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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGTCTTGCCTTCTGCAAGTTCATGGTAAAACCTTCAACTTTGCTAGTATTGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattcatttgttcctatccatattgagattactatctaccatgtgcattatagctttaagtttaattatcacttcatgattttttgaactctgtttgttctatcag

Basic information

species Vitis vinifera
transcript Vv07s0031g01640.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G15200.1 (Glycine max), 5'ss of exon 6
ACGTCTTGCCTTCTGCAAGTTCATGGTAAAACCTTCAACTTTGCTAGTATTGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattcatttgttcctatccatattgagattactatctaccatgtgcattatagctttaagtttaattatcacttcatgattttttgaactctgtttgttctatcag
||| || || || ||||| |||||||||||||| |||||| |||| || ||||||||||||||||||||||||||||||||| ||||||| ||||| ||||||||  ||| || | ||               |    | | |||| |  |          ||  |||  | |||| |       |  |||  |||  || ||||  |||
ACGGCTGGCTTTTTGCAAATTCATGGTAAAACCATCAACTCTGCTTGTGTTGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAGgtttgtctcacttttgccg--------------tgtgcttttccatataaa----------aaactta-ctgtcacctttcagcctactgatttctaattcttctcccag

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G39670.1 (Glycine max), 5'ss of exon 6
ACGTCTTGCCTTCTGCAAGTTCATGGTAAAACCTTCAACTTTGCTAGTATTGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattcatttgttcctatccatattgagattactatctaccatgtgcattatagctttaagtttaattatcacttcatgattttttgaactctgtttgttctatcag
||| || ||||| ||||| ||||||||||| || |||||| |||| || ||||||||||||||||||||||||||||||||| ||||||| ||||| ||||||||  ||| || |  |               ||   | | | || |  | || |     ||| ||  || |||| |       |  |||  |||| || ||||  |||
ACGGCTGGCCTTTTGCAAATTCATGGTAAAGCCATCAACTATGCTTGTGTTGGATGAACCAACCAATCACTTGGATATACCTTCTAAAGAAATGCTCGAGgtttgtctcacttttgtca--------------tatgcttttctatataaaataaa-----aagcttg-ttgtcacctttcagcctgctgatttctgattcttctcccag

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G09930.1 (Arabidopsis thaliana), 5'ss of exon 6
ACGTCTTGCCTTCTGCAAGTTCATGGTAAAACCTTCAACTTTGCTAGTATTGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattcatttgttcctatccatattgagattactatctaccatgtgcattatagctttaagtttaattatcacttcatgattttttgaactctgtttgttctatcag
||| ||||| |||||||| |||||||| ||||| || ||| | || || ||||| ||||| ||||||||||| || |||||| | ||||| ||||||||||| |             ||| ||||| |   ||  || |  |  | |   |      |||  || || | ||| |  |   |||| | ||   | |  || ||  |||||
ACGCCTTGCTTTCTGCAAATTCATGGTGAAACCATCCACTCTACTTGTGTTGGACGAACCCACCAATCACTTAGACATACCTTCAAAAGAAATGCTTGAGgtct-------------ctaaccatactcttat--ctgttcaataggccaaactgttcttggaggttgagtatgatct---gattctctg---tttccttctttcatcag

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT5G64840.1 (Arabidopsis thaliana), 5'ss of exon 5
ACGTCTTGCCTTCTGCAAGTTCATGGTAAAACCTTCAACTTTGCTAGTATTGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattcatttgttcctatccatattgaga-ttactatctaccatgtgcattatagctttaagtttaattatcacttcatgattttttgaactctgtttgttctatcag
 |||||||| |||||||| |||||||| |  || || ||||| || || ||||| ||||||||||||||||| || || ||| | ||||| ||||| |||||| |    |    |  |||    | |||||| |   |   ||| |||   || ||| || |     |     |      | | |  ||    || | |   ||  |||||
GCGTCTTGCTTTCTGCAAATTCATGGTGACGCCATCTACTTTACTCGTTTTGGACGAACCAACCAATCACTTAGACATTCCTTCAAAAGAAATGCTCGAGgttagtagtaggcatctctaatt-tgttgagaatctttggatacaatg---ataataactctgttcctggacctggagataggctaattct--ctttttcaattgaatcag

upper sequence: Vv07s0031g01640.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: PP1S495_14V6.1 (Physcomitrella patens), 5'ss of exon 4
ACGTCTTGCCTTCTGCAAGTTCATGGTAAAACCTTCAACTTTGCTAGTATTGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattcatttgttc-ctatccatattgagattactatctacc---atgtgcat-tatagctttaagtttaatt--atcacttcatgattttttgaactctgtttgttctatcag-------------------------------------------------------------------------------------
 || ||  | || |||||||||||||| | |||||||||| | |||||| |||| || || || |||||  ||||||| ||| | || || |||||||||||   | |  ||  | | || ||    |    |||  |   || |   ||||  ||  |   ||| || ||| | |  |||  |  ||  |||||   | | ||  | |   |                                                                                         
GCGGCTATCGTTGTGCAAGTTCATGGTCACACCTTCAACTGTCCTAGTACTGGACGAGCCCACAAATCATCTGGATATTCCTTCAAAGGAAATGCTTGAGgtaacagtttttgatcctctctcttcctctgtatttttccttagccggatgtagatacagcacttcaattttcagtcaatccttctatagtttttc--attttgcctctctcactcttattctccaattttactattttcttcaagttgattaccagtaggtactagcatgttaagctaacccagaagcttgtggtttgcag

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|37190151|gb|CF609500.1|CF609500
EST:     CCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAG                         GAGGCAATAACAGAGTACAAGGGCACTGTTGTTACAGTTTCTCATGATCGA
genomic: CCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
EST: gi|110391761|gb|EC956761.1|EC956761
EST:     TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAG                         GAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
EST: gi|30323437|gb|CD006699.1|CD006699
EST:     TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAG                         GAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
EST: gi|352772399|gb|FQ469924.1|FQ469924
EST:     TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAG                         GAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
EST: gi|27755077|gb|CB035832.1|CB035832
EST:     TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAG                         GAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
EST: gi|30301899|gb|CB978693.1|CB978693
EST:     TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAG                         GAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
EST: gi|32268733|gb|CD717892.1|CD717892
EST:     TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAG                         GAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
EST: gi|32248178|gb|CD713997.1|CD713997
EST:     TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAG                         GAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
EST: gi|30135054|gb|CB920392.1|CB920392
EST:     TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAG                         GAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
EST: gi|32269321|gb|CD718480.1|CD718480
EST:     TGGATGAACCAACCAATCACTTGGATATACCTACTANAGAGATGCTTGAG                         GAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA
genomic: TGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattca ... gttctatcagGAGGCAATAACGGAGTACAAGGGCACTGTTGTTACAGTGTCTCATGATCGA

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGTCTTGCCTTCTGCAAGTTCATGGTAAAACCTTCAACTTTGCTAGTATTGGATGAACCAACCAATCACTTGGATATACCTACTAAAGAGATGCTTGAGgtttgattcatttgttcctatccatattgagattactatctaccatgtgcattatagctttaagtttaattatcacttcatgattttttgaactctgtttgttctatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG