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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttataactaagacaagttttttgttatttgattttcttttttattaatgaggctaagctaagctgttctatatttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATCTTACAAATCG

Basic information

species Vitis vinifera
transcript Vv06s0009g01800.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os01g72790.1 (Oryza sativa), 3'ss of exon 6
gttataact---aagacaagttttttgttatttgatttt-cttttttattaatgagg---ctaagctaagctgttctata------tttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATCTTACAAATCG
|||    ||    ||| |  || ||||||  |   | || | | | ||| | |       || | ||||  |||| |||       ||  | |||| ||||| ||  | |||||||||||||| || ||||||||||| ||||||||||||||  | ||||| |||| ||| |||||||| ||  | ||||| ||
gttccttctttagagatatcttgtttgttcctacttcttgcatgtatatcagttttttccctgaactaatatgttgtatccgttctttcttgcagGATCTAACCTCTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCAAGTGACCACAATGGAAACTTAACAAACCG

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os05g32360.1 (Oryza sativa), 3'ss of exon 6
-------------------gttataactaagacaagttttttgttatt-tgattttctt-ttttattaatgaggctaagctaagctgttctatatttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATCTTACAAATCG
                   |||| |  | |  ||   |  | || ||  ||||||| |  ||||  |  | |       || |       | || |  | |||| || |||||  | ||||||||||| || || |||||||| || ||||||||||| ||  | ||||||||||||||||| || || ||||| || |||||
gtatacaacactaagcttcgttacattttattcat-ctcatagtgatcatgattttgtggtttttatgctaaaatattcctgattcaaaatctactcttgcagGATCCAATCTCTTGATAGACAATGAAGGTAACTTGAAGCTGGCTGATTTTGGCCTAGCAAGATCATTTTCAAATGATCATAACGGAAATCTCACTAATCG

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G019267_T02 (Zea mays), 3'ss of exon 6
gttataacta-agacaagttttttg----ttatttgattttcttttttattaatgaggctaagctaagctg---ttctatatttg----------tacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATCTTACAAATCG
||  || ||  | |||  | |  ||    ||  |||  || ||| ||   |  | | | |  | | ||||    | || ||||||          |  ||| ||||| ||| | |||||||||||||| || ||||||||||| ||||||||||||||  | ||||| || | |||||||||||| || ||||| || ||
gtcttagctgcaaacatctctgctgagtttttcttgtcttccttattcggtttttatgttttgttgagctaacatactgtatttggtactttgtttgtagGATCTAACCTTTTGATAGACAATGAGGGTAACTTGAAGCTTGCTGATTTTGGCCTTGCAAGATCATTCTCGAGTGATCACAATGGCAACCTTACTAACCG

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G44400.1 (Glycine max), 3'ss of exon 7
gttataactaagacaagttttttgttatttgattttc-ttttttattaatgaggctaagctaagctgttctatatttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATCTTACAAATCG
  | |   ||    ||   || |||| ||  ||  |  | ||  ||  ||    |  |  | |  | || | |  |  | ||||||| |||||||| ||||||||||| |||||| | ||||||||||||||||| || || || |||||||| ||||| || ||||  ||||||||||||||
-gtctgtgtattgaaaagattatgttcttacatcataatgttaaatctatttttcatatttgatgtattttgttctgttgcagGCTCAAATCTTCTTATAGACAATGAAGGAAATCTTAAGCTTGCAGATTTTGGACTGGCACGATCATTTTCTAATGACCAAAATGCAAATCTTACAAATCG

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA20G10960.1 (Glycine max), 3'ss of exon 5
-----------gttataact----aagacaagttttttgttatttgattttcttttttattaatgaggctaagctaagctgttctatattt--gtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATCTTACAAATCG
            | ||  ||    |||| |  | |     | |||| ||||   | || | ||      ||  |  |  || | ||| ||    | |||| || |||||||| ||||||||||| || ||| |||||||||| |||||||| || || ||||||||||| || || |||||||  ||||||||||||||
gtgtccttttgctaatgccttccaaagatacatgtacaaat-tttggttttagatcttgtcaaatctattactcctatttgatgtattttctgttgcagGTTCGAATCTTCTCATAGACAATGAAGGTAATCTGAAGCTTGCTGATTTTGGACTGGCACGGTCATTTTCTAACGAGCACAATGCAAATCTTACAAATCG

