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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgtatgtacctcagtgtttatttttccatctgtaaagctttgtttcctttaaaattctgaacgacatatttggtgattcactttttatcatttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA

Basic information

species Vitis vinifera
transcript Vv06s0004g04930.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------acttgtatgtacctcagtgtttatttt---tccatctgtaaagctttgtttcctttaaaattctgaa-cgacatatttggtgattcactttttat---cat-ttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA
                                                        ||   | ||  |    |   | |  |     |||| |  || |||  |||      |    | | || |   | || |      ||   | | ||   ||| |  ||| || || || || ||||||| |  |||||| ||  | |||||||||||||| |  |||||||||||||||||||| ||||| || || ||||||||||| 
gtgaattattagaattgtatttgtttcttggagatctgcgtgccttaatatttttgacccatttgagctaatggaataaaatggaaaccattttgaaggctgcgttgggaccacttgtataaatcagtaaatctaacccctctaatataatttccatgtcacagGACTCGAGTGACACTAAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGCACTTGGGTTGATTCT

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G114126_T01 (Zea mays), 3'ss of exon 6
---------------------------------acttgtatgtacctcagtgtttatttttccatctgta---aagctttgtttcctttaaaattctgaacgacatatttggtgattcactttttatcattt-------gcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA
                                 |  ||||||  | | |   | | || ||  |     |   || | || ||        ||||  || |      | |  |   |    |  ||| ||||        ||| ||  | || || || |||| |  |||||| ||  | |||||||||||||| |  |||||||||||||||||||| ||||| || || ||||||||||| 
gttaattgttagaattgtatttctttcttggagatctgtatg-gcttaaaaatattttattggaataaaatggaaacctttttgaaggctgaattgggaccagttattctaatccctgctgtaatataatttccatgtcacagGACTAGAGTGACACTTAAAAAATCTGGTGTCGTGTTGGATTTGGTGCCACCACTAACAAAGGTTAACAACCTGATATTTGGGCGTACTTGGGTTGATTCT

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 6
---acttgtatgtacctcagtgtttatttttccatctgtaaagctttgtt-tcctttaaaattctgaacgacatatttggtgattcactttttatcatttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA
   | |  |   | | | | | |||| |  |   | |    | ||  ||| |||| |    || | |    | |||||    |   |||| |     |||||||||||||||| || || || ||||||||||||||| ||||||||||||||||||| ||||||||||||||||| || ||||| || || ||| ||||||||
caaaataattcttgcttaaat-tttaatcctagttgttctgatctgagttatcctgttttgtttttatttgc-tatttaaaaaaggacttgta--tgtttgcagAACACGTGTGACCCTTAAGAGAGATGGTGTTGTCTTAGATTTGGTGCCACCTCCTACAAAGGTTAACAACCTCATATTTGGCCGAACTTGGATTGATTCA

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 6
acttgtatgtacctcagtgtttattt--ttccatctgtaaagctttg---tttcctttaaaattctgaacgacatatttggtgattcactttttatcatttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA
   || |   |    | | || ||||  | | |  |||   | | ||   | |||| |    || | |    | |||||    |      || |||  |||||||||| ||||| || || || ||||||||||||||| ||||||||||||||||||| ||||||||||||||||| || ||||| || || ||| ||||||||
-tatgcaacaaaacaattcttgatttaatcctagttgttctgatctgaattatcctgttttgttgttatttgc-tatttaaaaag--gacttgtat-gtttgcagAACTCGTGTGACCCTTAAGAGAGATGGTGTTGTCTTAGATTTGGTGCCACCTCCTACAAAGGTTAACAACCTCATATTTGGCCGAACTTGGATTGATTCA

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 6
--acttg-tatgtacctcagtgtttatttttccatctgtaaagctttgtttcctttaaaattctgaacgacatatttggtgattcactttttatcatttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA
  | ||| | |   | ||| | ||| | ||  ||   | |  |   | ||||  | |   |  ||   |  ||| ||   | ||   |  | ||  ||||||||||||| || || || || || |||||||| ||| |||||||||| || ||||| || |||||||| ||  |||| ||||| || |||||| ||||||||
agatttggtcttcgcttcactttttttgttcaca---gaattgtcatttttctatcattttcttgctaggaataattataggttttgtgatcattgtttgcagAACACGGGTAACCCTCAAGAGGGATGGTGTAGTCATAGATTTGGTTCCCCCTCCAACCAAGGTTAATAATTTGATATTTGGCCGAACATGGATTGATTCA

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 6
-----acttgtatgtacctcagtgtttatttttccatctgtaaagctttgtttcctttaaaattctgaacgacatatttggtgattcactttttatcatttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA
     |    || | |     ||| |       | || |    ||||||  |  |||  | | | | | | |   |  |  ||   |   | |  |   ||||||||| ||||| || || || | ||||||||| || || ||||||||||| |||| ||| ||| || |||| || || |||||||| || |||||||| |||
acgaaagagatacgaaagattgtgatgtaaccactatgttagtagcttttctgtctt--atactttcatcta---agctcatgcagccggtctattggcttgcagAACGCGTGTAACCCTCAAGAAAGATGGTGTGGTTCTGGATTTGGTGCCGCCTCTCACTAAGATTCACAATCTAATATTTGGACGAACCTGGGTTGACTCA

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|110688435|gb|EE066987.1|EE066987
EST:     TTAAAAACCAAATTTTTAGGGAACTTCCTGGATGTCTATCCTGTTGGAAG                         AACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACC
genomic: TTAAAAACCAAATTTTTAGGGAACTTCCTGGATGTCTATCCTGTTGGAAGgttagaatca ... tcatttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACC
EST: gi|30133371|gb|CB918710.1|CB918710
EST:     TTAAAAACCAAATTTTTAGGGAACTTCCTGGATGTCTATCCTGTTGGAAG                         AACACGTGTTACTCT
genomic: TTAAAAACCAAATTTTTAGGGAACTTCCTGGATGTCTATCCTGTTGGAAGgttagaatca ... tcatttgcagAACACGTGTTACTCT
EST: gi|30252454|gb|CB970005.1|CB970005
EST:     TTAAAAACCAAATTTTTAGGGAACTTCCTGGATGTCTATCCTGTTGGAAG                         AACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACC
genomic: TTAAAAACCAAATTTTTAGGGAACTTCCTGGATGTCTATCCTGTTGGAAGgttagaatca ... tcatttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcctttaaaattctgaacgacatatttggtgattcactttttatcatttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA
                                      ctttttatc  CT-rich tract
     tttaaaattctgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgtatgtacctcagtgtttatttttccatctgtaaagctttgtttcctttaaaattctgaacgacatatttggtgattcactttttatcatttgcagAACACGTGTTACTCTAAAAAGAGATGGTGTTGTCCTAGATTTGGTGCCACCTCCCACAAAGGTTAACAACCTGATTTTTGGACGGACATGGGTTGATTCA

- - -tatgtac
- - - - - - - - - - - - - - ccatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - -aaaattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgat