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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaattcacaatcttttaccactctacgcgtggctcatgtagcatggtgcatatcaaactcgagtaatgattaatgaatttgtttctgtttgtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTTTCATCTTCTAAATTGGTTGTTAAACCTGACATGTTATTTGGAAAGCGTG

Basic information

species Glycine max
transcript GLYMA02G04120.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G04120.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0127g00260.t01 (Vitis vinifera), 3'ss of exon 3
------aaattcacaatcttttaccactctacgcgtggctcatgtagcatggtgcatatcaaactcgagtaatgattaatgaatttgtttctgtttgtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTTTCATCTTCTAAATTGGTTGTTAAACCTGACATGTTATTTGGAAAGCGTG
      |||    |||    | |  | | |    |      || |  |   ||    ||  ||||     ||||||  ||   |||  || ||||  ||  ||| ||| || |  |||||||| |||| |||||||  |||||||||||| ||||| | |||    ||| |||| || |||||||||||||||||||| |||||||
ttgtgtaaaaattcaagacatgaagatttttttggatttatatatttc-cagttttgattgaactt---caatgatgtattgttttccttttgtt-atgcctca-gATCACAGAGTCAACTGACTTCAATGAGCTAGCAGAGAAGGAACCTTGGCTCTTATCAGGGAAACTGGTCGTGAAACCTGACATGTTATTTGGCAAGCGTG
















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|209701247|gb|BW652225.1|BW652225
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|192305509|gb|FG994303.1|FG994303
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|213590555|gb|DB973314.1|DB973314
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|5753577|gb|AI960864.1|AI960864
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|213601137|gb|DB956473.1|DB956473
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|213598625|gb|DB964247.1|DB964247
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|20498839|gb|BQ273769.1|BQ273769
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|17519242|gb|BM188284.1|BM188284
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|192306307|gb|FG995101.1|FG995101
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|7589883|gb|AW705648.1|AW705648
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|298178311|gb|HO024046.1|HO024046
EST:     AGCACTTTAAGAGACTCCCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|9986176|gb|BE660284.1|BE660284
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|151410816|gb|EV280631.1|EV280631
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|298174335|gb|HO017671.1|HO017671
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|213600410|gb|DB970304.1|DB970304
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|209697931|gb|BW670133.1|BW670133
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|213600535|gb|DB960083.1|DB960083
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|10847942|gb|BF070520.1|BF070520
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|213593143|gb|DB969885.1|DB969885
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|213601183|gb|DB956491.1|DB956491
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|208037383|gb|GD835312.1|GD835312
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
EST: gi|209699583|gb|BW678086.1|BW678086
EST:     AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAA                         ATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT
genomic: AGCACTTTAAGAGACTCTCTGGCAAGGAGTTGCCGATCAAGTCTGCACAAgtgagtacta ... gtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgcatatcaaactcgagtaatgattaatgaatttgtttctgtttgtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTTTCATCTTCTAAATTGGTTGTTAAACCTGACATGTTATTTGGAAAGCGTG
                      gattaat  putative branch site (score: 3)
                  taatgattaatgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaattcacaatcttttaccactctacgcgtggctcatgtagcatggtgcatatcaaactcgagtaatgattaatgaatttgtttctgtttgtgtttcaagATTACCGCATCAACTGATTTCACTGAGCTACAAGAGAAGGAACCCTGGCTTTCATCTTCTAAATTGGTTGTTAAACCTGACATGTTATTTGGAAAGCGTG

- attcaca
- - - - - - - - -ccactct
- - - - - - - - - - - - - gcgtggc
- - - - - - - - - - - - - - - - -tcatgta
- - - - - - - - - - - - - - - - - - - - gcatggt
- - - - - - - - - - - - - - - - - - - - - - - - - - tcaaact