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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtatagatgtgaaatacaaagccatctggaactttttataacccatgattaggcttataaaagttgtagtttgccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT

Basic information

species Vitis vinifera
transcript Vv18s0001g00480.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g48290.1 (Oryza sativa), 3'ss of exon 4
---------------------------------------------------------------------gtatagatgtgaaatacaaagccatctggaactttttataacccat-gattaggcttat-----aaaagttgtagtttgccatttgat---ggtcat-ccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------
                                                                       |||  | |||| |        |  |   | |||| ||||   || |  |   ||| |     ||   || || |     | |  |     || || |||||||    |   |||| || || ||||| |||||||| || || |||||||| || ||||| ||||||||||||||||| |||||||| || ||||| || ||||||||      
gtatcctttaatttgacccttttttattgctacaccggttaggtaatatcactgttttaaatctctgtttcatatgtatgaagtgtttt-ttacttcatatttttgataatttattggatcttcttgttggccaatctttataatgcaaaaataaaaaaaagttattccttaatgtgggcctcagACATCTCAAAAGTGCAAGATGACGAAGTAGGTGATGGAACTACTTCTGTTGTTGTTTTGGCTGGTGAGCTTTTGAGGGAAGCTGAAAAGTTGGTAAATAT

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g42220.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------------------------------gtatagatgtgaaatacaaagccatctg-gaactttttataacccatgat--------taggcttataaaagttgtagtttgccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------
                                                                             |   |  | |    || | ||| |  || | |||| |  |  | |||| |        |  |  | | | |  | |  | |  ||    |      |||||||  ||  |   ||| || || ||||||||||||||||| |||||||| ||||| || || || ||||||||||||||||| ||||| || || || || ||||| ||      
gtatcctttcatttgaatctgttgcttgatgatttttcatactaacacaatagcaagtcatagatgaagtggcaaaggggcaagtttcctttatacagcaacatgcgtacttatagtttctcatgctacctcatttgagtatttgatatgtatgatgtatcaaggaagttaagtccttaacgcattgt-tagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGACGGGACAACCTCTGTGGTTGTTTTGGCTGGAGAACTTTTGAGGGAGGCTGAAAAGTTAGTTAACAT

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 12
gtatagatgtgaaatacaaagccatctggaactttttataacccatgattaggcttataaaagttgtagtttgccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT-----------------------------------
                                                     || || ||||    ||   |||| ||| |      |||||||      |  ||| || || ||||||||||||||||| |||||||||||||| ||||| ||||||||| | |||||||| ||||| |  || || ||||||||  |                                   
-----------------------------------------------------ctaatgaaag--aaag---gccagttgct------ccttaat--ggttgctagacatctcaaaagttcaagatgatgaagttggtgatgggacaacttctgttgttgttctagCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACATGAAAATTCATCCGATGACTATTATTGCAG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 3
gtatagatgtgaaatacaaagcc-atctggaactttttataacccatgattaggcttataaaagttgtagttt--gccatttgatggtcatccttaattcaagG--GACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------
         | || | || |  |    ||  || |  | |  ||| |  |  |   || |||  || |  |       |    | || |||   |  || | |      ||| || || ||||||||||||||||| |||||||||||||| ||||| ||||||||| | |||||||| ||||| |  || || ||||||||  |      
--------ttaaacttcatattctgcttgtgacctcatttggcccctcttctg---tacaaatattattttcctaatgaaagaaaggccattactccttaatgatcattagACATCTCAAAAGTTCAAGATGATGAAGTTGGTGATGGGACAACTTCTGTTGTTGTTCTAGCTGGAGAACTTTTGAAGGAGGCTGAGAAGTTAATTAACAT

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 5
gtatagatgtgaaatacaaagccatctggaactttttataacccatgattaggcttataaaagttgtagtttg-ccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------
 |     | |  |||||    ||   ||  | |  ||| | |   ||||  || |  |        |  ||    |||  |||  |||||||||||  |||    ||| ||||| ||||||||||||||||| ||||| ||||| || || ||||||||||| |||||||| || |||||||| || ||||| ||| ||||      
-tcaccgtttataatacctgtcc---tgttattaattagagcat-tgatgtggatctttctttgcatgtttaaatcataagataatcatccttaatgtaagt--tagACATATCAAAAGTTCAAGATGATGAAGTTGGGGATGGAACTACCTCAGTTGTTGTGTTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAAC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 5
gtatagatgtgaaatacaaagccatctggaactttttataacccatgattaggcttataaaagttgtagtttg-ccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------
 |     | |  |||||    || ||  |   ||  ||  | |  || |  || || |        |  ||    |||  |||   |||||||||| ||||    ||| ||||| ||||| ||||||||||||||||| ||||| || || ||||||||||| |||||||| || |||||||| || ||||| ||| ||||      
-tcactgtttttaatac----ccgtccagttattaataagagcattggtgtggatttttctttgcatgtttaaatcataagataaccatccttaatgcaagt--tagACATATCAAAAGTACAAGATGATGAGGTTGGGGATGGAACTACCTCAGTTGTTGTATTGGCTGGTGAACTTTTAAGGGAGGCAGAAAAGCTGGTTGCAGC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatagatgtgaaatacaaagccat--ctggaactttttataacccatgattaggcttataaaagttgtagtttgccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------
||||  |  |    | | |     |  |  ||| |||| | |  |  |  ||   ||||     ||| |   |  |  || | ||    |  ||  |||      |||| || || ||||||||||||||||||||||||||||| || || || |||||||| ||||| || |||||| | || |||||||| ||| | ||      
gtatgtaatttccctgcgacattctggcatgaagttttcacattcgtttttt---cttagttgggttttctctcacagttcgttgtatctggtttgttctt----cagACATCTCGAAAGTTCAAGATGATGAGGTTGGTGATGGAACTACCTCTGTTGTTGTCTTGGCCGGCGAGCTTCTGAGGGAAGCAGAAAAGCTTGTGGCTTC

