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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctataaatccagtaaatgttccgtgttctttaaatgtattgatagaatgattgacaatatgttctgcactgaataatattcgttgcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAG

Basic information

species Glycine max
transcript GLYMA16G23590.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23590.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g13970.2 (Oryza sativa), 3'ss of exon 8
gtatgtctataaatccagtaaatgttccg-tgttctttaaatgtattgatagaatgattgacaatatgttctgcactgaataatattcgttgcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAG
||| || | |   |  |   ||||    | |  ||| || || | || || |  |   ||||    ||       |||  |  |   | ||     || |||| ||||| |||||||| ||||| || ||||| |||||||||||||| || |||||    |||   |||
gtaagtatttgtttagaaccaatgacatgctaatctatagatattttcattgcgta--tgac----tgactcttgctgttt--tcccccttcaaattgtagCTCCCTGGTGTTGACCCCAATGACCCCTCTGTGAAAGATTTGCTGGCATCATTGCATGGGCAGGGCGAG

upper sequence: GLYMA16G23590.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G147671_T01 (Zea mays), 3'ss of exon 8
----gtatgtctataaatccagtaaatgttccgtgttctttaaatgtattgatagaatgattgacaatatgttctgcactgaataatattcgttgcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAG
    ||||   | | || | | |         |||   ||||  || |  | |  ||| ||| |       || |    || | ||||             ||||||||||| ||||| || |||||||||||||| |||||||||||||| || ||||| |  |||   |||
gtatgtattattcttaaactaatggcatacaggtgcattttagctgca--gcttcaataatttattggccctttttatgtgtaaaata------------acagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG

upper sequence: GLYMA16G23590.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G165926_T02 (Zea mays), 3'ss of exon 8
----gtatgtctataaatccagtaaatgttccgtgttctttaaatgtattgatagaatgattgacaatatgttctgcactgaataatattcgttgcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAG
    ||||   ||| || | | | |       ||    ||| |     ||| |  | | ||| |    |  || |  | ||  | | ||             |||||||||| ||||| || |||||||||||||| |||||||||||||| || ||||| |  |||   |||
gtatgtattattattaaactaatgacatacatgtacatttttagc-cgttgctttattaatttattggacctttttta-tgtgtgaaata----------atagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG

upper sequence: GLYMA16G23590.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G078663_T03 (Zea mays), 3'ss of exon 2
----gtatgtctataaatccagtaaatgttccgtgttctttaaatgtattgatagaatgattgacaatatgttctgcactgaataatattcgttgcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAG
    ||||   | | || | | |         ||    ||||  || |  | |  ||| ||| |       || |    || | ||||             ||||||||||| ||||| || |||||||||||| | |||||||||||||| || ||||| |  |||   |||
gtatgtattattcttaaactaatggcatacaggtacattttagctgca--gcttcaataatttattggcccttttatg-tgtaaaata------------acagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG

upper sequence: GLYMA16G23590.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------------------------gtatgtctataaatcca-gtaaatgttccgtgttctttaaatgtattgat-agaatgattgacaatatgttctgcactgaataatattcgttgcttc-tgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAG
                                                          |     | | |  ||   ||  |    | | |    ||||| |  ||| || ||      || |  |   | || |||| |  |||      ||  |||||||||| || |||||||| |||||||| || |||||||||||||| || ||| |||||||| |||| |||
gtatgtgactgaaccctcacttttccaaaaagtaaaaaggaaaaacaagcacaggcacacacacacacacacacacaagagagaggagatggaaaaatg-acagatgaggatctgctgcagttagcatttca-tgaaaagcattttcgattttgtgcagCTTCCAGGAGTTGACCCCAATGATCCTTCAGTCAAAGATTTGCTAGCATCCATGCAAAATGAGTCAGAG

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|192323832|gb|FK018598.1|FK018598
EST:     TGAGTAAGCTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCG                         CTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: TGAGTAAGCTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCC
EST: gi|22933789|gb|BU550928.1|BU550928
EST:     TGAGTAAGCTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCG                         CTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: TGAGTAAGCTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCC
EST: gi|21675640|gb|BQ627991.1|BQ627991
EST:     TGAGTAAGCTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCG                         CTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: TGAGTAAGCTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagaatgattgacaatatgttctgcactgaataatattcgttgcttctgcagCTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCCTTGCAAAATCAGTCTGAG
         gattgac  putative branch site (score: 3)
                                           ttgcttct  putative PPT
                              tgaataatatt  TA-rich tract