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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtagtttccttctacttgatcactgtcatttgttggtatctgctattaggttgccctttggtcagtttgaggtgaaatttgggttggtggttaagtgagtttattctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT

Basic information

species Vitis vinifera
transcript Vv01s0137g00580.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g27520.4 (Oryza sativa), 3'ss of exon 4
gtaagtgtagtttccttctacttgatcactgtcatttgttggtatctgctattaggttgccctttggtcagtttgaggtgaaatttgggttg-gtggttaagtgagtttattctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
      ||   | |  |        |  | ||      |  ||| ||| |  |   |  |  | || |    |||    | ||| | | |||  |   ||||   || ||||  ||||||||| | |||||| ||||||||||||||||||||||||||||| ||||||
------gtgagtcctatggttcacttttccgtttcccttaagtaactgttgatctat--ctgtgtgctttacttg---cgcaatattgcttgtatatataagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G179308_T03 (Zea mays), 3'ss of exon 4
gtaagtgtagtttccttctacttgatcactgtca-tttgttggtatctgctattaggttgccctttggtcagtttgaggtgaaatttgggttggtggttaagtgagtttattctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
                              || | |||| |||| || | ||  |   | |  | || |     |      ||  |||  |   |   ||||   || ||||  ||||||||| | |||||| ||||||||||||||||||||||||||||| ||||||
------------------------------gtgagtttgctggt-tcggttaacacccttctgtatgctttacattcat--aagattgcttgtatatataagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

upper sequence: Vv01s0137g00580.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G063792_T04 (Zea mays), 3'ss of exon 4
gtaagtgtagtttccttctacttgatcactgtca-tttgttggtatctgctattaggttgccctttggtcagtttgaggtgaaatttgggttggtggttaagtgagtttattctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
                              || | |||| |||| || | ||  |  |       || | |  || |  | | |||   | | ||   ||||   || ||||  ||||||||| | |||||| ||||||||||||||||||||||||||||| ||||||
------------------------------gtgagtttgctggt-tcagttagcacctatatgcgtgcttacgttca--taagatt---gcttgtatataagctggtctatt--ttgcagTTGTGTTCAAATTCGGAACTGGTTTGACTATCGTAACCATATCTGTATT

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|110709438|gb|EE084898.1|EE084898
EST:     GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCG                         TTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
genomic: GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCGgtaagtgtag ... ttctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
EST: gi|110732680|gb|EE108178.1|EE108178
EST:     GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCG                         TTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
genomic: GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCGgtaagtgtag ... ttctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
EST: gi|161716341|gb|FC064657.1|FC064657
EST:     GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCG                         TTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
genomic: GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCGgtaagtgtag ... ttctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
EST: gi|110698778|gb|EE076668.1|EE076668
EST:     GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCG                         TTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
genomic: GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCGgtaagtgtag ... ttctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
EST: gi|110712429|gb|EE090038.1|EE090038
EST:     GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCG                         TTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
genomic: GAAGTTGAAGTGCTACAGTTGCTTGGAAAATATGATAAAAGTGGCTCTCGgtaagtgtag ... ttctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtcagtttgaggtgaaatttgggttggtggttaagtgagtttattctttgcagTTGCGGTCAAATACGGAACTGGTTTGACTATCGTAACCATATTTGTATT
                                         tttattcttt  CT-rich tract
                                         tttattcttt  TA-rich tract