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S116_55V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatagatgtgaaatacaaagccatctggaactttttataacccatgattaggcttataaaagttgtagtt----tgccatttgatggtcatccttaatt-caagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------
         | || |  ||||  || |    ||||  || | |  |   || |||| | |     || |||     | |    |   ||  ||  |  |   |   | ||||||| ||||| || ||||||||||||||||| ||||| || || || || || || ||||| || ||| |  ||||||| ||||||||||||||      
-------cat-aattgtaaaggaatttt---ctttacatcatcagttggtatgcttgtgagctgcgtggttgatacgacgagcggctgtgctctctgttcgtatttggcagATATTTCCAAGGTCCAAGATGATGAGGTTGGAGATGGTACAACATCTGTGGTAGTCTTGGCGGGGGAGTTGCTAAGAGAGGCAGAGAAGTTGGTCGCTCT

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S307_63V6.1 (Physcomitrella patens), 3'ss of exon 4
gtatagatgtgaaatacaaagccatctggaactttttataacccatgattaggcttataaaagttgtagtttgccatt-tgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT------
 |  | |      | |  ||||  | | |  ||  | |||  |||   | ||  | ||    |    | || |  | | || |   |  ||||  ||     ||||||||| || || || ||||||||||||||||| ||||| || || || || || || |||||||||||| |  ||||||| || |||||| ||||      
cttaaaacagtccacagtaagcatttttg--ctgatcatatgccagtgtaagtttaatggttgacacaattggggactgtgctccccgcccttgttt-----gacagATATTTCTAAGGTGCAAGATGATGAGGTTGGAGATGGCACAACATCTGTAGTAGTGTTGGCTGGAGAGTTGCTAAGAGAGGCGGAGAAGCTGGTTGCTCT

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|352769329|gb|FQ471478.1|FQ471478
EST:     CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTG                         --A----TATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
genomic: CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttac ... ttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
EST: gi|71880141|gb|DT029196.1|DT029196
EST:     CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTG                         --A----TATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
genomic: CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttac ... ttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
EST: gi|352782455|gb|FQ470358.1|FQ470358
EST:     CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTG                         --A----TATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
genomic: CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttac ... ttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
EST: gi|161714038|gb|FC064113.1|FC064113
EST:     CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTG                         --A----TATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
genomic: CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttac ... ttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
EST: gi|352765070|gb|FQ473718.1|FQ473718
EST:     CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTG                         --A----TATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
genomic: CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttac ... ttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
EST: gi|352773730|gb|FQ472512.1|FQ472512
EST:     CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTG                         --A----TATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
genomic: CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttac ... ttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
EST: gi|352777695|gb|FQ466748.1|FQ466748
EST:     CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTG                         --A----TATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
genomic: CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttac ... ttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
EST: gi|352781730|gb|FQ469028.1|FQ469028
EST:     CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTG                         --A----TATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
genomic: CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttac ... ttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
EST: gi|352777783|gb|FQ466836.1|FQ466836
EST:     CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTG                         --A----TATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT
genomic: CATCTTAAAGTCCCTTCATATTGACAACCCAGCTGCTAAAGTCCTTGTTGgtatccttac ... ttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattaggcttataaaagttgtagtttgccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT
                                           ccttaat  putative branch site (score: 4)
                                       tcatcctt  CT-rich tract
         ttataaaagttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagatgtgaaatacaaagccatctggaactttttataacccatgattaggcttataaaagttgtagtttgccatttgatggtcatccttaattcaagGGACAGATATATCCAAAGTTCAAGATGATGAGGTTGGTGATGGGACCACTTCAGTTGTTGTTTTGGCTGGAGAGCTTTTAAGAGAAGCAGAGAAGTTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - gaaatac
- - - - - - - - - - gccatct
- - - - - - - - - - - - - - - - - - - taaccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatggt