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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 16
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
  | |||   | |||  |           |   |  || || ||||    ||    | |  ||| || |  |    | |  || |   |||||||||||||| ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  | ||||| || |||||  ||||||| || || || 
--gtgtgttttcttgataa----------tactgcctgcttattgt----ctggtgt-tgaattcttgaactaacatatttttcttgttgcagTGTCATGGGGTACACATTACTTCTTAGTTTGATTGAGTACAAGACACTTGTGATGCGTGGGGATATTGAACGTGCAAATGATATTTTACCATCCATACCA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G086015_T01 (Zea mays), 3'ss of exon 1
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtat-tgctaacatcttt-attattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
      | |  |||    ||||       |         |||| | || || |||  ||| | | ||  || | | ||            | ||||||||| || ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || 
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagctt----------ggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 16
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtat-tgctaacatcttt-attattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
      | |  |||    ||||       |         |||| | || || |||  ||| | | ||  || | | ||            | ||||||||| || ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || 
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctgttaatttctctgactaacaaatagctt----------ggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G448913_T01 (Zea mays), 3'ss of exon 5
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtat-tgctaacatcttt-attattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
      | |  |||    ||||       |         |||| | || |  |||  ||| | | ||  || | | ||            | ||||||||| || ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  |||| |  || ||  || ||||| | || || || 
------gtatgttttctcgaaaacaatgcttcctttcctttgtagcatctattaatttctctgactaacaaatagctt----------ggtacagTGTCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGATCATGCAAACAAAATTTTATCATCCATACCA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G095348_T01 (Zea mays), 3'ss of exon 16
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
    |||  ||||    | ||      | ||     |   | |||||       | | || |||  |  |       |      |  || |||| |||| || ||||| |||||||| |||||||||||||||||||| |||||||||||||| ||  ||||||  || |||||| ||||| | || || || 
----gtgcgctttctctaaaac-----aatgtttcctttcttttgtaacatctgc-tgttaatttctgtgactaacatataagcttgatacagTATCATTGGGTACACATTACTTCTGAGTTTGATTGAGTACAAGACCCTTGTGATGCGTGGGGATTTGGAACATGCAAATGAAATTTTATCATCCATACCA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 17
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgc-taacatctttatta-ttaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
            |  |||| | |  | | |      |  |  |  | || | | |  | ||| |   ||| |       ||  |||| | | ||||||  |||| || || ||||| |||||||||||||||||||| || |||||||||||||| ||  ||||||  || |||    ||||||| || || || 
-----------gtaagcagcatgcagca-tacctacttctgatcttcttacatgatgtgtttttgggttatgacaacaatt--tttttattacagTGTGGTGGGTTATACTTTACTACTCAGTTTGATTGAGTACAAAACACTTGTGATGCGTGGGGATTTGGAACATGCGAATATTATTTTACCATCCATACCA

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 16
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
|| ||||||    |||     |     | |  |       | |   | |||    ||| | ||||||       ||||  || ||  |  |||||| |||||||||||| ||||| | ||||||||||| |||||||| ||||| |||||||||||  ||||| ||||||||||| || |||| |||||||| 
gtaagtggatcaatggtttgcatt---attcaaaa-----tatctcaatgcagtaatcctgattatt-------ttttaactgttttactcagTGTTATGGGATACACGCTACTTTTAAGTTTGATTGAATACAAGACACTTGTCATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 16
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
|| |||| |  ||  ||    |         |       |||  ||| |  | ||  ||||  | || | |   |||||  | |      |||||| |||||||||||  | ||| | || ||||||||||||||||| |||||||||||||||||  ||||| ||||||||||| || |||| ||||| |||
gtaagtgaaacttctgcttggattattcaaagttttaaattgcagtaatcttgactacttttctgttta-tcaattttttttct------cagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATCCCC

