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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctcttggagttagacttaatcacagcgattctgtcattgttttttatgagcatgaagaatttacttttcatagcaaggctttggttaaatggtaattaatttattatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT

Basic information

species Glycine max
transcript GLYMA12G00600.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G00600.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv16s0013g00290.t01 (Vitis vinifera), 3'ss of exon 3
gtaagtctcttggagttagacttaatcacagcgattctgtcattgttttttatgagcatgaagaatttacttttcatagcaaggctttggttaaatggtaattaatttattatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT
            | |||    ||     |      | |   ||| | |    |     |||| | ||| ||| |||   ||||| |||   | |         ||| ||||   |||||| |||||||||||| || | ||||||||| || ||||| ||||||||||| ||||| ||  ||||||||||| | |||||||| | |
------------gcgtttcctttgcattccattccttttaaattatgtagcttagaagtgaatatttttcttctcact-caaggtttttactgagaa------aatatatttcatgcagAGTTCAGCAAATCTGAAACTATATTATGCTACATGTTTCTCTCTTATTGCTGGGATCATCATTTTTGGTGGTTTACTTGCACCAACT
















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|120491443|gb|EH219610.1|EH219610
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|6566524|gb|AW234167.1|AW234167
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|7924908|gb|AW830934.1|AW830934
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|19269603|gb|BM885859.1|BM885859
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|13479753|gb|BG509096.1|BG509096
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|33389909|gb|CA853116.1|CA853116
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|298167160|gb|HO010599.1|HO010599
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|13480083|gb|BG509426.1|BG509426
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|22525484|gb|BU084295.1|BU084295
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|33389270|gb|CA852477.1|CA852477
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|12689436|gb|BG155833.1|BG155833
EST:     AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: AGAATGAACTCCCTAACTTCCCATCATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
EST: gi|192307757|gb|FK001701.1|FK001701
EST:     CATTCATTCCTTTCTTGCCTCCTTTG                         ACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC
genomic: CATTCATTCCTTTCTTGCCTCCTTTGgtaagtctct ... ttatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttacttttcatagcaaggctttggttaaatggtaattaatttattatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT
                                   aattaat  putative branch site (score: 3)
                     tttggttaaatggtaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctcttggagttagacttaatcacagcgattctgtcattgttttttatgagcatgaagaatttacttttcatagcaaggctttggttaaatggtaattaatttattatttgcagACTTCAGCAAATCTCAAGCAATATTATGCAACCTGTTTTTCTCTTATTGCCGGGATAATTCTTTTTGGTGGTCTCCTTGCACCTAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG