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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttttttcattcagatttttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA

Basic information

species Vitis vinifera
transcript Vv14s0006g00820.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g02510.2 (Oryza sativa), 3'ss of exon 1
tcttttttcattcagatttttg-tgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttaca-gGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
  |  | |  |   |||||||| ||   || ||         ||| | | ||  |   |   |   || || |     ||||||||   ||   |    | ||||||||||||| ||||| ||||| ||  | || ||||||||||||||||| || |||||||| |||||||| || ||||| ||||| || || ||||| 
--taatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtaggtaagGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCCGCAAG

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g02510.3 (Oryza sativa), 3'ss of exon 1
---tcttttttcattcagatttttg-tgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttaca-gGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
     |  | |  |   |||||||| ||   || ||         ||| | | ||  |   |   |   || || |     ||||||||   ||   |    | ||||||||||||| ||||| ||||| ||  | || ||||||||||||||||| || |||||||| |||||||| || ||||| ||||| || || |     
ttcagtaatctggtgtggatttttgctgcaactgttagtaagagctgttaggaaggaatcgcatgatgcttatggtttgtgtttgtttgatttggtgtagGTAAGGTAAGCCATGGTGAAGCACAACAACGTCATCCCGAATGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCAGCCCGCCC-----

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g37970.1 (Oryza sativa), 3'ss of exon 1
-tcttttttcattcagatttttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattt-tgtttgtgctgccatttacagGTAAGCC---------------ATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
 | |  |    | |   |   | || |      |   ||| | | |  |  | ||  ||||  |  |   | | || ||  |||||||| ||      |||||||||                 ||||| ||||| ||||| ||| | || ||||| ||||||||||| || |||||||| |||||||| || ||||| |||               
atgtgctcgattgcgcgtgcatatggtctcgccgctgtatatcgggttgttggtag-tcgctgatgtgaggtttgtgttcgtgtttgtg-tgatgcgcacagGTAAGAAGGAGAGGAGGAGAAAATGGTGAAGCACAACAACGTTATCCCCAATGGCCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAAC---------------

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G409407_T01 (Zea mays), 3'ss of exon 1
-----------------tcttttttcattcagatttttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaat--ttgtgatggtattttgtttgtgctgccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
                 |  |  |    | |      ||    | |   |  |   |||||     ||||  ||  |    |  |||   ||   |   | |      |  |   | |||   |  ||||| ||||| ||||| ||| | || || |||||||||||||| || |||||||| |||||||| || |||||                   
tgcctgctttgatatcgtgctgctgggctaacgaggatggagctttggcggctccgtttgttgttcagctggatgacgtggttattgcattgacgtgcagGTAAGAAGGTAAGGAAGAGG-GCGAAATGGTGAAGCACAACAACGTTATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTC------------------

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G081102_T03 (Zea mays), 3'ss of exon 1
-------------tcttttttcattcagatttttgtgtttcttttga-gttattttgtgacggagctaa-atcgcaaaatttgtgatggtattttgtttgtgctgccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
                |  || ||||   ||   ||| |    | |  | |  | | ||  |  ||    |  |     ||  ||||| | |   | |      |  |   | |||   |  ||||| ||||| ||||| ||  | || || |||||||||||||| || |||||||| |||||||| || ||||| |||||             
tggagctggcggcagctcgttgattcttgttcccgtggtgtgctcgttgctcgtctctgctgatgccgtcactgttgcgttgttgatg-tgtacaggtaagAAGGAGAGAAAGAGG-GCGAAATGGTGAAGCACAACAACGTCATCCCCAACGGGCACTTCAAGAAGCACTGGCAGAACTATGTCAAGACATGGTTCAACCA-------------

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G17370.1 (Glycine max), 3'ss of exon 1
--tcttttttcattcagatttttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggt-attttgtttgtgctgccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
  |  | | | | |  |  ||| ||  ||  ||||  || |||| | | |    ||  |||      ||||  |  |  || | ||  |||||  ||||  |||||||| |||||||||||||| |||||| | || ||||||||||||  |||||| ||||| || ||||| || ||||||||||| ||||| || || || 
tatagtatgttaattggggttt-gtagttgatttgtctt-ttttat-atgatcttatgtcgaccctgttgttttatttgttcttttattgctgtaatttgtagGTAAGCAATGGTTAAGCATAATAATGTTATCCCCAATGGGCACTTCCGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCCCGAAAG

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G08090.1 (Glycine max), 3'ss of exon 1
--tcttttttcattcagatttttgtgtttcttttgagttattttgtga-cggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
  |  | ||| | |  |  |||   | |  |||    ||  |   ||| |  |  |  | |      ||| |  || | |||| ||   | || |||||  |||||||  ||||||||||||||||| ||| | || ||||||||||||| |||||| ||||| || ||||| || ||||||||||| ||||| || || || 
catagtattttaattggggtttgcagctgatttgtcttttatacatgatcatatgttgaccctgttgttttttttgttcttttatt---gttgtcatttgtagGTAAGATATGGTTAAGCATAACAACGTTATCCCCAATGGGCACTTCAGGAAACACTGGCAAAACTATGTGAAGACTTGGTTTAATCAACCAGCACGGAAG

