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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtctataaatccagtaaattttccatgttctttaaatgtattaatagaatgattgacaatatgttcttaactgaataatattcattgcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG

Basic information

species Glycine max
transcript GLYMA02G05250.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g13970.2 (Oryza sativa), 3'ss of exon 8
----gtatgtctataaatccagtaaattttccatgttctttaaatgtattaatagaatgattgacaatatgttcttaactgaataatattcattgcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG
    |||| | | || | ||| | |  |    ||   || || || | || || |  |   ||||    ||    |  |||  |  |   | ||     || |||| ||||| |||||||| |||||||| ||||| |||||||||||||| ||  ||||    |||   |||
gtaagtatttgtttagaaccaatgacatgctaat---ctatagatattttcattgcgta--tgac----tgactcttgctgttt--tcccccttcaaattgtagCTCCCTGGTGTTGACCCCAATGACCCCTCTGTGAAAGATTTGCTGGCATCATTGCATGGGCAGGGCGAG

upper sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G147671_T01 (Zea mays), 3'ss of exon 8
----gtatgtctataaatccagtaaattttccatgttctttaaatgtattaatagaatgattgacaatatgttcttaactgaataatattcattgcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG
    ||||   | | || | | |    |     ||   ||||  || |    |  ||| ||| |       || |||  || | ||||             ||||||||||| ||||| || ||||| |||||||| |||||||||||||| ||  |||| |  |||   |||
gtatgtattattcttaaactaatggcatacaggtgcattttagctgcagc--ttcaataatttattggccctttttatgtgtaaaata------------acagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG

upper sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G165926_T02 (Zea mays), 3'ss of exon 8
----gtatgtctataaatccagtaaattttccatgttctttaaatgtattaatagaatgattgacaatatgttcttaactgaataatattcattgcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG
    ||||   ||| || | | | |  |     |    ||| |     ||  |  | | ||| |    |  || || | ||  | | ||             |||||||||| ||||| || ||||| |||||||| |||||||||||||| ||  |||| |  |||   |||
gtatgtattattattaaactaatgacatacatgtacatttttagc-cgttgctttattaatttattggacctttttta-tgtgtgaaata----------atagCTTCCTGGTGTTGATCCCAATGATCCATCTGTTAAAGATTTGCTGGCATCGTTGCACAGCCAGGGAGAG

upper sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G078663_T03 (Zea mays), 3'ss of exon 2
gtatgtctataaatccagtaaattttccatgttctttaaatgtattaatagaatgattgacaatatgttcttaactgaataatattcattgcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG
   | | ||| | ||   |||| |    |||   |  |  |  |||  |||    |    |||||  || ||  |    | || |  |         ||||||||||| ||||| || ||||| |||||| | |||||||||||||| ||  |||| |  |||   |||
--gtatgtattattct--taaacta---atggcatacaggtacattt-tagctgcagcttcaataatttattggcccttttatgtgtaaaata---acagCTTCCTGGTGTTGATCCCAATGATCCATCTATTAAAGATTTGCTGGCATCATTGCACAGCCAGGGAGAG

upper sequence: GLYMA02G05250.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0023g03620.t01 (Vitis vinifera), 3'ss of exon 8
--------------------------------------------------------gtatgtctataaatcca-gtaaattttccatgttctttaaatgtattaatagaatgattgacaatatgttcttaactgaataatattcattgcttc-tgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG
                                                          |     | | |  ||   ||         | |    |||||    |  || ||      || |  |   || | |||| |  |||      ||  |||||||||| || |||||||| ||||| || || |||||||||||||| || |||||||||||| |||| |||
gtatgtgactgaaccctcacttttccaaaaagtaaaaaggaaaaacaagcacaggcacacacacacacacacacacaagagagaggagatggaaaaatgacagatgaggatctgctgcagttagcatttca-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|207736317|gb|GD710796.1|GD710796
EST:     TATCCTTGCATCG                         CTTCCTGGGGTTGACCCAAATGATCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: TATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
EST: gi|254335038|gb|GR844823.1|GR844823
EST:     TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCG                         CTTCCTGGGGTTGACCCAA-TGACCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
EST: gi|207802077|gb|GD774273.1|GD774273
EST:     AGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCG                         CTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: AGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
EST: gi|213602974|gb|DB974139.1|DB974139
EST:     TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCG                         CTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
EST: gi|254335039|gb|GR844824.1|GR844824
EST:     TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCG                         CTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
EST: gi|308099085|gb|HO760926.1|HO760926
EST:     TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCG                         CTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
EST: gi|31470062|gb|CD412090.1|CD412090
EST:     TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCG                         CTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC
genomic: TGAGTAAACTGTTGGCAGATCAGTCCTTTGTATCTTCTATCCTTGCATCGgtatgtctat ... gcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatagaatgattgacaatatgttcttaactgaataatattcattgcttctgcagCTTCCTGGGGTTGACCCAAATGACCCATCTGTCAAAGATTTGCTGGCTTCCATGCAAAATCAGTCTGAG
                       tcttaac  putative branch site (score: 2)
                                           ttgcttct  putative PPT
                         ttaactgaataatatt  TA-rich tract