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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctcatcaaaatattatttacaatcttctttgattatatcttatactgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA

Basic information

species Vitis vinifera
transcript Vv14s0108g01230.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 3'ss of exon 9
gctcatcaaaatattatttacaatcttctttgattatatcttatactgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA
           | ||||      |  | |  | || |   |||| |   |||  |||| | ||   | |  | |||   || ||        ||| |||||||||||| || ||  || | ||||| ||||||||||| |||||||| ||||| || ||||| || ||||| |||||||| ||||| |||||||||||||
----------gttttatgc-tgttactataaggttcttatttattc-actttatttattataagtta-tcctaattcatttgtctgtatttatttaacagTCTCGAGCACATCCACGAGAAATAATAACTGAAGTTCTTAAAGCTCTGCAAGAGCTAAATGTTTGCTGGAAGAAGATTGGACATTATAACATGAAATGCA

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G077278_T01 (Zea mays), 3'ss of exon 9
gctcatcaaaatattatttacaatcttctt--tgattatatcttatactgttttgcttataagaaaa-gaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA
                     ||| |||||  | | || |||||||  ||| || | |  |  |    ||||   ||||   || ||    |   | | |||||||||||| || ||  || | ||||| | |||||| || |||||||| |||||||||||||| |  |||||||||||||| || ||||||||||||||||
-------------------gtaattttcttgttaagtacatcttatgatgtgtttcatgaattattccgaattccgattcatttatctgtaattgtctaacagTCTCGAGCACATCCACGAGAAATAATAAGTGAAGTGCTTAAAGCTCTGCAAGAACTGAATGTTTACTGGAAAAAGATTGGACACTACAACATGAAATGCA

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA18G49770.1 (Glycine max), 3'ss of exon 10
gctcatcaaaatattatttacaatcttctt--tgattatatcttatactgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA
    ||| |||   | |||    |  |  |  ||   ||     | | |||  |  | ||          || | | |  |||||    || ||| ||||||||||||||||| ||| |  | ||||||||||| ||||| |||||| | |||||| | ||||| |||||||| |||||||| || ||||||||||| || |
--atatctaaaagctgtttgtttttgtaatagtggccatcagaaaaattgtagtcttgatgtcttgttggtagttacttactttttgtttatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTTCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G05700.1 (Glycine max), 3'ss of exon 9
gctcatcaaaatattatttacaatctt----ctttgat-tatatcttatactgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA
  | || ||    ||||    ||| ||     | |||| ||  | || |  || ||  ||| | |   | |  |  || |  |  | |    |||||| ||| ||||||||||||| ||  |  | ||||||||||| || || ||||||||||||||| | ||||| |||||||| |||||||| || || |||||||| ||||
--ttattaatg-gttatcagaaatattgaagttctgatgtacttattttgatggtt-acttgtgactgaggtctt-tgttggttatgtttgttaacttgtgatagTCTCGAGCCCAACCACGTGAAATAATGACTGAGGTCCTTAAAGCTCTACAAGAATTAAATGTTTGTTGGAAGAAGATTGGACACTATAACATGAAGTGCA

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G26180.1 (Glycine max), 3'ss of exon 9
----gctcatcaaaatattatttacaatcttctttgattatatcttatactgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA
    |    |   ||| ||  | | | |   | |     | ||  ||    |||||| |     |     | | ||     | || |  | || ||| ||||||||||||||||| ||| |  | ||||||||||| || || |||||| | |||||| | ||||| |||||||| |||||||| || ||||||||||| || |
taacggctgtttgaatttttgtaatagttgccatcagaaaaattgta----gttttgatgtcttgttggtagttatatactttttgttcattatcttgtgacagTCTCGAGCCCATCCTCGTGAAATAATGACTGAGGTCCTTAAAGCTTTGCAAGAATTAAATGTTTGTTGGAAGAAGATTGGTCACTACAACATGAAGTGTA

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G29160.3 (Arabidopsis thaliana), 3'ss of exon 9
------------------------------gctcatcaaaatattatttacaatcttc-tttgattatat-cttatactgttttgct-tataagaaaagaataatgattatcttttcaactaactttt---gacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA
                               |||| || ||  |  | |  |  |  |     || | ||   | |||| |||  || || |     | |   || || ||  | | | ||   | ||    ||||||||  || || ||| |  | || |||| ||||||| | |||||||| |||||||| |||||||||||||| |||||||| || ||||||||||||||  
gtttgttcctgattactgattctttttgttcctcaccataaagtcttctgaatgcaacacacaatcagatatctgtactctttgcctctacatagccaaatcgataatcattctgttaccttgttgttttgaacagTCTCATGCGCATCCTCGTGAAATCATGAATGAAGTTTTGAAAGCTCTTCAAGAACTCAATGTGTGTTGGAAGAAGATTGGTCACTACAACATGAAATGTC

upper sequence: Vv14s0108g01230.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G01090.2 (Arabidopsis thaliana), 3'ss of exon 9
gctcatcaaaatattatttacaatcttctttgattatatcttatactgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA
                |||   || |||| |  ||||    || |   ||  |||| | | | |    | || | |||  |  ||| |   |    ||||||||| || || ||  |  | |||||||| ||||| || ||||| || |||||  ||||||| |||||||| ||||| ||||| ||||||||||| ||||
--------------gttttgatattttctgtatttatggtataaagacttcagcttttgatatatatgtgattaatattgtaacaatttgatcgc-acagTCTCGGGCTCATCCCCGTGAAATAATGACGGAAGTCCTGAAAGCCCTGCAAGATTTGAATGTATGTTGGAAGAAGATAGGGCACTACAACATGAAGTGCA

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|110375190|gb|EC940152.1|EC940152
EST:     GTTTAAGAACCCAGTTCCCAGCTGAGAGGAAATGGGCTCTTGGGCTTCAG                         TCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAA
genomic: GTTTAAGAACCCAGTTCCCAGCTGAGAGGAAATGGGCTCTTGGGCTTCAGgttagactct ... cttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAA
EST: gi|110369736|gb|EC933904.1|EC933904
EST:     GTTTAAGAACCCAGTTCCCAGCTGAGAGGAAATGGGCTCTTGGGCTTCAG                         TCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAA
genomic: GTTTAAGAACCCAGTTCCCAGCTGAGAGGAAATGGGCTCTTGGGCTTCAGgttagactct ... cttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA
                                       aactaac  putative branch site (score: 1)
                                             ctttt  CT-rich tract
         ttataagaaaagaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctcatcaaaatattatttacaatcttctttgattatatcttatactgttttgcttataagaaaagaataatgattatcttttcaactaacttttgacagTCTCGAGCCCAGCCTAGACAGATAATGACTGAAGTTCTCAAAGCTCTACAAGAACTGAATGTGTGTTGGAAAAAGATTGGGCATTACAACATGAAATGCA

- - - caaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaaaa