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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtagaagcttatcatccatttatccatgttctttatataacaacgaactctcatctccaattttcttcctcag

Basic information

species Vitis vinifera
transcript Vv08s0007g08690.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G323479_T01 (Zea mays), 5'ss of exon 13
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtagaagcttatcatccatttatccatgtt---ctttatataacaacgaactctcatctccaattttcttcct-cag
 | |||||||| ||| || |||||||| |||||| ||||||| |||||||| || ||||||||||| ||||| || |||||||||||    || | ||||||| |     |||     |||||   | |    |||| |  || |   |  ||| ||||  || || | ||||  ||
TACCAAATGCTTTTTACTTGACTGTGGGGCTGAGCTATTTGTGTGGGTTGGTCGGGTAACACAGGTAGAGGACAGGAAAGCTGCCAGTGCGGCAGTTGAGgtaaacctacatcccaagtttattgctttcttgctttgttcaaaacatatatcttatctaaaagttacctcctgtag

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G081322_T01 (Zea mays), 5'ss of exon 8
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtagaagcttatcatccatttat--ccatgttctttatataacaacgaactctcatctccaattttcttcct-cag
|| ||| |||| ||| || ||||| || |||||| |||| || |||||||| || ||||||||||| ||||| || |||||||||||   ||| | ||||||| |  | || |     |||||  |  | ||   |   | ||||   |  || ||||  || || | ||||  ||
CACCAAGTGCTTTTTACTTGACTGCGGGGCTGAGCTATTCGTGTGGGTTGGTCGGGTAACACAGGTAGAGGACAGGAAAGCTGCCAGTGCAGCAGTTGAGgtaaacccatagcccaattttattgctttcttgccttgttcacaatataacct-atctaaaagttacctcctgtag

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G180988_T01 (Zea mays), 5'ss of exon 8
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtaga------agcttatcatccatt-tatccatgttctttatat--aacaacgaactctcatctccaattttcttcctcag
 | |||||| |  || || |||||||| |||||  ||| ||| ||||||||||| ||||||||  | |||||||||||| ||||||   |||| | ||||||| |      | || ||  ||  || || || | | |   || |     |   |||  |    |  | || |||||  |||
TACCAAATGTTTCTTACTTGACTGTGGGGCTGAAATATATGTATGGGTTGGCCGGGTAACACAAATGGAGGATAGAAAATCTGCCACTAAAGCAGTTGAGgtaaattcttgaactaattttcttttgtaaccttttcccccatttcttgtagttaacattttcatgaatttctcttctgcag

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA10G21350.2 (Glycine max), 5'ss of exon 7
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtagaagc---ttatcatccat----ttatccatgttc-tttatataacaa--cgaactctcatctccaattttcttcctcag
||||||||||||||| |||||||||||||||||||| ||||| |||||||| ||||| ||||| || || ||  ||||| | ||| ||||||| | |||||||    |    ||  ||| ||    | || ||| | | ||| | |   ||   | | ||     | | |       |  |||
CAACAAATGCTATTTACTGGACTGTGGTGCTGAGGTGTTTGTCTGGGTTGGTCGTGTGACACAAGTTGAAGAACGAAAATCAGCCTGCCAAGCCGTTGAGgtaaggccattgtagaatctataatctaattcatttccatttgtttgttaaattggattcattaattctaccaatacctccag

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA19G32010.1 (Glycine max), 5'ss of exon 8
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtag---aagcttatcatccatttatccatgttctttatataacaacgaactctcatctccaattttcttcctcag
| ||||||||||| |  ||||||||||| ||||||||||||| ||||||||||| |||||||| || || ||| ||||||| ||  | ||||| |||||||||    ||    |   ||||||| | ||| | ||   | | | |  | | ||     |   | |    |  ||||
CTACAAATGCTATCTATTGGACTGTGGTACTGAGGTATTTGTCTGGGTTGGCCGGGTAACACAAGTTGAAGATCGAAAAGCAGCTTGTCAAGCAGCTGAGgtaatgcaattgcaagttccatttcttcatatgctg-gtttga-agtggagtcattaatgttactgatatgttcag

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA03G29280.1 (Glycine max), 5'ss of exon 7
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtagaagcttatcatccatttatccatgttctttatataacaac--gaactctcatctccaattttcttcctcag-----
| ||||||||||| |  |||||||||| |||||||||||||| ||||||||||| |||||||| || || ||  ||||||| ||  | ||||| |||||||||      |||      ||   |||| ||||| ||||        ||| |    ||   ||| ||  |  |  |     
CTACAAATGCTATCTATTGGACTGTGGAGCTGAGGTATTTGTCTGGGTTGGCCGGGTAACACAAGTTGAAGAACGAAAAGCAGCATGTCAAGCAGCTGAGgtaatg--ctattgcaagttccaccat-ttcttcatatgttggtttgaagtgaagtcattaatgttactaatatgttcag

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA02G32100.1 (Glycine max), 5'ss of exon 6
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtag----------aagcttatcatccatttatccatgttc--tttat--ataacaacgaactctcatctccaattttcttcctcag
||||||||||||||| |||||||||||||| ||| | ||||| |||||||| || || ||||| || || ||  ||||||| ||| ||||||| | |||||||            |   ||  ||| | || |   |  ||  ||| |   | | |  | | ||     | | |      ||  |||
CAACAAATGCTATTTACTGGACTGTGGTGCCGAGATGTTTGTCTGGGTTGGTCGCGTGACACAAGTTGAAGAACGAAAAGCAGCCTGCCAAGCCGTTGAGgtaatgctattctagaatctagaatctaattcttacttctccatttgttagttaaagtggattcattaattctacaaatatctccag

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT2G41740.1 (Arabidopsis thaliana), 5'ss of exon 8
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgta-------gaagcttatcatccatttatccatgttctttata----------taacaacgaactctca-tctccaattttcttcctcag
||  ||||||||  |  |||||||||| |||||| ||| | | |||||||||||||| || || || || || || |||||||| || ||| |||||||||||       |||   ||| |   |  | ||   | || ||| |           ||  | |   ||||| | |  |  |||| ||  |||
CACTAAATGCTACCTCTTGGACTGTGGCGCTGAGATATATATCTGGGTTGGCCGTGTCACTCAAGTAGATGAGAGGAAAGCTGCTAGTCAATCTGCTGAGgtaaagaatggaaatctattaaaaacatttctccggtccttagaatatctatctcaatcatggcttctcactttttacctttcatctacag

upper sequence: Vv08s0007g08690.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT3G57410.1 (Arabidopsis thaliana), 5'ss of exon 9
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtagaagct--tatcatccatttatccatgttctt---tatataacaacgaactctcatctccaattttcttcctcag
||| ||||||||  |  ||||||| ||| ||||| | ||| | ||||||||||| ||||| || || || || |||||| |||| | |||||||||||||||| |||||   ||| || |  |  |   |   |    ||| | |  |     |||||| |  |   ||| ||  |||
CAATAAATGCTACCTTTTGGACTGCGGTTCTGAGATCTTTATCTGGGTTGGCCGAGTAACTCAAGTGGAAGAGAGAAAAACTGCTATCCAAGCTGCTGAGgta-aagctagaatcgtctaacttgcttagccttagaatatctgaggattggttctcattttta-ccttcctctacag

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|30133877|gb|CB919216.1|CB919216
EST:     GCCAGCCAAGCTGCTGAG                         GAATTTGTTTCTAGCCAAAATAGACCAAAGGCAACTCGTGTAACCCGGGTT
genomic: GCCAGCCAAGCTGCTGAGgtagaagctt ... tcttcctcagGAATTTGTTTCTAGCCAAAATAGACCAAAGGCAACTCGTGTAACCCGGGTT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACAAATGCTATTTGCTGGACTGTGGTGCTGAGGTATTTGTTTGGGTTGGCCGTGTAACACAGGTCGAGGATAGAAAAGCTGCCAGCCAAGCTGCTGAGgtagaagcttatcatccatttatccatgttctttatataacaacgaactctcatctccaattttcttcctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT