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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctcccactgttcaaaagagatgtagtagtttcagtccaaaacatttttttttttttttggtccttgtgctaattttgactgtttgtttgatgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAAGTTTTCTACATTGACTATGGGAATCAAGAAGTAGTTCCTTATGATCGGT

Basic information

species Vitis vinifera
transcript Vv14s0068g00720.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os02g32350.1 (Oryza sativa), 3'ss of exon 14
tctcccactgttcaaaagagatgtagtagtttcagtccaaaacatttttttttttttttggtccttgtgctaattttgactgtttgtttgatgtatca-------agATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAAGTTTTCTACATTGACTATGGGAATCAAGAAGTAGTTCCTTATGATCGGT
      ||  ||  |  |   || | | |||    |  | |      ||| |  ||| ||||  |       | || |   || | |    | || |        ||||||| |||| ||  |||||||||||   ||| | | | ||  | |||||||| ||||||||||||||||| || |||||||| ||||||||   |||  
-----aaccatttta--gtcctggacttgttaagttgaacattcccgtttctagtttctggttttcaaaaataattaggaagtatatccattttaactgatctgcagATTGTGAATGGACCTCGAGGAGCTGTATCATCTCAAGACGACAAGTTTGAAGTATTCTACATTGACTATGGCAACCAAGAAGTCGTTCCTTACAGTCGCA

upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA08G00910.1 (Glycine max), 3'ss of exon 15
-----tctcccactgttcaa-aagagatgtagtagtttcagtccaaaacatttttttttttttttggtccttgtgctaattttgactgtttgtttgatgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAAGTTTTCTACATTGACTATGGGAATCAAGAAGTAGTTCCTTATGATCGGT
      | |   || ||    || | || | | | ||  | |    | ||  |  | | ||   |    ||| |     || |||     | |  ||||| |  || | ||||||| ||  |||||| ||||  ||||  |||| ||    |||||||| ||||||||||| ||||| |||||||||||||| |||||   || | 
tttgtgcacatgctatttgtcaacacattttgcacttgtactttgtaccacctagtctgttcagtcaaacttct-----ttatgaaatggtatgggatgt-tgtagGTAGTCAATGGACCTCGAGGACCTGTTGAATCTTCAAATGACATGTTTGAAGTATTCTACATTGATTATGGAAATCAAGAAGTAGTACCTTACTCTCAGC

upper sequence: Vv14s0068g00720.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT5G61780.1 (Arabidopsis thaliana), 3'ss of exon 14
tctcccactgttcaaaagagatgtagtagtttcagtccaaaacatttttttttttttttggtccttgtgctaattttgactgtttgtttgatgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAAGTTTTCTACATTGACTATGGGAATCAAGAAGTAGTTCCTTATGATCGGT
           | | ||    | ||    |  ||  |||  |  | || |||||||  |    ||| || |  |||    | |||  |   ||| | |||||||| |||| ||  |||||||| || ||||| ||| | || ||||||||||| |||||||| || ||||| || |||||| ||||||| ||        
------gtaaattataaagtttctaaatatgccaa-ccatgatttcttctttttttactatcacttatggttgtttattgtatttcgtatttgtgttaagATTGTTAATGGACCTCGAGGAGCAGTTCAATCTCCAGAGGAGGAATTTGAAGTGTTCTACATCGATTATGGAAACCAAGAAATAGTTCCGTACAGCGCAA

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|71861153|gb|DT010208.1|DT010208
EST:     ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATG                         ATTGTCAATGCACAACGAGGAG
genomic: ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATGgtaagagtta ... atgtatcaagATTGTCAATGCACAACGAGGAG
EST: gi|30252445|gb|CB969996.1|CB969996
EST:     ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATG                         ATTGTCAATGCACGACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
genomic: ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATGgtaagagtta ... atgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
EST: gi|110381283|gb|EC946607.1|EC946607
EST:     ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATG                         ATTGTCAATGCACGACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
genomic: ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATGgtaagagtta ... atgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
EST: gi|161721331|gb|FC070058.1|FC070058
EST:     ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATG                         ATTGTCAATGCACGACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
genomic: ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATGgtaagagtta ... atgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
EST: gi|30256375|gb|CB972218.1|CB972218
EST:     ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATG                         ATTGTCAATGCACGACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
genomic: ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATGgtaagagtta ... atgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
EST: gi|110731966|gb|EE106841.1|EE106841
EST:     ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATG                         ATTGTCAATGCACGACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
genomic: ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATGgtaagagtta ... atgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
EST: gi|30304038|gb|CB980832.1|CB980832
EST:     ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATG                         ATTGTCAATGCACGACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
genomic: ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATGgtaagagtta ... atgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
EST: gi|30304101|gb|CB980895.1|CB980895
EST:     ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATG                         ATTGTCAATGCACGACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA
genomic: ATATTGTTCTTGCTCAATTTACTGCTGATAATTCTTGGAACCGAGCTATGgtaagagtta ... atgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttttttttttggtccttgtgctaattttgactgtttgtttgatgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAAGTTTTCTACATTGACTATGGGAATCAAGAAGTAGTTCCTTATGATCGGT
     ttttttttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctcccactgttcaaaagagatgtagtagtttcagtccaaaacatttttttttttttttggtccttgtgctaattttgactgtttgtttgatgtatcaagATTGTCAATGCACAACGAGGAGCTGTCCAATCCCCAAAAGATGAATTTGAAGTTTTCTACATTGACTATGGGAATCAAGAAGTAGTTCCTTATGATCGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
tctccca
- - - - - - -aaaagag
- - - - - - - - - - - - - - - - - - ccaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactgt