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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttggttctcacttatggtcgaccaacagtgctttgtgtgcgtctctctgatctgcactcattcatgtcactaaaattttcttaatgggaacttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGATGAGACTGCAAAAGCTGAGTTTGGCGAGTGGTCATGGATGTCACCGGAT

Basic information

species Vitis vinifera
transcript Vv08s0056g00030.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0056g00030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G33600.1 (Glycine max), 3'ss of exon 4
tttggttctcacttatggtcgaccaacagtgctttgtgtgcgtctctctgatctgcactcattcatgtcactaaaattttcttaatg---ggaacttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGATGAGACTGCAAAAGCTGAGTTTGGCGAGTGGTCATGGATGTCACCGGAT
   |  |              | ||  | ||    |  ||             | |  |  | | |  |   | | | || || |        |      |||||||||| |||| ||||||||| | ||  | ||||| ||||| ||||||||||  ||||  |||||||||||||| || ||||||||||| ||||| || 
---gagtgcagggggcaaggcatcagaattggaaggcatggaagaagggatctttcgtttttgctttgctaaatagtgtttttgacacttttgatacgcacagGTTTCTTTTTAAGTTCACTGGACAAGATCAAGAAATTAATCTTTTGGGTGATGGTACTGAGAAAGCTGAGTTTGGGGAATGGTCATGGATATCACCTGAA

upper sequence: Vv08s0056g00030.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G33990.1 (Glycine max), 3'ss of exon 4
---tttggttctcacttatggtcgaccaacagtgctttgtgtgcgtctctctgatctg-cactcattcatgtcactaaaattttcttaatgggaacttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGATGAGACTGCAAAAGCTGAGTTTGGCGAGTGGTCATGGATGTCACCGGAT
      ||     |   ||         |  |          | |    | || | || |  | | |  |||   | | | |||    ||    ||  |  |||||||||| |||| ||||||||  | ||  | ||||| ||||| ||||||||||  ||||  |||||||||||||| || ||||||||||| ||||| || 
agtgcaggggacaaggcatcagaattggaaggcatggaagaagggatattttgttttggctttaagtagtgtttttgacacttttgatat----acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGATGGTACTGAGAAAGCTGAGTTTGGGGAATGGTCATGGATATCACCTGAA
















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|32245104|gb|CD710923.1|CD710923
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|30128721|gb|CB914060.1|CB914060
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|32247573|gb|CD713392.1|CD713392
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|30322778|gb|CD006040.1|CD006040
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|110703134|gb|EE079712.1|EE079712
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|351033064|gb|FQ446417.1|FQ446417
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|110702464|gb|EE081204.1|EE081204
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|351026488|gb|FQ428500.1|FQ428500
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|34361910|gb|CF403495.1|CF403495
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|77584900|gb|DV221533.1|DV221533
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|27582290|gb|CB004985.1|CB004985
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|71870980|gb|DT020035.1|DT020035
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|30303216|gb|CB980010.1|CB980010
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|110382971|gb|EC947304.1|EC947304
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|18458074|gb|BM436352.1|BM436352
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
EST: gi|71867829|gb|DT016884.1|DT016884
EST:     AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTG                         GTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA
genomic: AGACTTAAAAATCAATGGGGATCAGACTGGAAAGGTCAAGTACAGAAGTGgtgagtgcat ... acttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgatctgcactcattcatgtcactaaaattttcttaatgggaacttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGATGAGACTGCAAAAGCTGAGTTTGGCGAGTGGTCATGGATGTCACCGGAT
                        actaaaattttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttggttctcacttatggtcgaccaacagtgctttgtgtgcgtctctctgatctgcactcattcatgtcactaaaattttcttaatgggaacttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGATGAGACTGCAAAAGCTGAGTTTGGCGAGTGGTCATGGATGTCACCGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - -cttatgg
- - - - - - - - - - -accaaca
- - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cactcat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actaaaa