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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAATGTTATGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgatagagctagcctttttgttctctgagtagttctatcaatatattggcctaaacgcagaaatatttgtgggattctacag

Basic information

species Vitis vinifera
transcript Vv12s0028g03130.t01
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA12G13410.1 (Glycine max), 5'ss of exon 20
GTCAATGTTATGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgatagagctagcctttttgttctctgagtagttctatcaatatattggcctaaacgcagaaatatttgtgggattctacag
|||||||||||||| || |||||||||||||||||||| || ||| |||||||||| |||||| | ||       ||| || |||   || |||  | ||   || |||| ||      | |  | ||  |||| |  | |||     
GTCAATGTTATGGATACCTTAAGCAGACTTAGCCATGATACTGATTCAGAAGTAGCTATGgtaagatg------ttagtctcttta--ctttgaacatttgggtctatattttatttgtagc-taaaacaatttatatgcttcag---

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: GLYMA06G44340.1 (Glycine max), 5'ss of exon 20
GTCAATGTTATGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgatagagctagcctttttgttctctgagtagttctatcaatatattggcctaaacgcagaaatatttgtgggattctacag
|||||||||||||| || |||||||||||||||||||| || ||| | |||||||| |||||| | || |||        | | | |||| |||  | ||   || |||| ||      | |  | ||  |||  |  | |||     
GTCAATGTTATGGATACGTTAAGCAGACTTAGCCATGATACTGATTCGGAAGTAGCTATGgtaagatgttag--------tctcttttctttgaacatttgggtctatatcttatttgtagc-taaaacaattaatatgcttcag---

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: AT4G28470.1 (Arabidopsis thaliana), 5'ss of exon 18
GTCAATGTTATGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtg--atagagctagcctttttgttctctgagtagttctatcaatatattggccta-aacgcagaaata----tttgtgggattc-tacag
|| | |||||||||||| || |||||||| ||||||||||||||| ||||||| ||||||||  | |    |   || |  | |  |       |||||||| | ||  |   |||   |  | ||  | | |     ||  |  ||||| |||||
GTGACTGTTATGGACACTTTGAGCAGACTAAGCCATGACACAGATTCAGAAGTTGCAATGgtgagttatcttttcgccactcatggttgaggtagagtagttatttctttgacttgctatgcagcgttggactgatgtttcatctgattcctacag

upper sequence: Vv12s0028g03130.t01 (Vitis vinifera), 5'ss of exon 20
lower sequence: EFJ26022 (Selaginella moellendorffii), 5'ss of exon 19
GTCAATGTTATGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgatagagctagcctttttgttctctgagtagttctatcaatatattggcctaaacgcagaaatatttgtgggattctacag
   ||||| ||||||||||| ||||| || ||||||||||||||  | ||||| || ||||||||       ||||   |   || ||||| || |       | | | |  |  |||         |                    
---AATGTCATGGACACATTGAGCAGGCTGAGCCATGACACAGACTCGGAAGTCGCGATGgtatg-------agctttacgagttcttctccgaatgaaatcgttattgttctctcctgtttttcccag-------------------

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|110370776|gb|EC932910.1|EC932910
EST:     TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATG                         GCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
genomic: TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgat ... gattctacagGCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
EST: gi|37183929|gb|CF603283.1|CF603283
EST:     TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATG                         GCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
genomic: TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgat ... gattctacagGCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
EST: gi|37188290|gb|CF607639.1|CF607639
EST:     TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATG                         GCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
genomic: TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgat ... gattctacagGCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
EST: gi|110699529|gb|EE076605.1|EE076605
EST:     TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATG                         GCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
genomic: TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgat ... gattctacagGCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
EST: gi|110416060|gb|EC982014.1|EC982014
EST:     GCAGACTTAGCCATGACACAGATACAGAAGTAGCAATG                         GCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
genomic: GCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgat ... gattctacagGCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
EST: gi|30305288|gb|CB982082.1|CB982082
EST:     TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATG                         GCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
genomic: TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgat ... gattctacagGCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
EST: gi|110708175|gb|EE085416.1|EE085416
EST:     TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATG                         GCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
genomic: TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgat ... gattctacagGCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
EST: gi|161716967|gb|FC068834.1|FC068834
EST:     TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATG                         GCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA
genomic: TGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgat ... gattctacagGCTGCTGTCATCTCCTTGGGTTTGATAGGTGCGGGTACCAACAATGCTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAATGTTATGGACACATTAAGCAGACTTAGCCATGACACAGATACAGAAGTAGCAATGgtatggtgatagagctagcctttttgttctctgagtagttctatcaatatattggcctaaacgcagaaatatttgtgggattctacag

- - - - - - - - - - - - - - - - - - - - - - -  AGAAGT