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G04410.1 (Glycine max), 3'ss of exon 6
gttataactaagacaa-gttttttgttatttgattttcttttttattaatgaggctaagctaagctgttctatatttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATCTTACAAATCG
||      ||| | |   | ||||   ||  || | |    | ||||| |    |||   | |  | || | |  |  | ||||||| |||||||| ||||||||||| |||||| | ||||||||||||||||| || || || |||||||| ||||| || ||||  |||||||| |||||
gtctgtgttaaaagattatgtttttacatcagaatgttaaatctattattattcctat-ttgatgtattttgttctgttgcagGCTCAAATCTTCTTATAGACAATGAAGGAAATCTTAAGCTTGCAGATTTTGGACTGGCACGATCATTTTCTAATGACCAAAATGCAAATCTTACTAATCG

upper sequence: Vv06s0009g01800.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S121_162V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------gttataactaagacaagttttttgttatttgattttcttttttattaa--tgaggctaagcta-----agctgttct-atat---ttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATC---TTACAAATCG
                                         |||  | ||| |    |||| | ||| |     ||    | ||| ||       || | |||      | | |||| ||||   || | |||| || |||||||| || |||||  | |||| |||||||||||| |||||||| |||||  |||| ||||| |||||||| |||||  | |   | |||||   
gtaagttgtacggtttttcagctgaaccagctttccattgattaggaataacagtccttttgtattaatcttggtttagatctatcaagtcatatcttacctacttgtggattttctgatatctctttttcagGTTCAAATCTTCTTATCGACAACAATGGAATTTTGAAGCTTGCTGATTTTGGGCTTGCAAGGTCGTTTTCTAATGATCAGAATGGTCAACCACTGACAAA---

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|110724472|gb|EE100331.1|EE100331
EST:     GGGGCTTCACTACTGTCATGTGAATCAAGTTCTTCATCGGGATATCAAAG                         GCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTG
genomic: GGGGCTTCACTACTGTCATGTAAATCAAGTTCTTCATCGGGATATCAAAGgttataacta ... atttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTG
EST: gi|110707937|gb|EE084906.1|EE084906
EST:     GGGGCTTCACTACTGTCATGTGAATCAAGTTCTTCATCGGGATATCAAAG                         GCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTG
genomic: GGGGCTTCACTACTGTCATGTAAATCAAGTTCTTCATCGGGATATCAAAGgttataacta ... atttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTG
EST: gi|110707837|gb|EE084694.1|EE084694
EST:     GGGGCTTCACTACTGTCATGTGAATCAAGTTCTTCATCGGGATATCAAAG                         GCTCTAATCTTCTAATAGACAATGAAGGAAATTTGAAGCTTGCAGATTTTG
genomic: GGGGCTTCACTACTGTCATGTAAATCAAGTTCTTCATCGGGATATCAAAGgttataacta ... atttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTG
EST: gi|28962085|gb|CB341118.1|CB341118
EST:     GGGGCTTCACTACTGTCATGTAAATCAAGTTCTTCATCGGGATATCAAAG                         GCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTG
genomic: GGGGCTTCACTACTGTCATGTAAATCAAGTTCTTCATCGGGATATCAAAGgttataacta ... atttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTG
EST: gi|161712182|gb|FC061554.1|FC061554
EST:     GGGGCTTCACTACTGTCATGTGAATCAAGTTCTTCATCGGGATATCAAAG                         GCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTG
genomic: GGGGCTTCACTACTGTCATGTAAATCAAGTTCTTCATCGGGATATCAAAGgttataacta ... atttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgattttcttttttattaatgaggctaagctaagctgttctatatttgtacagGCTCTAATCTTCTAATAGACAATGAGGGAAATTTGAAGCTTGCAGATTTTGGCCTTGCCCGGTCATTTTCAAATGATCACAATGGGAATCTTACAAATCG
               tattaat  putative branch site (score: 2)
     ttttcttttttattaa  TA-rich tract