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 16
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttcctt-ttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
|| |||| |  ||  ||     ||   | |  | | |     ||  ||||| |  ||||| | ||||    || || |   || ||     |||||| |||||||||||  | ||| | || ||||||||||||||||| |||||||||||||||||  ||||| ||||||||||  || | || ||||| |||
gtaagtgaaacttctgctt---ggattattcaaagtt-----ttaaattgcaataatcttgactatttttctgtttatcaattgtttttctcagTGTTATGGGATACACACTGCTTTTAAGCTTGATTGAGTACAAGACACTTGTGATGCGTGGTGATTTGGAAAGGGCCAATGATATTCTGCCATCAATCCCC

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 5
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
|| ||||||    |||     |     | |  |      |   || | || |      ||| ||  |   |   ||||  || |   |  ||||||  ||||||||||  ||||| | ||||||||||| |||||||| || || ||||| |||||  ||||| ||||||||||| || |||| |||||||| 
gtaagtggatcaatggtttgcatt---attcaaaatctctcaatgcagtggtcctgattttttttct---tcttttttaactgtgttactcagTGTTGTGGGATACACACTACTTTTAAGTTTGATTGAATACAAGACACTAGTCATGCGCGGTGATTTGGAAAGGGCCAATGAAATTCTACCATCAATTCCT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 20
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
|| ||  ||  |||  | |  | |     |  |   || ||  |   || || || ||| | |                | || | | | |||||| || |||||||| |||||| | ||||||||||||||||||||||||||||||||||| ||  |||||| ||| |||||| | |||||||||||||| 
gtaagcagatgttttactgttatgattgcta-acaatgttttgtaacttactgacttctgtgtc-------------cactttatgattacagTGTTATTGGATACACTTTACTTTTAAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGAGATTTGGAACAGGCTAATGAAGTCTTACCTTCAATTCCT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 16
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
|| ||||    || |        |   |    |  | | ||||| ||      |  | | |  |  |    |     |   || |  ||||||||| || || ||||| ||  | || ||  |||||||||||||||||||||||||||| |||||  | ||    |||| |||| | |||||| ||||||| 
gtaagtg---cttagatttgtgtgtttatataattgagattgttcta-----gaagtttctgatgctg---ttcccctgttttgtggatgcagTGTTATAGGGTACACCTTGTTGCTAAGCCTGATTGAGTACAAGACTCTTGTGATGCGGGGTGATTTAGACAAAGCCAGTGAAATCTTACCTACAATTCCT

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 16
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 16
gtgagtggacttttggcagaaagggggagtggagggtggttgttgtattgctaacatc-tttattatta-agttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
    ||    |  |   | | | |   | | |||  || ||  | | ||||  ||||  |||  ||  | | ||   |||| |||   ||||||||||||| ||||| ||  | || || ||  ||||||| |||||||||||||||||||| || ||  ||||  | |||||| || |||||||| ||||||| 
----gtacgttcctt-tatatatgtttatttgagactgttt--tatcttgcatacataatttgctaacatatttccctttttcttgggaatgcagTGTCATAGGATATACCCTGCTGCTTAGCCTGATTGAATACAAGACTCTTGTGATGCGAGGCGATTTGGATAGAGCCAATCAAATTTTACCTACAATTCCT

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|351030017|gb|FQ430759.1|FQ430759
EST:     GATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTTCA-                         TGTTATGGGATACACGTTACTTCTCAGT
genomic: GATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTT-CAAgtgagtggac ... ttcaatgcagTGTCATGGGATACACGTTACTTCTCAGT
EST: gi|110728301|gb|EE103751.1|EE103751
EST:     GGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAA                         TGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTATAAGACTCTTGT
genomic: GGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAAgtgagtggac ... ttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGT
EST: gi|161716849|gb|FC068107.1|FC068107
EST:     GGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAA                         TGTTATGGGATACACGTTACTTCTCAGTTTGATTGAGTATAAGACTCTTGT
genomic: GGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAAgtgagtggac ... ttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttgtattgctaacatctttattattaagttggtttttccttttcaatgcagTGTCATGGGATACACGTTACTTCTCAGTTTGATTGAGTACAAGACTCTTGTGATGCGTGGTGACCTGGAACGGGCCAATGAACTTTTACCTTCAATTCCC
          tgctaac  putative branch site (score: 1)
                                ttggtttttccttttc  putative PPT
             taacatctttattatt  TA-rich tract