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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacaaaaatttagtaatgagtatgatttcagcctatactgtccattttgtagcagaaaattgaatcaaattgtatggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACGTACTGGTGGAGCCACGCCATGATCTCTGATAAAACGTACCGGCAGCTCA

Basic information

species Vitis vinifera
transcript Vv14s0068g00260.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g00260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G879749_T01 (Zea mays), 3'ss of exon 6
-----------------gtaacaaaaatttagtaatgagtatgatttcagcctatactgtccattttgtagcagaaaattgaatcaaattgtatggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACGTACTGGTGGAGCCACGCCATGATCTCTGATAAAACGTACC-GGCAGCTCA
                 | |          |   | ||| | |    | |||       |||| | |  | |  ||         |||    |   |   ||||| ||||| || || || ||||||||||| |||||| | || || ||||| ||||||||||  |||||||||||||| ||    || |||  |||    | 
gtgagtatcgtatctatgcatgctgctgccaaacacgagcaggccgccggccggccggctccagtcta-atcttaacccctccaaaaaaaaaacaccgatcagGTGGGCAACGCGGTGACCGACAACTACTACGACAACATCGGCACGGTCACCTACTGGTGGACGCACGCCATGATCTCCGACCGCACCTACAAGGCCATCC-

upper sequence: Vv14s0068g00260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G50170.1 (Glycine max), 3'ss of exon 3
--------gtaaca-aaaatttagtaa--tgagtatgatttca-gcctatactgtccattttgtagcagaaaattgaatcaaattgt--atggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACGTACTGGTGGAGCCACGCCATGATCTCTGATAAAACGTACCGGCAGCTCA
         ||| | || || ||  |   | |  ||| | | |     |    |   || |||  |  |||  ||  || | |||    |||  |||||||| || |||||||| ||||||||||||||||| ||| |||| ||||| ||||| ||||||||||| || |||||||| ||  | || |||||||| || |
ttgacattttaagataagatgtaaaagattaaagatggtattataagaaggaggagaatattgatggtgaagttttgataatattaatgatgcaatgcagGTAGGAAATGCAGTGACAGACAACTACTATGATAACTTGGGCACAGTGACGTATTGGTGGAGCCATGCTATGATCTCCGACCAGACTTACCGGCAACTAA

upper sequence: Vv14s0068g00260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA08G26930.1 (Glycine max), 3'ss of exon 3
-------gtaaca----aaaatttagtaatgagtatgatttcagcctatactgtccatt-ttgtagcagaaaattgaatcaaattgt--atggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACGTACTGGTGGAGCCACGCCATGATCTCTGATAAAACGTACCGGCAGCTCA
        | |||    || ||    | ||    ||| | | |    |    ||  | | |||  |  |||  ||   | | |||    |||  |||||||| || |||||||| ||||||||||||||||| ||| |||| ||||| ||||| ||||||||||| || |||||||| ||  | || | |||||| || |
taatatcttgacattttaagataagattatatagatgttgttataagaaggggtggaatattgatggtgaagttttgttaatattaataatgcaatgcagGTAGGAAATGCAGTGACAGACAACTACTATGATAACTTGGGCACAGTGACGTATTGGTGGAGCCATGCTATGATCTCCGACCAGACTTTCCGGCAACTAA

upper sequence: Vv14s0068g00260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G02110.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaacaaaaatttagtaatgagtatgatttcagcctatactgtccattttgtagcagaaaattgaatcaaattgtatggcat--gcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACGTACTGGTGGAGCCACGCCATGATCTCTGATAAAACGTACCGGCAGCTCA
              ||||| |  |       |  || |  | | ||||    |  ||||   ||  |  ||  |    |  |  | ||||||| || || || || |||||  ||||||| ||||| ||||| ||  |||| |||||||||||||| ||||||||||||   ||||| |  ||| | |
--------------gtaattaagaaaccaaaatactctgtttttcattac-caaaagaatggtgtttgtaaccgctgcgtttttgtagGTTGGAAACGCGGTGACGGACAATCACTATGATAACCTAGGAACGGTTTCGTATTGGTGGAGCCACGCGATGATCTCTGATCGGACGTATCATCAGTTGA

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|30255072|gb|CB971519.1|CB971519
EST:     TGGCCTACAACGCCAAATACAAGCATGCCATAAATCTCAAAGGAATAATG                         GTTGGAAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
genomic: TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATGgtaacaaaaa ... tggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
EST: gi|349832475|gb|FQ421036.1|FQ421036
EST:     TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATG                         GTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
genomic: TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATGgtaacaaaaa ... tggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
EST: gi|110689497|gb|EE065771.1|EE065771
EST:     TGGCCTACAACGCCAAATACAAGCATGCCATNAATCTCAAAGGAATAATG                         GGTGGCAATGCANTAACAGACAACTACTATGAACAAC-TGGGAACAG
genomic: TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATGgtaacaaaaa ... tggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGA-CAACCTGGGAACAG
EST: gi|351027112|gb|FQ439973.1|FQ439973
EST:     TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATG                         GGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAAC
genomic: TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATGgtaacaaaaa ... tggcatgcagG-TTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAAC
EST: gi|349829923|gb|FQ422236.1|FQ422236
EST:     TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATG                         GTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
genomic: TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATGgtaacaaaaa ... tggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
EST: gi|351015449|gb|FQ447278.1|FQ447278
EST:     TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATG                         GTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
genomic: TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATGgtaacaaaaa ... tggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
EST: gi|349832339|gb|FQ420900.1|FQ420900
EST:     TGGCCTACAACGCCNAATATAAGCATGCCATAAATCTCAAAGGAATAATG                         GTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
genomic: TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATGgtaacaaaaa ... tggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
EST: gi|110684702|gb|EE062281.1|EE062281
EST:     TGGCCTACAACGCCAAATACAAGCATGCCATAAATCTCAAAGGAATAATG                         GTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
genomic: TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATGgtaacaaaaa ... tggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
EST: gi|349828534|gb|FQ417276.1|FQ417276
EST:     TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATG                         GTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG
genomic: TGGCCTACAACGCCAAATATAAGCATGCCATAAATCTCAAAGGAATAATGgtaacaaaaa ... tggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcctatactgtccattttgtagcagaaaattgaatcaaattgtatggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACGTACTGGTGGAGCCACGCCATGATCTCTGATAAAACGTACCGGCAGCTCA
                          aaaattgaatcaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacaaaaatttagtaatgagtatgatttcagcctatactgtccattttgtagcagaaaattgaatcaaattgtatggcatgcagGTTGGCAATGCAGTAACAGACAACTACTATGACAACCTGGGAACAGTCACGTACTGGTGGAGCCACGCCATGATCTCTGATAAAACGTACCGGCAGCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA