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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT

Basic information

species Vitis vinifera
transcript Vv17s0000g09500.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggt-taaatgagtttatt--ctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
||||||  |         | ||   |         |  |||||||       | |  ||||| ||  ||    | |   | || || || || |  |    ||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||
gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctatctgtgtgctttactt-gcgcaatattgcttgtatatataagctggtctattttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
  | | |||| || ||   |||||| || |   |||  |   ||  || ||  ||||| ||   |    || |           ||    || ||||  |||||||||||| ||||| ||||||||||||||||||||||||||||||||||||
--gtgagtttgctggttcggttaacaccct--tctgt-atgctttacattc--ataagattgcttgtatatat-----------aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 4
gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
  | | |||| || ||   |||| | |||  |   |    || |  |  ||  ||||| ||   |    ||             ||    || ||||  |||||||||||| ||||| ||||||||||||||||||||||||||||||||||||
--gtgagtttgctggttcagttagcacctatatgcg----tgcttacgttc--ataagattgcttgtatat-------------aagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G36360.1 (Glycine max), 3'ss of exon 3
gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| ||| |||    |   ||  |  |   | || ||  |    || || | | | |  |  |  |        |  || |||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||| ||||||||||||
gtaagtatttt---gacctgaaacttttcttacatgttatatatgccagtatgacataccatatttgattccattgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G18530.1 (Glycine max), 3'ss of exon 3
gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
        | | || | ||        |||  | ||  |    || || |   | |  |  |  |           || |||||||||| |||||||| |||||||||||||||||||||||||||||||||||||||||| ||||||||||||
-------gtaagtatttttacctgaaacttttcttgttatacatgccagtacgacataccatctttgattccagtgcattggttaaatgggtttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA17G13440.1 (Glycine max), 3'ss of exon 3
gtgagtgtttactagtgttgttaactccttaacctgccac-tgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
             |||  | ||||||  | ||  || ||| | |    |||   || |   |   | |     ||| || |||||||||| | |||||| |||||||||||||||||||||||||||||||||||||||||| ||||||||||||
----------gtaagtaattttaact--taaatttgtcacgtatgcatactacaatgaaaatccttgattccattg-cattggttaaatgggcttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G02740.1 (Glycine max), 3'ss of exon 3
gtgagtgtttactagtgttgttaactccttaacctgccactgttggcactcttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| |||   |  ||      |||| |   | || |      ||    |||   || |   |   | |     ||| || |||||||||| | |||||| |||||||||||||||||||||||||||||||||||||||||| ||||||||||||
gtaagtagat-ttaac----ttaaatttgtcacgtatgctagtacatactacaatgaaaatccttgattccattg-cattggttaaatgggcttattccttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAATCATATCTGTATT

upper sequence: Vv17s0000g09500.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G24740.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtgtttactagtgttgttaactccttaacctgccactgttg-gcactcttataagcttttctaag---cattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
|| |||  |  ||  ||   ||  || | |      | | | |   | | ||    |   ||||| |||   | ||||  ||| |||||||| | | ||||| |||||||||||| ||||| ||||||||||||||||||||||||||||||||||||
gtaagtactgtctgttgactttttcttcatgcatcactaatctgatgaagtcaagcatagttttccaagattcttttttgcaaaggttaaatcattgtattccttgcagTTGTGTACAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

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|30322713|gb|CD005975.1|CD005975
EST:     GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCGgtgagtgttt ... ttctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
EST: gi|32272087|gb|CD721246.1|CD721246
EST:     GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCGgtgagtgttt ... ttctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
EST: gi|32268109|gb|CD717268.1|CD717268
EST:     AAATTGAAGTCTTACAACAGNCTTGCTAAACATGACAAGGGTGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: AAATTGAAGTCTTACAACAG-CTTGCTAAACATGACAAGGGTGGCAATCGgtgagtgttt ... ttctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
EST: gi|30324825|gb|CD008087.1|CD008087
EST:     GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCGgtgagtgttt ... ttctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
EST: gi|32268970|gb|CD718129.1|CD718129
EST:     GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCGgtgagtgttt ... ttctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
EST: gi|32248754|gb|CD714573.1|CD714573
EST:     GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCGgtgagtgttt ... ttctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
EST: gi|71856051|gb|DT005106.1|DT005106
EST:     GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCG                         TTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
genomic: GAAATTGAAGTCTTACAACAGCTTGCTAAACATGACAAGGGTGGCAATCGgtgagtgttt ... ttctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttataagcttttctaagcattttgtcaatggttaaatgagtttattctttgcagTTGTGTGCAAATACGGAACTGGTTTGACTATCGTAACCATATCTGTATT
                                         tttattcttt  CT-rich tract
                                ttaaatgagtttatt  TA-rich tract