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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgggcattgcaacaaaatagtcaaccatcctaggttttagctcatgatgcttaatcataagattcataactaaatgttgttcttttggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG

Basic information

species Vitis vinifera
transcript Vv08s0007g07400.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA19G28770.1 (Glycine max), 3'ss of exon 6
--ttgggcattgcaacaa-aatagtcaaccatcctaggttttagctcatgatgcttaatcataagattcataactaaatgttgttcttttggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG
   |   |||   | ||| | | |      ||  || |    || || | | ||| | |  |     | |||| |   | |   ||||||||| || ||| |||||||||||||||||||| || |||||||||||| | |||||||| || || || || ||||| || || ||||||
gtctcctcatataagcaatagttgaattatataataaggaaaaggtc-taaggctaatttgtttttattataattt--tatccatcttttggtacggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAGGCTGATGAG

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G04560.2 (Glycine max), 3'ss of exon 7
----ttgggcattgcaacaaaatagtcaaccatcctaggttttagctcatgatgcttaatcataagattcataactaaatgttgttcttttggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG
     |  ||| |     ||| | |      ||  || |    |  || | | ||| | |  |    || |||| |   | ||  |||||||||  | ||| |||||||||||||||||||| || |||||||||||| | |||||||| || || || || ||||| ||||| ||||||
tgatataagcaatattctaaagttgaattatataataaggaaaatgtc-taaagctaatttgttct-tttataattt--tattcatcttttggtatggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGCTAATCACCCAACTGACCCAGAAGCTGATGAG

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G26940.1 (Glycine max), 3'ss of exon 6
ttgggcattgcaacaaaatagtcaaccatcctaggttttagctcatgatgcttaatcataagattcataa--ctaaatgttgttcttt---------tggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG
            |||| || |           |  || | ||     || ||||| |||   |  |||||  |||||  || ||||||         |  |  | ||| |||||||| |||||||| ||||| |||||||||||| ||||||||||||| || || || ||||| || || ||||||
-----------gacaatattgcttgttgcataaacttattgcctgcaatccttaagcatcctaaacataagtctaaacctttttctttacctcttttttatatggttgaagGGAAAACGCAAATGAGATTAAGGCCAAATTTATTGTTGAAGCAGCCAATCACCCAACTGACCCGGAGGCTGATGAG

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G16320.1 (Glycine max), 3'ss of exon 8
--ttgggcattgcaacaa-aatagtcaaccatcctaggttttagctcatgatgcttaatcataagattcataactaaatgttgttcttttggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG
  ||   |||   | ||| | | |      ||  || |    || || | | ||| | |  |     | |||| |   | |   |||||||||  | ||| |||||||||||||||||||| || |||||||||||| | |||||||  || || || || |||||  |  ||||||||
gtttcctcatataagcaatagttgaattatataataaggaaaaggtc-taaagctaatttgtttttattataattt--tatccatcttttggtatggttgaagGGAAAATGCAAATGAAATCAAGGCCAAATTTATTGTGGAAGCAGATAATCACCCAACTGACCCAAAGCCAGATGAG

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA02G07940.1 (Glycine max), 3'ss of exon 7
ttgggcattgcaacaaaatagtcaaccatcctaggttttagctcatgatgcttaatcataagattcataa----ctaaatgttgttcttttggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG
|    | ||  | ||  | |  || | |||    ||| ||  |   |||   |||| |  |||  | |||     |   | |   ||||||  |  | ||| |||||||| |||||||| ||||| ||||||||| || ||||||||||||| || || || ||||| || || ||||||
tccatcctta-agcatcagaaacatctatct---gttctaaatggagatatataatgaacagaagcgtaaacctttttctttccctctttttatatggttgaagGGAAAACGCAAATGAGATTAAGGCCAAATTTGTTGTTGAAGCAGCCAATCACCCAACTGACCCGGAGGCTGATGAG

upper sequence: Vv08s0007g07400.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G03910.1 (Arabidopsis thaliana), 3'ss of exon 6
ttgggcattgcaacaaaatagtcaaccatcctaggttttagctcatgatgcttaatcataagattcataactaaatgttgttcttttggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG
        |     | | |       | ||  |  | |||    ||    ||  ||||| |  | |    |||||  |  |   ||||||| |||| ||||||||||||||| ||||| ||||||||||| || |||||||  || || || || || || ||||| || || |||
-------gtcttttatagtttcttgtc-tcaaaaatattaatctatt---ctctatcatgatttcct---ctaaacctc-tggctttggtctgttt-tagGGAAAATGCAAACGAAATAAAAGCCAAATTCATCATTGAAGGTGCTAATCACCCAACTGATCCTGAGGCTGACGAG

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|110695999|gb|EE074656.1|EE074656
EST:     CGTCCTCATCCCAGCAGCCCTTGGGGGTGTGATCAACAG                         GGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCA
genomic: CGTCCTCATCCCAGCAGCCCTTGGGGGTGTGATCAACAGgttcttctca ... ccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCA
EST: gi|33404831|gb|CF210458.1|CF210458
EST:     GAAGATTGTGACGTCCTCATCCCAGCAGCCCTTGGGGGTGTGATCAACAG                         GGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCA
genomic: GAAGATTGTGACGTCCTCATCCCAGCAGCCCTTGGGGGTGTGATCAACAGgttcttctca ... ccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCA
EST: gi|33404746|gb|CF210373.1|CF210373
EST:     GAAGATTGTGACGTCCTCATCCCAGCAGCCCTTGGGGGTGTGATCAACAG                         GGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCA
genomic: GAAGATTGTGACGTCCTCATCCCAGCAGCCCTTGGGGGTGTGATCAACAGgttcttctca ... ccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCA
EST: gi|110428368|gb|EC994837.1|EC994837
EST:     GAAGATTGTGACGTCCTCATCCCAGCAGCCCTTGGGGGTGTGATCAACAG                         GGCAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCA
genomic: GAAGATTGTGACGTCCTCATCCCAGCAGCCCTTGGGGGTGTGATCAACAGgttcttctca ... ccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgcttaatcataagattcataactaaatgttgttcttttggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG
                       aactaaa  putative branch site (score: 2)
                                            tccgttt  putative PPT
      ttaatcataagatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgggcattgcaacaaaatagtcaaccatcctaggttttagctcatgatgcttaatcataagattcataactaaatgttgttcttttggtccgtttgtagGGAAAATGCAAATGAAATTAAAGCCAAATTTATTATTGAAGCAGCCAACCATCCTACAGACCCTGAAGCAGATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - -aacaaaa
- - - - - - - - - - - - -ccatcct
- - - - - - - - - - - - - - - - - - - - -ctcatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aactaaa