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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatatttgctttatcataatgtatttccattaacccctttcctttttgcaatggttacttatatttggtgtttaatttccttgatgtttttttctctagGGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAAGATGGCTCTCAGGCAATGCAAGGCTTGACGATACGATAAGTTAATCACT

Basic information

species Vitis vinifera
transcript Vv14s0068g00220.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G06410.1 (Glycine max), 3'ss of exon 9
---ttatatttgctttatcataatgtatttccattaacccctttcctttttgcaatggttacttatatttggtgtttaatttccttgatgtttttttctctagGGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAAGATGGCTCTCAGGCAATGCAAGGCTTGACGATACGATAAGTTAATCACT
   | ||  | |  ||||  | ||| | |  ||||    |    |   |   |  |  ||  ||        || || ||| |  || | ||  | | || |||| || ||||||||||| |||| ||||||||| |||||||| ||||  || ||||| |||||||||   ||||| |||    |  | | ||   |    |
ttttgattgtggagttattttgatgaaatgtcattgcttcaacacgagtaaccggtttttgattggcgacaatgcttgattac--tggt-ttcctatttccagGGAAACATTGCAAATGTTATCAGTACCATTCAGGCCAACAAAATAACGGAGGATGGGTCTCAGGCAGCCCAAGGTTTGGTAGTTAGGTGAGAGGACGTTT

upper sequence: Vv14s0068g00220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G22090.1 (Glycine max), 3'ss of exon 9
---ttatatttgctttatcataatgtatttccattaacccctttcctttttgcaatggttacttatatttggtgtttaatttccttgatgtttttttctctagGGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAAGATGGCTCTCAGGCAATGCAAGGCTTGACGATACGATAAGTTAATCACT--
   |  ||    ||||    | ||| | |  | ||    |    |   |     ||  ||  ||   | || ||||||||| |||     ||  | | ||||||| || ||||||||||| |||| ||||||||| |||||||| ||||  || ||||| || ||||||   |||||||||    | || | ||   |  | |  
ttttcgtaacaacttttatttgatggaatggcgttgcttcaacacaagtgactgattttttatttgctatgatgtttaattgcctgt---ttcctatttctagGGAAACATTGCAAATGTGATCAGTACCATTCAGGCCAACAAAATAACGGAGGATGGGTCCCAGGCAGCCCAAGGCTTGGTAGTTCGGTGAG--GACGATTGA
















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|30326179|gb|CD009441.1|CD009441
EST:     TTGGGCAGCAGCAGTGGCAAAACCTTCGATCAAAGCTACTGACATGGAGG                         GGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAA
genomic: TTGGGCAGCAGCAGTGGCAAAACCTTCGATCAAAGCTACTGACATGGAGGgtaatgaact ... ttttctctagGGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAA
EST: gi|37187675|gb|CF607028.1|CF607028
EST:     TTGGGCAGCAGCAGTGGCAAAACCTTCGATCAAAGCTACTGACATGGAGG                         GGTAATATTGCAAATGTCATCAA
genomic: TTGGGCAGCAGCAGTGGCAAAACCTTCGATCAAAGCTACTGACATGGAGGgtaatgaact ... ttttctctagGGTAATATTGCAAATGTCATCAA
EST: gi|87586086|gb|DY474543.1|DY474543
EST:     TTGGGCAGCAGCAGTGGCAAAACCTTCGATCAAAGCTACTGACATGGAGG                         GGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAA
genomic: TTGGGCAGCAGCAGTGGCAAAACCTTCGATCAAAGCTACTGACATGGAGGgtaatgaact ... ttttctctagGGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAA
EST: gi|110421499|gb|EC987796.1|EC987796
EST:     TTGGGCAGCAGCAGTGGCAAAACCTTCGATCAAAGCTACTGACATGGAGG                         GGTAATATTGCAAATGTCATCAATACCATTCAAG
genomic: TTGGGCAGCAGCAGTGGCAAAACCTTCGATCAAAGCTACTGACATGGAGGgtaatgaact ... ttttctctagGGTAATATTGCAAATGTCATCAATACCATTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcaatggttacttatatttggtgtttaatttccttgatgtttttttctctagGGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAAGATGGCTCTCAGGCAATGCAAGGCTTGACGATACGATAAGTTAATCACT
                               tttccttgatgttttt  CT-rich tract
          ttacttatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatatttgctttatcataatgtatttccattaacccctttcctttttgcaatggttacttatatttggtgtttaatttccttgatgtttttttctctagGGTAATATTGCAAATGTCATCAATACCATTCAAGCCAACAAGATAAGTGAAGATGGCTCTCAGGCAATGCAAGGCTTGACGATACGATAAGTTAATCACT

- - - - - - - - - - - - -ttccatt
- - - - - - - - - - - - - - - - aacccct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccttg