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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattcactgatgtatcattatcatttcatttgaaaccttttttgatagagtagttttacttacagtatggtcttcttgttccagGTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGATGACTATGGCTGTGATTGGTATTTTAGGCCATTTTAG

Basic information

species Glycine max
transcript GLYMA10G16320.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G827205_T02 (Zea mays), 3'ss of exon 6
gtattcac--tgatgtat-catt--atcatttcatttgaaaccttttttgatagagtagttttactt-----acagtatggtcttcttgttccagGTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGATGACTATGGCTGTGATTGGTATTTTAGGCCATTTTAG
||||   |  |||   |  || |  |||  ||||  | | |  ||| || |     |  |||   |      | |  |||       ||   ||||||||| ||    ||||||||||||||||| || || || |||||||| ||| || |||||||||| || ||||| || ||||| ||
gtatgggccatgagaaacacactggatctgttcaaatcagagttttatttacctttttttttctttggagaaaaatcatgacacctatgcatcagGTATCCTTCAATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG

upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G137707_T01 (Zea mays), 3'ss of exon 6
------gtattcactgatgtatcattatcatttcatttgaaaccttttttgatagagtagttttacttacag-----tatggtcttcttgttccagGTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGATGACTATGGCTGTGATTGGTATTTTAGGCCATTTTAG
      |  || |   |   |  |      ||| | |   |   || |||       |   |||    | |       |||       ||   ||||||||||||    ||||||||||||||||| || || || |||||||| ||| || |||||||||| || ||||| || ||||| ||
gtatgggccttgagaaacacactagatctgtttaaatcagagttttgtttacctttttttctttggaaaaaaataatcatgacacctatgcatcagGTATCCCTCGATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAG

upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM5G827205_T01 (Zea mays), 3'ss of exon 6
gtattcac--tgatgtat-catt--atcatttcatttgaaaccttttttgatagagtagttttactt-----acagtatggtcttcttgttccagGTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGATGACTATGGCTGTGATTGGTATTTTAGGCCATTTTAG-------------
||||   |  |||   |  || |  |||  ||||  | | |  ||| || |     |  |||   |      | |  |||       ||   ||||||||| ||    ||||||||||||||||| || || || |||||||| ||| || |||||||||| || ||||| || ||||| ||             
gtatgggccatgagaaacacactggatctgttcaaatcagagttttatttacctttttttttctttggagaaaaatcatgacacctatgcatcagGTATCCTTCAATTGTTTTTGTTGGTGATACCTACACCTATTTTGCTGGAATGGCTTTGGCTGTGATAGGAATTTTGGGACATTTCAGGTAAACATCCTTA

upper sequence: GLYMA10G16320.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv08s0007g05920.t01 (Vitis vinifera), 3'ss of exon 6
----gtattcactgatgtatcattatcatttcatttgaaaccttttttg----atagagtagttttacttacagt---------atggtcttcttgttccagGTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGATGACTATGGCTGTGATTGGTATTTTAGGCCATTTTAG
    ||| |  |    |  || | |   |||| ||  ||    ||| |     |||    ||| || || |||||          |    | | | |||||||||||| ||||||||||||||||| || || || || || |||||||| ||||| ||||||||  |||| |||||||||||||||||
agaagtacttccaagagagtcctaa--gtttctttaaaatttgtttctcctgcataatcaagtcttgctaacagttcatttgttgtatcttgcatattccagGTATCCTTCTTCAGTTTTTGTTGGAGACACTTACACGTATTTTGCTGGAATGACAATGGCTGTAGTTGGCATTTTAGGCCATTTTAG

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|208131743|gb|GD928220.1|GD928220
EST:     TTAGCTCAGCCCTTGCTAGCTACCTCTTTGGCTTTACTTTCTTACAACTG                         GTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGAT
genomic: TTAGCTCAGCCCTTGCTAGCTACCTCTTTGGCTTTACTTTCTTACAACTGgtattcactg ... cttgttccagGTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGAT
EST: gi|192332055|gb|FK026335.1|FK026335
EST:     TTAGCTCAGCCCTTGCTAGCTACCTCTTTGGCTTTACTTTCTTACAACTG                         GTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGAT
genomic: TTAGCTCAGCCCTTGCTAGCTACCTCTTTGGCTTTACTTTCTTACAACTGgtattcactg ... cttgttccagGTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGAT
EST: gi|17518507|gb|BM187549.1|BM187549
EST:     TTAGCTCAGCCCTTGCTAGCTACCTCTTTGGCTTTACTTTCTTACAACTG                         GTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGAT
genomic: TTAGCTCAGCCCTTGCTAGCTACCTCTTTGGCTTTACTTTCTTACAACTGgtattcactg ... cttgttccagGTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaaaccttttttgatagagtagttttacttacagtatggtcttcttgttccagGTATCCCTCTTCAGTTTTTGTTGGTGATACATATACATACTTTGCTGGGATGACTATGGCTGTGATTGGTATTTTAGGCCATTTTAG
                           tacttac  putative branch site (score: 1)
                                         tcttcttgttcc  putative PPT
        ttttttgata  TA-rich tract