCAGATTGCTTCGGACCCGTATTCGAGTGGGTGATGCTGCACCGATGGCCTATATCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC