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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctaatttttgttgtatctagttgtactccaattctctctttggtacatcaaagttaattctaatacttaactgcttttttgtataccaatttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTCCCGCCTCCCCATCAGGATGGAGCAGTTGGATTCCCTCACACATCACGCA

Basic information

species Vitis vinifera
transcript Vv17s0000g00620.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA05G38410.1 (Glycine max), 3'ss of exon 6
tgctaatttttgttgtatctagttgtactccaa--ttctctctttggtacatcaaagttaattctaatacttaactgcttttttgtataccaatt--tttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTCCCGCCTCCCCATCAGGATGGAGCAGTTGGATTCCCTCACACATCACGCA-
    |  |  || |  || |  | ||  |||||  ||  | |||  | |        ||  || |  |    |||      | ||| | |  | |  ||| |||| |||||||||  |||  |  |||||| |  | || ||||| |||||||| || ||||| |||||||||||||| |||||||  || |    || |  || 
----atctaatggtccatgtcatggttatccaagctttccacttcagcattgtcttatttgttttcttgagcaacattacatgtgtcttctcactaattttcagAGGTGGAGAGTTGTGACCCATGCAAATGCAAAAAGTAAGAGTGAGAAATTTCCACCTCCTCATCAGGATGGAGCTGTTGGATATCCGC-TGGATGATTCAA

upper sequence: Vv17s0000g00620.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G01250.1 (Glycine max), 3'ss of exon 6
tgctaatttttgttg--tatctagttgtactccaa--ttctctctttggtac-atcaaagttaattc-taatacttaactgcttttttgtataccaatttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTCCCGCCTCCCCATCAGGATGGAGCAGTTGGATTCCCTCACACATCACGCA-
    ||||||  |||   || |  | ||  |||||  ||  | |||  | |   ||  | ||  ||| |    |   | | | | | |    || || |||  |||| |||||||||  |||  |  |||||  |  | || ||||| |||||||| || ||||| |||||||||||||| |||||||  || |    || |  || 
----aattttgtttgatcatgtcatggttatccaagctttccacttcagcattgtcttatttgtttccttgagcaacattacatgtcttctcactaacttt--cagAGGTGGAGAGTTGTGACCCATGCAAACGCAAAAAGTAAGAGTGAGAAATTTCCACCTCCTCATCAGGATGGAGCTGTTGGATATCCAC-TGGATGATTCAA
















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|352795543|gb|FQ480131.1|FQ480131
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|351046377|gb|FQ452993.1|FQ452993
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGAAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTC
EST: gi|351055934|gb|FQ453395.1|FQ453395
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCCAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCA
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCA
EST: gi|351043417|gb|FQ451469.1|FQ451469
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|351043887|gb|FQ452681.1|FQ452681
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|351038967|gb|FQ457642.1|FQ457642
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAATGGAGAGTGATGAGTCCAGCAAATTTCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|351055161|gb|FQ440500.1|FQ440500
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAAT-C
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|110382073|gb|EC938409.1|EC938409
EST:     GGGCAGTTCCAGCTCCGGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAATCCTGCAAATTCCGAGAGCAAGAGTGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|351032086|gb|FQ460343.1|FQ460343
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCCAATTCCGAGA
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGA
EST: gi|351043841|gb|FQ452635.1|FQ452635
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGGT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|349824254|gb|FQ417641.1|FQ417641
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|351013309|gb|FQ425014.1|FQ425014
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|352795551|gb|FQ480139.1|FQ480139
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|351034440|gb|FQ463253.1|FQ463253
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|352790536|gb|FQ478176.1|FQ478176
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCCAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGACCGAGAAATT
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATT
EST: gi|352791008|gb|FQ480001.1|FQ480001
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAGTCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
EST: gi|33408038|gb|CF213665.1|CF213665
EST:     GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGAT                         AAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC
genomic: GGGCAGTTCCAGCTCCAGAAGCCAATGCAGAGCTCCAAGCAAACTTGGATgtatgtcttg ... atttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatcaaagttaattctaatacttaactgcttttttgtataccaatttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTCCCGCCTCCCCATCAGGATGGAGCAGTTGGATTCCCTCACACATCACGCA
                                              tttttcc  CT-rich tract
      aaagttaattctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctaatttttgttgtatctagttgtactccaattctctctttggtacatcaaagttaattctaatacttaactgcttttttgtataccaatttttccagAAGTGGAGAGTGATGAATCCAGCAAATTCCGAGAGCAAGAGCGAGAAATTCCCGCCTCCCCATCAGGATGGAGCAGTTGGATTCCCTCACACATCACGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - actccaa
- - - - - - - - - - - - - - - - - tctctct
- - - - - - - - - - - - - - - - - - - - - - - acatcaa