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G14640.2 (Glycine max), 3'ss of exon 1
--tcttttttcattcagattt--ttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttacagGT--AAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
  | | |  |   || | | |  ||  | ||  ||    ||||    | ||     || ||     || ||||  | ||   |    |||  ||        | |   |||||||||||||||||||||||||| | || ||||| ||||||   || || |||||||| ||||| || || ||||| || || || ||       
tgtttgtgattgatctgctatggttacgctttcttgtgcttatccaattaccttattacataatctaacttgttgtcgtggatgacctgttatgtgtaagGTAAGCCAAAGCCATGGTTAAGCATAACAATGTTATCCCCAATGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACCTGGTTCAATCAGCCAGCA------

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G14640.1 (Glycine max), 3'ss of exon 1
tcttttttcattcag-atttttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttacagGT--AAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
   |  || ||     ||  ||  | ||  ||    ||||    | ||     || ||     || ||||  | ||   |    |||  ||        | |   |||||||||||||||||||||||||| | || ||||| ||||||   || || |||||||| ||||| || || ||||| || || || || || || 
--gtgattgatctgctatggttacgctttcttgtgcttatccaattaccttattacataatctaacttgttgtcgtggatgacctgttatgtgtaaggtaagCCAAAGCCATGGTTAAGCATAACAATGTTATCCCCAATGGACACTTCCGTAAGCACTGGCAGAACTATGTGAAGACCTGGTTCAATCAGCCAGCACGGAA-

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G49010.1 (Arabidopsis thaliana), 3'ss of exon 1
tcttttttcattcagatttttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttg--tgctgccatttacagG--TAAGCCATGG---TTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
  |||| |  || |  |||  |  ||| |  |  | | |  |    | |    || |  ||  |||||   |   | | ||| ||  || ||   |||    |  | ||     |   | ||||| ||||||||| | || ||||| |||||||| || || ||||||||||||||||| || ||||| ||||| |||||  |    
--ttttgtttttgaagtttgaggttttatcatttgatttccttgagctgtttaaagtttcatcatttgatttaa-agtgtgtctgattgatgttttttggcagCTTGAGTTGAAGAAATGAAGCACAACAATGTTATCCCCAATGGTCACTTCAAAAAGCACTGGCAGAATTATGTCAAGACATGGTTCAACCAGCCTGCCAG----

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G23900.1 (Arabidopsis thaliana), 3'ss of exon 1
tcttttttcattcagatttttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA------
  |  | |   |    |       ||    ||||  | | |  | |     ||     |   | ||| |  |  | || |        |    |||   | | ||  |   | ||||| ||||| ||| | || |     |||||    || || ||||||||||||||||| |||||||||||||| |||||  | ||       
--taatgttgcttgtgtaacatgattagggttgaaatctatgattattttacttctctgtttagtttattctcatgttgta---acatttgtgtttgttgcttagAAA-AATGAAGCACAACAACGTTATCCCGAGCTCACACTTTCGCAAGCACTGGCAGAATTATGTCAAGACTTGGTTTAACCAGCCTGCCAGGAAGACAAGG

upper sequence: Vv14s0006g00820.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S126_52V6.1 (Physcomitrella patens), 3'ss of exon 1
tcttttttcatt-cagatttttgtgtttcttttgagttattttgtgacggagctaa-atcgcaaaatttgtgatggtattttgtttgtgctgc---catttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
| |  |    |  |  |||||||||||  | |||   || || |||| | |   |  |  |    |||  |||||      | |||||| ||      |  | || | |  |||||| ||||||||||||||| | || ||||| |||||||||||  | ||||| || ||||| |  || ||||||||||| || || ||||  
tgtgatggagtggcgtatttttgtgttgttgttg---taattcgtgaagcaataattagggtcggattgttgatgtcgcaatttttgtgatgtgtatgtgaagAGTTGAAACATGGTGAAGCATAACAATGTTATCCCCAATGGCCACTTCAAGAAGGACTGGCAAAACTATGTGAGGACCTGGTTTAACCAGCCCGCCCGCA--

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|26256908|gb|CA807971.1|CA807971
EST:     AGGCAGTGCTNAGGGGGTATCAGTCTTTAAG                         GTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAA
genomic: AGGCAGTGCT-AGGGGGTATCAGTCTTTAAGgtatgcttgc ... ccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAA
EST: gi|29781900|gb|CB346727.2|CB346727
EST:     GGCAGTGCTAGGGGGTATCAGTCTTTAAG                         GTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAA
genomic: GGCAGTGCTAGGGGGTATCAGTCTTTAAGgtatgcttgc ... ccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAA
EST: gi|30303531|gb|CB980325.1|CB980325
EST:     GCAGTGCTAGGGGGTATCAGTCTTTAAG                         GTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAA
genomic: GCAGTGCTAGGGGGTATCAGTCTTTAAGgtatgcttgc ... ccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAA
EST: gi|26256977|gb|CA808040.1|CA808040
EST:     AGGCAGTGCTAGGGGGTATCAGTCTTTAAG                         GTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAA
genomic: AGGCAGTGCTAGGGGGTATCAGTCTTTAAGgtatgcttgc ... ccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA
    agctaaa  putative branch site (score: 3)
                             tattttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttttttcattcagatttttgtgtttcttttgagttattttgtgacggagctaaatcgcaaaatttgtgatggtattttgtttgtgctgccatttacagGTAAGCCATGGTTAAGCATAACAATGTTGTGCCTAATGGGCACTTCAAGAAACATTGGCAGAATTATGTCAAAACTTGGTTTAACCAACCTGCTCGCAAA

- - - - cattcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caaaatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgatgg