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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacatttctggactggtcttgcaaataaaggcttatcatcttttactctccaactgactatctttttcatcctttttattattatttttgtatacctcagGTCCAAATTGATGTGGAGAGCTTTGTGAATTCTTTCCGGCCTGATATCATGGAGGCTGTGCATGCTTGGGCCAAAGGGTCCAAATTCTATCAGATTATGG

Basic information

species Vitis vinifera
transcript Vv06s0009g01750.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01750.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os12g18140.1 (Oryza sativa), 3'ss of exon 13
--------------------------tacatttctggactggtcttgcaaataaaggcttatcatcttttactctccaactgactatctttttcatcctttttattattat--ttttgtatacctcagGTCCAAATTGATGTGGAGAGCTTTGTGAATTCTTTCCGGCCTGATATCATGGAGGCTGTGCATGCTTGGGCCAAAGGGTCCAAATTCTATCAGATTATGG
                          |  |||  | |  || | |      || |    ||       || |||   || ||  ||||||  |  |       | | || |  | |||   |   ||| |||||||||| |||||||| |||||||| ||||||||||||||||| ||||| || ||| || | ||||||||||| |||||||||||||| || ||||
gtaattgatataactaagccatcatatggattgtttg-ttgatataattgttataaagctaggtggacttgctccagaattg--tatcttaatgctgaaacaaaatgttctcgtcttgccgatgacagATCCAAATTGACGTGGAGAGTTTTGTGAACTCTTTCCGGCCTGATATAATGGAAGCGGTGTATTCATGGGCCAAAGGATCCAAATTCTATCAAATCATGG

upper sequence: Vv06s0009g01750.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA08G47700.1 (Glycine max), 3'ss of exon 13
tacatttctggactggtcttgcaaataaaggcttatcatcttttactctccaactgactatctttttcatcctttttattattattt-ttgtatacctcagGTCCAAATTGATGTGGAGAGCTTTGTGAATTCTTTCCGGCCTGATATCATGGAGGCTGTGCATGCTTGGGCCAAAGGGTCCAAATTCTATCAGATTATGG
    |||     || ||        || ||  |  |||| || || |     | ||  |       |  |  ||| | | || ||||     | |   |||||  ||||||| || ||||| ||||| || || ||  ||||||| || |||||||||||| |||||||||| ||||| || || |||||| |||| ||||
agagtttgctatctcgtagctttt-tagagtgtcttcattttatagttgtacaatgctttgacgaattcttttttctttgatcatttaccaaaaaaaacagGTGGAAATTGACGTTGAGAGTTTTGTTAAGTCGTTTAGGCCTGACATTATGGAGGCTGTGTATGCTTGGGCGAAAGGTTCAAAGTTCTATGAGATCATGG

upper sequence: Vv06s0009g01750.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT1G59760.1 (Arabidopsis thaliana), 3'ss of exon 13
tacatttctggac-tggtcttgcaaataaaggcttatcatcttttactctccaactgactatctttttcatcctttttattattatttttgtatacctcagGTCCAAATTGATGTGGAGAGCTTTGTGAATTCTTTCCGGCCTGATATCATGGAGGCTGTGCATGCTTGGGCCAAAGGGTCCAAATTCTATCAGATTATGG
   |||     || |  |||  |   | |      |     ||| ||  |   |  ||   | |  | |||   |||   | |  ||| ||       |||||| |||| || |||||||| |||||| | |||||| | |||||||| |||||||| ||| |||||||||| |||||||||||||||||| || | ||||
-gtattcactaacatattctctctgctcagctaaaagtgaatttgaccatttgaa-gaggctttggtccataactttc--tgtcttttatgacattgacagGTCGAAATAGACGTGGAGAGTTTTGTGCAGTCTTTCAGACCTGATATAATGGAGGCGGTGTATGCTTGGGCAAAAGGGTCCAAATTCTATGAGGTCATGG

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|110377496|gb|EC942564.1|EC942564
EST:     AGTTACAAGATACAGCTAGGAGGGTTGCCAAAGTTCAGCTGGAGAGCAAG                         GTCCAAATTGATGTGGAGAGCTTTGTGAATTCTTTCCGGCCTGATATCATG
genomic: AGTTACAAGATACAGCTAGGAGGGTTGCCAAAGTTCAGCTGGAGAGCAAGgtattagtgg ... tatacctcagGTCCAAATTGATGTGGAGAGCTTTGTGAATTCTTTCCGGCCTGATATCATG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctccaactgactatctttttcatcctttttattattatttttgtatacctcagGTCCAAATTGATGTGGAGAGCTTTGTGAATTCTTTCCGGCCTGATATCATGGAGGCTGTGCATGCTTGGGCCAAAGGGTCCAAATTCTATCAGATTATGG
      aactgac  putative branch site (score: 2)
                                       tttttgt  putative PPT
             tatctttttcatcctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacatttctggactggtcttgcaaataaaggcttatcatcttttactctccaactgactatctttttcatcctttttattattatttttgtatacctcagGTCCAAATTGATGTGGAGAGCTTTGTGAATTCTTTCCGGCCTGATATCATGGAGGCTGTGCATGCTTGGGCCAAAGGGTCCAAATTCTATCAGATTATGG

- - - - -ggactgg
- - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - -ctctcca