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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatatttgagtatcagataatggattatgccccataactttcattcagaatatgtgttgcaattttgtggttgatatgattttgatttttctttatcagGTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGGAATCGTGCTGCTCGCCAACGGATTTCCAATAGGATTTGGACTGATGAAG

Basic information

species Vitis vinifera
transcript Vv02s0033g01350.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0033g01350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G174236_T02 (Zea mays), 3'ss of exon 5
ggatatttgagtatcagataatggattatgccccataactttcattcagaatatgtgttgcaattttgtggttgatatgattttgatttttctttatcagGTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGGAATCGTGCTGCTCGCCAACGGATTTCCAATAGGATTTGGACTGATGAAG
                         || |     || |  ||  ||     ||  |  |    ||||     |  ||    ||| || | | ||| | ||||   |   || |||||   |||||||||||| ||||||||||||| ||| || ||||| ||||| ||| | ||| | |||| ||||||||| ||||| |
------------------------gttttcgttgatgatgttattttcctgtagatagttgtgttttccctctcttactggttttatatat-tttgttagGTCACGTCAAGGATTGGCCACCCTATTACTGGATATGGCCAGGAAACTAGAAACCGTGCAGCTCGGCAAAGAATTCCAAATAAGATTTGGACAGATGAGG

upper sequence: Vv02s0033g01350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G31810.1 (Glycine max), 3'ss of exon 3
ggatatttgagt--atcagataatggattatgccccataactttcattcagaatatgtgttgcaattttgtggttgatatgattttgatttttctt-tatcagGTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGGAATCGTGCTGCTCGCCAACGGATTTCCAATAGGATTTGGACTGATGAAG
 ||| | |||||  |        |||   |||     |  ||    |||   |  ||| | ||  ||||   |||||  ||   | |||||   || |   || | || || || |||||||  || |||||||||||||| ||||| ||||| ||||| |||||||||||| | ||| |  | ||| | ||||||||||| |
tgatttgtgagttaactttggtttggggaatgaatagtggctg--gttctatacctgt-tggctgtttttatgttgacttgcgatggatttactttgtgctagATACGAGTAAGGATTGGATTTCCAATTACTGGTTATGGTCAGGAGAGTAGAAATCGAGCTGCTCGCCAAAGAATTCCTCACAGGGTATGGACTGATGAGG

upper sequence: Vv02s0033g01350.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G35830.3 (Glycine max), 3'ss of exon 3
ggatatttgagt--atcagataatggattatgccccataactttcattcagaatatgtgttgcaattttgtggttgatatgattttgatttttctt-tatcagGTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGGAATCGTGCTGCTCGCCAACGGATTTCCAATAGGATTTGGACTGATGAAG
 ||| | | |||  |        |||   |||    ||| |      |   |    || ||||  ||||   ||| |  ||   | |||||   || || ||||| ||||| || |||||||  || |||||||||||||| ||||| ||||| || || |||||||||||| | ||| |  | ||| | ||||||||||| |
tgatttgtaagttaactttgctttggggaatga---atagcggctggttctataccgttttgctgtttttgtgttcacttgggatggatttgctttgtaccagGTACGGGTGAGGATTGGATTTCCAATTACTGGTTATGGTCAGGAGAGTAGAAACCGAGCTGCTCGCCAAAGAATTCCTCACAGGGTATGGACTGATGAGG

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|33409166|gb|CF214793.1|CF214793
EST:     GTACAAAATTTTTGGGAAGGCTCTCAAAAGGGTTCAAGAAGACGGTCAG                         GTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGG
genomic: GTACAAAATTTTTGGGAAGGCTCTCAAAAGGGTTCAAGAAGACGGTCAGgtttgtgcga ... tctttatcagGTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGG
EST: gi|33409087|gb|CF214714.1|CF214714
EST:     GTACAAAATTTTTGGGAAGGCTCTCAAAAGGGTTCAAGAAGACGGTCAG                         GTTCGGGTCAGAATTGGAT
genomic: GTACAAAATTTTTGGGAAGGCTCTCAAAAGGGTTCAAGAAGACGGTCAGgtttgtgcga ... tctttatcagGTTCGGGTCAGAATTGGAT
EST: gi|110726779|gb|EE102857.1|EE102857
EST:     GTACAAAATTTTTGGGAAGGCTCTCAAAAGGGTTCAAGAAGACGGTCAG                         GTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGG
genomic: GTACAAAATTTTTGGGAAGGCTCTCAAAAGGGTTCAAGAAGACGGTCAGgtttgtgcga ... tctttatcagGTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGG
EST: gi|161714198|gb|FC062943.1|FC062943
EST:     GTACAAAATTTTTGGGAAGGCTCTCAAAAGGGTTCAAGAAGACGGTCAG                         GTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGTAAAGTAGG
genomic: GTACAAAATTTTTGGGAAGGCTCTCAAAAGGGTTCAAGAAGACGGTCAGgtttgtgcga ... tctttatcagGTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagaatatgtgttgcaattttgtggttgatatgattttgatttttctttatcagGTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGGAATCGTGCTGCTCGCCAACGGATTTCCAATAGGATTTGGACTGATGAAG
                                   ttttgat  putative branch site (score: 4)
                                   ttttgatttttcttt  CT-rich tract
                             atatgattttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatatttgagtatcagataatggattatgccccataactttcattcagaatatgtgttgcaattttgtggttgatatgattttgatttttctttatcagGTTCGGGTCAGAATTGGATCCCCTATTACTGGTTATGGCCAGGAAAGTAGGAATCGTGCTGCTCGCCAACGGATTTCCAATAGGATTTGGACTGATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - tatgccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggttg