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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttgcttgacttaggtgggccccttgctcttctaaacatatagacgcattttaaagtcataaggagaaagagttattacatgtaccttgtttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC

Basic information

species Vitis vinifera
transcript Vv12s0059g02280.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g33850.2 (Oryza sativa), 3'ss of exon 5
-atttgcttgac---ttaggtgggccccttgctcttctaaacatatagacgcattttaaagtcataag-gagaaagagttattacatgtaccttgtttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC
 || ||   | |   | | || ||      |    |   ||  | |     | || ||   |  |    ||   ||  || ||   | |  ||    |||  ||||| || || ||||| |  ||  | || || || ||||||||||| ||| | ||  ||||||| |||||||||||||||||||| |||||||| || || |
catatgtcagtcccttaaagtcggaggacagtaagttagaaggtttttttccgttgtattcttgtttctgatggaggattttt---tttttctgaaattt--cagGCCAGGGCATACGCGAGAGCGATGAAGGCGACCCTCTTCTTCTCCAGCTCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC

upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G125507_T01 (Zea mays), 3'ss of exon 5
atttgcttgacttaggtgg-gccccttgctcttctaaacatatagacgca-ttttaaagt-cataaggagaaagagttattacatgtaccttgtttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC
   | |    |    |||| |      |   ||| |  | ||| ||  || |  ||| || | |   ||     |   | |     |    ||||     ||||| ||||| ||||| |  ||  | || || || ||||||||||||||||| ||  ||||||| |||||||||||||||||||| |||||||| || || |
---tacagctccagagtggagtgttgcgaagttccattcctatcgaaacaatactaatgtgcgtgtcgatcgctaacaaatgtggtttgtgtgttcccaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC

upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G027344_T01 (Zea mays), 3'ss of exon 5
atttgcttgact-taggtgggccccttgctcttctaaacatatagacgcattttaaagtcataaggagaaagagttattacatgta--ccttgtttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC
   | |   |||   | ||  |  |    | || | ||  |  |  |  ||   |||        | |      ||  || | ||   |  ||||  |  ||||| ||||| ||||| |  ||  | || || || ||||||||||||||||| ||  ||||||| |||||||||||||||||||| |||||||| || || |
---tacagcactgctgctgcacagcggagtgttgtgaagttccattcctatcggaaacaatctgtgcgcgttgattgctaaaagtgatctgtgttcctaacagGCCAGAGCATACGCAAGAGCGATGAAGGCGACCCTCTTCTTCTCGAGCGCGACGCACAACATCAACGTGAACAAGATCTTCAAGTTCATCACGGCCAAGC

upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G46250.1 (Glycine max), 3'ss of exon 3
-atttgcttgacttaggtgggccccttgctcttctaaacatatagacgcattttaaagtc-ataaggagaaagagttattacatgtaccttgtttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC
 | |   | || |  |    | |      |  ||      |  |||     ||| | ||  || | ||  | | ||  |   ||||   |    ||   |||||||||   || || |||||||| ||||| ||  | ||||| || || |||||||||||||| || ||||||||||||||||| |||||||| || ||||
taatacatcgattatgcaaagGCAAGAAATTCTCAGGTTTTCAAGATAAGATTTGATGTTGATGATGATGATGTGTGTTGCGATGTG--TGACATTGAACAGGCAAGAAATTATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCATCACTGCTAAAC

upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G10670.1 (Glycine max), 3'ss of exon 5
atttgcttgacttaggtgggccccttgctcttctaaacatatagacgcattttaaagtcataa--ggagaaagagttattacatgtaccttgtttttgg-cagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC
 || |  ||   || |  |||         |   ||| | ||       |||| |||  |  |   ||  | || || |    |||    ||   |||  |||||||||   || || |||||||| ||||| ||  | ||||| || || |||||||||||||| || ||||| ||||||||||| |||||||| || ||||
-ttggaatg--ctatgcaggctttccaagatagcaaaaaaattcttatgttttcaagataagatttgatgatgatttgtgttgtgttttgtgacattgaacagGCAAGAAAATATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAATAAGATCTTCAAGTTCATCACTGCTAAAC

upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G46120.1 (Glycine max), 3'ss of exon 5
atttgcttgacttaggtgggccccttgctcttctaaaca--tatagacgcattttaaagtcataaggagaaagagttattacatgtaccttgtt--------tttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC
           |    ||        ||| | | ||| |  || |||   ||| | | ||  | | || ||    | || |  |||     | |        ||   |||||||||   || || |||||||| ||||| ||  | ||||| || || |||||||||||||| || ||||||||||||||||| ||| |||| || ||||
----------ttggaatgctatgtaggctttccaaaatagctaaagaaaaattctcaggttttcaagataagatttgatgatgtgtgttacgatgtgtgacattgaacagGCAAGAAAATATGCAAAGGCCCTCAATGCCACCTTGTTCTTTTCAAGTGCAACCTACAACATCAATGTGAACAAGATCTTCAAGTTCGTCACTGCTAAAC

upper sequence: Vv12s0059g02280.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G21700.3 (Arabidopsis thaliana), 3'ss of exon 4
atttgcttgacttaggtgggccccttg---ctcttctaaacatatagacgcattt-taaagtcataaggagaaagagttatt--acatgtaccttgtttt---tggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC
   |  |    |||       |  |||      ||  ||   ||   ||  ||   || ||| | |   |  |  | |||||  |||| |    ||||||   |  ||||| ||| | || || |||||  |||| || ||||||||||||||||| ||  | ||||||||||||||||| |||||||| || ||  | || || || |
--gtaatgtttttaaccatatcttttgaagtcatttgaattctagtaacaaatcaatacagtgaaattcaatataatttattttacatttggaatgttttgtgtaacagGCGAGAACATATGCGAAGGCTTTAAACGCGACGCTCTTCTTCTCGAGTGCTTCATACAACATAAACGTGAATAAGATCTTTAAGTTTGTGACGGCGAAGC

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|26265133|gb|CA816196.1|CA816196
EST:     ACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAG                         GCAAGAGCATACGCTAAGGCCCTAAATGCGACGCTCTTCTTCTCGAGCGCA
genomic: ACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAGgtaaattttt ... tttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCA
EST: gi|110383289|gb|EC947654.1|EC947654
EST:     ACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAG                         GCAAGAGCATACGCTAAGGCCCTAAATGCGACGCTCTTCTTCTCGAGCGCA
genomic: ACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAGgtaaattttt ... tttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCA
EST: gi|34544942|gb|CF513174.1|CF513174
EST:     ACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAG                         GCAAGAGCATACGCTAAGGCCCTAAATGCGACGCTCTTCTTCTCGAGCGCA
genomic: ACGATTTCATCCAACTTCCCATTGACCTGCAATGGACAGTTGCAAGTCAGgtaaattttt ... tttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcattttaaagtcataaggagaaagagttattacatgtaccttgtttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC
                                        ccttgttttt  CT-rich tract
                            ttattacat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttgcttgacttaggtgggccccttgctcttctaaacatatagacgcattttaaagtcataaggagaaagagttattacatgtaccttgtttttggcagGCAAGAGCGTACGCTAAGGCCCTAAATGCAACGCTCTTCTTCTCGAGCGCAACCTACAACATAAACGTGAACAAGATCTTCAAATTCATCACAGCAAAAC

- - gcttgac
- - - - - - -aggtggg
- - - - - - - - - - ccccttg
- - - - - - - - - - - - - - - - ctaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtac