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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcttcatttttatggatcttcacctgtttcactcatactctggtttaatagtcaaaagattgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGGTGAAGAAAATG

Basic information

species Glycine max
transcript GLYMA08G44410.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0187g00170.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------------gtaatcttcattttta---tggatcttcacctgtttcactcatactctg---gtttaatagtcaaaag--attgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGGTGAAGAAAATG
                                                 ||||||    |||    | ||| || |||| |   || | |   |||   || |  || |     |  ||    | |||||||||||||||| ||||| |||||||| || || |||||||||||  |||| ||||||||||
gtacttgcttaatatcaagaacaagaaagctattacttccagcctgtcaaatcttttgctttgaatttgatattaacctttagaacac-tgggctgaatgtcttctaatttgctgtaatcttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG

upper sequence: GLYMA08G44410.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0187g00220.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------------gtaatcttcattttta---tggatcttcacctgtttcactcatactctg---gtttaatagtcaaaag--attgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGGTGAAGAAAATG
                                                 ||||||    |||    | ||| || |||| |   || | |   |||   || |  || |     |  ||    | |||||||||||||||| ||||| |||||||| || || |||||||||||  |||| ||||||||||
gtacttgcttaatatcaagaacaagaaagctattacttccagcctatcaaatcttttgctttgaatttgatattaacctttagaacac-tgggctgaatgtcttctaatttgctgtaatcttttatcagGTACTTCCTCAACCTGTTCGGATTAAGGGGTTTATTTAGTCTCATTCTGGGAGAAGAAAATG
















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|208135014|gb|GD926661.1|GD926661
EST:     GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTG                         GTACTTCCTACAATCTGTTTGG
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCT-CAATCTGTTTGG
EST: gi|31462046|gb|CD404074.1|CD404074
EST:     GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTG                         GTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
EST: gi|192312658|gb|FK004346.1|FK004346
EST:     GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGTTCTTG                         GTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
EST: gi|9565805|gb|BE475314.1|BE475314
EST:     GGAATAGACCTTAGCCCAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTG                         GTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
EST: gi|10255339|gb|BE823105.1|BE823105
EST:     GGAATAGANNTTAGCNNAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTG                         GTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
EST: gi|192312657|gb|FK004345.1|FK004345
EST:     GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGTTCTTG                         GTACTTCCTCAATCTGTTTGGAT-AAGAGGATTCTTTAGTCTCATCTTGGG
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
EST: gi|208142885|gb|GD941497.1|GD941497
EST:     GGAATAGACCTTAGCACCGTAGATGTTAGCTATGTCAGCAGTCGCTCTTG                         GTACTTCCTCAATCTGTTTGGATTAAGAGGA
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGA
EST: gi|192294522|gb|FG987451.1|FG987451
EST:     GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTG                         GTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
EST: gi|11274440|gb|BF324793.1|BF324793
EST:     GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTG                         GTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGG
EST: gi|7588400|gb|AW704196.1|AW704196
EST:     GGAATAGACCTTANCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTG                         GTACTTCCTCAATCTGGTTGGATTA
genomic: GGAATAGACCTTAGCACAGTAGATGTTAGCTATGTCAGCAGTCGCTCTTGgtaatcttca ... tgcatttcagGTACTTCCTCAATCTGTTTGGATTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttcacctgtttcactcatactctggtttaatagtcaaaagattgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGGTGAAGAAAATG
                           gtttaat  putative branch site (score: 4)
                            tttaatagtcaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatcttcatttttatggatcttcacctgtttcactcatactctggtttaatagtcaaaagattgcatttcagGTACTTCCTCAATCTGTTTGGATTAAGAGGATTCTTTAGTCTCATCTTGGGTGAAGAAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA