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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgatttttccagtcacccaaagaaaatgcctcctattccaatacatctaaaatttttcttcatcatcattcacaactcgtctaaatcctgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG

Basic information

species Vitis vinifera
transcript Vv03s0038g03750.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g03750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os06g51160.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------------gatgatttttccagtcacccaaagaaaatgcctcctattccaatacatctaaaatttttcttcatcatcattcacaactcgtctaaatcctgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG
                                                         |  ||   | | |||    ||   ||   | | | | | |||  ||  |   |||| ||||     |  ||||           |||    ||||||||||||| ||| | |  || ||||| || |   | ||||| || |||||||| |||||||||||||||||||| |||||| |||| |  |||||||||||||
gtaagtagtggaacaagaaagctgtgcttgattatattgttcgaatacatttatcccaccatgcattctgtctatgaactgaaggtcatgcaactgcaa--caattggtatttatcttttgtttgtttcatttgataagagaatgtgtttttgcagAATGAGGATCGTAAGCTGTGGAAGCTGGATACATTGCCTCCAGGACTGATTACTTTCTACAACCTGACATACCCATTGAATCGCACTTGGCATGTGTTGG

upper sequence: Vv03s0038g03750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os10g21890.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------------------------gatgatttttccagtcacc------caaagaaaatgcctcctattccaatacatctaaaatttttcttcatcatcattcacaactcgtctaaatcctgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG
                                                     | | ||  | |||  ||        | | |||  | | | | |||  || |  |   || || |  ||  |   | |     | |     || | |||||| ||||||||| ||| | |  || ||||| || ||  |  |||| || |||||||| ||||| |||||||||||||| |||||| |||| |  |||||||||||||
gtaagtaatggaacgagaaaagctagcagtggttaattatattgttcaaataggtttatcctaccatgcattttctgtctatgaaggt-catgcaattataacagctggtaatttatcttttgttggcttcatttaataagggaatttctgttt-gcagAATGAGGATCGCAAGCTGTGGAAGCTGGGCACACTGCCTCCAGGACTGATTACTTTTTACAACCTGACATACCCATTGAATCGCAATTGGCATGTGTTGG

upper sequence: Vv03s0038g03750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G028501_T01 (Zea mays), 3'ss of exon 7
-----------------------gatgatttttccagtcacccaaagaaaatgcctcctattccaatacatctaaaatttttcttcatcatcattcacaactcgtctaaatcctgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG
                         || |  || || |  | |   | | ||  | | |  |  | |  | ||  |||   | ||  |  |    |  | ||  |  ||  ||| ||  ||||||||| ||  | |  || ||||| || ||  || |||| || ||  | || |||||||||||||||||||| || ||| ||||||  |||||||| ||||
gtaagtagtggaatgagaaatgtactgctgattgcattgcctcgttgcatatagcccatcatttagtgaacctgtaatgaatttt-gttgtttcgctta-ctaatagaagacctatt--gcagAATGAGGACCGTAAGCTGTGGAAGCTGGGTACGCTGCCTCCAGGTTTAATTACTTTCTACAACCTGACATACCCGTTGAATCGTACTTGGCATGTCTTGG

upper sequence: Vv03s0038g03750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G09200.1 (Glycine max), 3'ss of exon 4
---gatgatttttccagtcacccaaagaaaatgcctcctattccaatacatctaaaatttttcttcatcatcattcacaactcgtctaaatcctgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG
   |        | ||   ||   |||   | |  | || ||    | ||| || |   |    |  || || |     |   ||  || |  |  |||||||||||| |||||||| |||||||| |||||| | || || || ||||| ||||| || || || ||||| ||||| || |||||  |||||||||| ||||
tcaggcctcaacttcaaatactggaaggccaagtttactgttttg-tgcatgtagatagtagtgttgtcttcttatctgat--gtagaattaatcctttgcagAATGAGGATAGAACCCTCTGGAAGCTTGGAACCTTACCCCCAGGACTAATCACCTTTTATAATCTGACCTATCCGTTAGATCGAGGCTGGCATGTTTTGG

upper sequence: Vv03s0038g03750.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT4G38270.2 (Arabidopsis thaliana), 3'ss of exon 8
gatgatttttccagtcacccaaagaaaatgcctcctattccaatacatctaaaatttttcttcatcatcattc-acaactcgtctaaatcctgttt--tgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG
             || |  ||  | ||||  |||  |    ||||||| |||| | ||| |  || || | |  |    ||   |||    || ||  ||||||||||||| ||||| || ||||| || ||||||||||||||||| ||||| || || ||||||||||| ||| || ||||| | |||||||| ||  | |
-------------gtaaggcattggaaatttctcaaaaga-aatacatataaa-tatttttggatgatgaatggatgtgtcaattaatatatgattgatgcagAATGAAGACAGAACACTGTGGAAGCTGGGATCGTTGCCACCGGGGCTGATAACATTTTACAACCTGACGTATGCAATGGATAGGAGCTGGCACGTACTAG

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|351026754|gb|FQ436407.1|FQ436407
EST:     AGTGGAGGAAGCGAAACATGACTGGAATATATCATTATTGGCAAGACATG                         AATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATC
genomic: AGTGGAGGAAGCGAAACATGACTGGAATATATCATTATTGGCAAGACATGgtaaggaagc ... tgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATC
EST: gi|110694156|gb|EE071016.1|EE071016
EST:     AGTGGAGGAAGCGAAACATGACTGGAATATATCATTATTGGCAAGACATG                         AATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCCGGGACTGAT
genomic: AGTGGAGGAAGCGAAACATGACTGGAATATATCATTATTGGCAAGACATGgtaaggaagc ... tgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACC-GGGACTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctaaaatttttcttcatcatcattcacaactcgtctaaatcctgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG
                                   gtctaaa  putative branch site (score: 3)
                                          tcctgtttt  CT-rich tract
     aaaatttttcttcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgatttttccagtcacccaaagaaaatgcctcctattccaatacatctaaaatttttcttcatcatcattcacaactcgtctaaatcctgttttgcagAATGAAGATAGAACTCTCTGGAAACTTGGATCGTTGCCACCGGGACTGATCACTTTCTACAACCTGACATATCCATTGGATCGTAGCTGGCATGTGTTGG

- - - - - - - tcaccca
- - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - cctccta
- - - - - - - - - - - - - - - - - - - - caataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcacaac