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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgtttctgtttctataactgagatcaagtttgtcctgattataatgttcccggctcactcgtgtgattccactgaattctccaattttactagGAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAAAAAACGAAAGCTGACAATGTCAAACTCTATGGGAAGATTCGTTATGTCC

Basic information

species Vitis vinifera
transcript Vv17s0000g03970.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: LOC_Os03g50300.1 (Oryza sativa), 3'ss of exon 13
gtatgttgtttctgtttctataactgagatcaagtttgtcctgattataatgttcccggctcactcgtgtgattccactgaatt----ctccaattttactagGAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAAAAAACGAAAGCTGACAATGTCAAACTCTATGGGAAGATTCGTTATGTCC
   ||  ||     | | ||||  |    | | | ||    |  |    |||| ||    |   | || |  ||       |||     |     | | ||||||| ||| |    | |||||||||   |   |||||   || ||| |||||||||| ||||| || |||||  |||| ||||||||||||||||| || |
---tgaagtggggatctgtatatgtttatttatgatttcatttttatctatgtgcctctttgttttgttttgttttgacttattgccattttgtgtctcctagGAACTAAGAAGACTAAAAGAGAAGTATGAAATGCTAGTTGTAGAATTGGAAAAAACTAAAGCAGATAATGTTCAACTGTATGGGAAGATTCGTTACGTGC

upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GRMZM2G011219_T02 (Zea mays), 3'ss of exon 13
----gtatgttgtttctgtttctataactgagatcaagtttgtcctgattataatgttcccggctcactcgtgtgattccactgaattctccaattttactagGAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAAAAAACGAAAGCTGACAATGTCAAACTCTATGGGAAGATTCGTTATGTCC
      |  |   ||  | || | | |   | || | || |  | ||  || |     |  |  |   |        |  | ||   | |   |   || |||||| | |      | |||||||||   | | |||| || || |||||||||||||| |||||||| |||||  |||| ||||| |||||||| |||||||
tgtcacacttccctttagatttttttatc-acatgatgtct--cttgtctacatgaaacatgaatgtgtgtcactgattaattgccatttttgaggataatagGAACTGAGGAGACTAAAAGAGAAGCATGAGATGCTGACTGTTGAACTGGAAAAAACTAAAGCTGATAATGTGCAACTGTATGGAAAGATTCGATATGTCC

upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA07G09890.3 (Glycine max), 3'ss of exon 14
gtatgttgtttctgtttctataactgagatcaagtttgtcctgattata-atgttcccggctcactcgtgt-gattccactgaattctccaattttactagGAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAAAAAACGAAAGCTGACAATGTCAAACTCTATGGGAAGATTCGTTATGTCC
            | | | |||||   |   ||| |||     ||||||  || |  | |  | ||  |||| || |    |||||| | || ||||| |||||| |||  |||||||| |||||||| ||| |  ||||||||||||||||||| |  |||||||| ||||||||||| |||||||||||||||||||| |
-----------gtatgtttataatcaa--ccaaattt---tagattatggatatgacagtgtaacgagtgttgacttgggtgaatttttcacttttaatagGAAATAAGGCAGTTGAAGGAGAAGATTGGGGTATTAACAGTGGAACTGGAAAAGAGCAAAGCTGATAATGTCAAACTATATGGGAAGATTCGTTATGTAC

upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA09G31920.1 (Glycine max), 3'ss of exon 16
gtatgttgtttctgtttctataactgagatcaagtttgtcctgattataatgttcccggctcactcgtgtgattccactgaattctccaattttactagGAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAAAAAACGAAAGCTGACAATGTCAAACTCTATGGGAAGATTCGTTATGTCC
            | | | |||||   ||  ||| ||||   | |  ||| || |   |   |    || ||| |    |||||| | || ||||| |||||| |||  |||||||| |||||||| ||| |  ||||||||||||||||||| |  |||| ||| ||||||||||| || ||||||||||||||||| |
-----------gtatgtttataatc-agcccaattttggattaaggata-tggtagtgtaacgagtgt-tgacttgggtgaatttttcacttttattagGAAATAAGGCAGTTGAAGGAGAAGATTGGGGTATTAACAGTGGAACTGGAAAAGAGCAAAGTTGATAATGTCAAACTATACGGGAAGATTCGTTATGTAC

upper sequence: Vv17s0000g03970.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G18480.1 (Arabidopsis thaliana), 3'ss of exon 14
gtatgttgtttctgtttctataactgagatcaagtttgtcctgattataatgttcccggc-----tcactcgtg-tgattccactgaattctccaattttactagGAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAAAAAACGAAAGCTGACAATGTCAAACTCTATGGGAAGATTCGTTATGTCC
|||   | |   |||   ||||| |||  ||   ||    |||  |    | |  || |      | | | |   ||| |    ||  |||||  |   |   ||||| |||  |  || ||||||||||||||  | || ||||  ||| |||| || || ||||| ||||| ||||||||||||||||| || ||||||||||
gtacagt-tagttgtacatataaatga--tcctcttccctctgtattctctatctccagttaaatttatttgaactgaattttatgtgttctcttaacattgcagGAAATAAGGCGATTAAAAGAGAAGATAGGTTTTCTCACAGACGAATTGGAGAAGACCAAAGCAGACAACGTCAAACTCTATGGGAAAATCCGTTATGTCC

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|30125770|gb|CB911109.1|CB911109
EST:     TCTGCAATCAGCGAGATCGGTTTAGAGCACGGTTGCGAGAGACAGAAGAG                         GAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAA
genomic: TCTGCAATCAGCGAGATCGGTTTAGAGCACGGTTGCGAGAGACAGAAGAGgtatgttgtt ... attttactagGAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttataatgttcccggctcactcgtgtgattccactgaattctccaattttactagGAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAAAAAACGAAAGCTGACAATGTCAAACTCTATGGGAAGATTCGTTATGTCC
             ggctcac  putative branch site (score: 3)
                                              ttttact  putative PPT
                                            aattttacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttgtttctgtttctataactgagatcaagtttgtcctgattataatgttcccggctcactcgtgtgattccactgaattctccaattttactagGAAGTAAAACAGTTGAAAGAGAAGATAGGGCTGCTAACAGTGGAACTGGAAAAAACGAAAGCTGACAATGTCAAACTCTATGGGAAGATTCGTTATGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA