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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactttgcttatgttaaaagggtggaagagaacaagttgtttaagtgttccattttttcctttttttacaaatatgtggtgatacgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG

Basic information

species Vitis vinifera
transcript Vv14s0219g00120.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G015869_T02 (Zea mays), 3'ss of exon 2
-ttactttgcttatgt-taaaagggtggaagagaacaagttgtttaagtgttccattttttcctttttttacaaatatgtggtgatacgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG
  ||       ||| |   | |   |    ||  | |  || || || | |   ||  |   ||    |  ||  |    | | ||      |||||  |||||||| ||||| |||||||||||||||||||| ||| | ||||||||    |||||||| |||||  | |||||| |    || ||||||
aataaaacatctatttgccataacatctgtgaacagacatttttcaactatgaaatggtagtctccaatc-catttgacagttcatttttcctttat-gcagATGATTCCTGTTGCTGCAAATGATGTTGCTTTTTCACTGCATGCTGTAGCATTGACAGCCTTTACCGTTTTTCAAGTATTCATATATGAG

upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA16G07110.1 (Glycine max), 3'ss of exon 2
---ttactttgcttatgttaaaagggtggaagagaacaagttgtttaagtgttccattttttcctttttttacaaatatgtggtgatacgctt-tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG
   ||||   ||| ||   |||        |   ||    |  | | | |  |  |  | ||     ||    ||   ||| ||  ||   |  ||| || |||||||||||||| ||||||||||||||||||||||| || ||||||||| |  |||||||| |||| ||||| || |||||||||||||| 
attttacaaagctcat-ccaaacacacactaagtaatgtctgttcttatttatataaatatttggagttccctaa---tgtagttttagtttcatttgtttcagATGATACCTGTTGCTGCAAATGATGTTGCTTTCTCGATCCATGCTGTTCTACTGACAGCAATTACATTGTTCCAGATTGCAATCTATGAA

upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G23610.1 (Glycine max), 3'ss of exon 2
-ttactttgcttatgttaaaagggtggaagagaacaagttgtttaagtgt-tccattttttcctttttttacaaatatgtgg--tgatacgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG
 | ||| |  || | ||       ||    | ||| |  || | |  | | | |||   ||| ||   | |     ||   |  | ||    | |||||| ||||||||||| ||||| |||||||||||||||||||||   ||||||||| | ||||||||| || | ||||| || |||||||||||||| 
atcactctttttcttttcct----tgttgaataactatatgatgatatatctgcataaattcattagctaaagtccattctgcttcattttttatttatttcagATGATACCCGTGGCAGCAAATGATGTTGCTTTCTCAGCCCATGCTGTTCTGTTGACAGCAATTTCCTTGTTCCAGATTGCAATCTATGAT

upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G07750.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------ttacttt--gcttatgttaaaaggg----tggaagagaacaagttgtttaagtgttccattttttcctttttttacaaatatgtggtgatacgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG
                                                        ||||     |  || | ||||       ||     |  |||  |  |||  | |||   || |    |||      |  || |  || ||    ||  ||| |||||||| ||||| || || ||||||||||||||||| |||||| | || || || |    | |||   |||  |||||| |||| | ||| 
gtgggacttgaatttttcaaatggctagcaaaataatacaacacgagtcaccaatgtactgccaacaaatatcaaaatcaactttgtctttgtgcaaaatcattagatattcacgttatctagtttagctttatgatctcttgttat-tattgcattgcagATGATTCCTGTAGCCGCTAATGATGTTGCTTTCTCCATTCATTCAGTCATATTAAATTTAATTATACTGTCCCAAATTTCAATGTTTGAA

upper sequence: Vv14s0219g00120.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G40670.1 (Arabidopsis thaliana), 3'ss of exon 2
ttactttgcttatgttaaaagggtggaagagaacaagttgtttaagt-gttccattt--tttcctttttttacaaatatgtggtgata--cgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG
     ||| |  | |  ||      | | | || ||    ||||  | |||| |  |  |||  |||||||  |    | | || |||   | |  ||||| |||||||||||||||||||||||||||||||| ||||| || ||||| ||| |  |||||||  ||||  |||| || ||    |||||||| 
-----ttgttcctttctaagtttcagcaaaaaaaaaacgctttagattgttcgagctggtttaattttttttgagtcgttttgttataattgttgcttatttcagATGATACCTGTGGCTGCAAATGATGTTGCATTCTCGATCCATGCAGTTGTAATGACAGCTGTTACACTGTTCCAGATCTTTATCTATGAA

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|110723575|gb|EE101045.1|EE101045
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTCATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|351045861|gb|FQ441046.1|FQ441046
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|351030795|gb|FQ438633.1|FQ438633
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|349811028|gb|FQ406016.1|FQ406016
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|110699274|gb|EE076127.1|EE076127
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|294966259|gb|GW837510.1|GW837510
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|349820300|gb|FQ403916.1|FQ403916
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|349809992|gb|FQ398617.1|FQ398617
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|161711864|gb|FC059173.1|FC059173
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGAT
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGAT
EST: gi|110696243|gb|EE075180.1|EE075180
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|110724366|gb|EE100141.1|EE100141
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
EST: gi|34549515|gb|CF517747.1|CF517747
EST:     TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAG                         ATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC
genomic: TTAGCTCTGCTGTCCAGAGGCAGTACCGTGAGAAATATGGAATTGGACAGgtttgtgttt ... tttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgttccattttttcctttttttacaaatatgtggtgatacgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG
                                          ctttttatt  CT-rich tract
       attttttccttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactttgcttatgttaaaagggtggaagagaacaagttgtttaagtgttccattttttcctttttttacaaatatgtggtgatacgctttttattacagATGATACCTGTGGCTGCAAATGATGTTGCTTTCTCAATTCATGCTGTTATCTTGACAGCATTTACTTTGTTTCAAATTGCAATCTATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - -gcttatg
- - - - - - - - - - gggtgga
- - - - - - - - - - - - - - -agaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtggtg