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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaataatgaataggtgggatgatgttcaatgtttcccagaataaaagttaattttggataacattattacaataccattatctacaatcattgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTACTTCA

Basic information

species Glycine max
transcript GLYMA07G03360.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03360.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g06980.t01 (Vitis vinifera), 3'ss of exon 2
--------------------------------------------aaataatgaatag-gtgggatgatgttcaatgtttcccagaataa-------aagttaattttggataac--attattacaataccattatctac--aatcattg---tctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTACTTCA
                                             |||  |||   |  || ||  || |||  | | |  | ||  ||        | ||   |||||| |    ||||| |   |  ||| | || |  |||| ||    | | ||||   |||||||| |||||||| | ||||||| ||||||||||| ||||||| ||||| |||||||||||||| ||||||| ||| 
gtatgtgccctcatttttctaccaagccaatcttttcgtcattttaatgttgagaggcatgcgagaattttctttctcttgctgataaatttctttgacttctgtttggaaattgaattataattttgtcatcacctgctaaatcctttactttttcagGGTTAAGCTTCCTTCATGGGCGATGTTTGAACTTGGGAGGGCTCCTGTCTACTGGAAGACCATGAATGGCCTTCCTCCTAGTTCT
















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|20813310|gb|BQ297788.1|BQ297788
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|19270363|gb|BM886619.1|BM886619
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|20815004|gb|BQ299482.1|BQ299482
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|22522339|gb|BU081150.1|BU081150
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|5678007|gb|AI939137.1|AI939137
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|20812780|gb|BQ297258.1|BQ297258
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|19053187|gb|BM731854.1|BM731854
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|21994672|gb|BQ786200.1|BQ786200
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|20498211|gb|BQ273141.1|BQ273141
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|15000090|gb|BI320904.1|BI320904
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|16349259|gb|BI974854.1|BI974854
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|9901740|gb|BE610708.1|BE610708
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|20813584|gb|BQ298062.1|BQ298062
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|20497978|gb|BQ272908.1|BQ272908
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|10234637|gb|BE803525.1|BE803525
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
EST: gi|213595810|gb|DB966225.1|DB966225
EST:     NTCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGA                         GTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA
genomic: ATCAGTGCTGCTGCTGTTGCAACAACAACAACAACTGAGGAAATTCAAGAgtatgaattc ... ttgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttaattttggataacattattacaataccattatctacaatcattgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTACTTCA
          ggataac  putative branch site (score: 3)
            ataacattattacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaataatgaataggtgggatgatgttcaatgtttcccagaataaaagttaattttggataacattattacaataccattatctacaatcattgtctacagGTACAAGCTTCCATCATGGGCTAAGTTTGAAATTGGGAGGGCTGCTGTCTATTGGAAAACCATGAATGGCCTCCCTCCTACTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT