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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacctctttgttgcaatttactattatggggaaattcatactgtatttgtgctgttcaatctagggtgaataattcttgaatatggttttgatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACG

Basic information

species Vitis vinifera
transcript Vv04s0008g03720.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G062953_T01 (Zea mays), 3'ss of exon 1
-aacctctttgttgcaatt-tactattatggggaaattcatactgta-tttgtgctgt--tcaatctagggtgaataattcttgaatatggttttgatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACG
   | | ||  || |  || | ||   |  |         || | |  ||||  |||   ||| |||    |  ||  | | |   |||| || | |     ||||||| |||| ||||| ||||| |   |||| || || |||||    ||||||||||||||||||||||||||||| || 
gctcatgttcatttcgtttctgctgaaacagaagcccatttaatttgctttgccctgctgtcattctgttattgattgtccatatctatgcttgtaa-----cagGCAATCAAAAGATGTCGTCAAGGCACTAAAGAAACGGATTGGCCACAAGAATCCAAAAGTTCAACTTCTTGCACTAACT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G153138_T02 (Zea mays), 3'ss of exon 1
aacctctttgttgcaatttactattatggggaaattcatactgtatttgtgctgttcaatc-tagggtgaataattcttga----atatggttttgatt-tatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACG
      ||  || || || ||    |  |         || | |  || |||| | |  || |  ||| |  | || ||||    | ||     || || |  ||||||| | || ||||| ||||| |   | || || || |||||    |||||||||||||||||||||||||| || || 
-----gttcatttcatttcaccggaacagaagtccatttaatctgctt-tgctctgctgtcgttcggttatcacttattgattgtacatatccatgcttgtcacagGCAATCGAAAGATGTCGTCAAGGCACTGAAGAAACGGATTGGCCACAAGAATCCAAAAGTTCAACTTCTTGCGCTAACT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G21410.1 (Glycine max), 3'ss of exon 1
aacctctttgttgcaatttactatt--atggggaa-attcatactgtatttgtgctgttcaatctagggtgaataattcttgaatatggttttgatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACG
    | |  || | | |  | ||||  |||   ||  ||   | | |  |  |  | |  | |      |    |   ||    | ||||| ||||| |||||||||||||||||||| || ||||||||||| ||||| ||||||||||| ||| ||||||| |||||||||||||| || 
-gtgtttaagtggaattagagtatttgatgtataatgtttgaatttttctctttgtttatacttccaaatattcagaactctgtt-tggttatgatt-atcagGCAAGCAAAGGATGTTGTTAAAGGCATAAAGAAGCGGATTGGAAGTAAAAATTCAAAAGTCCAACTTCTTGCACTAACT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G26440.1 (Glycine max), 3'ss of exon 1
aacctctttgttgcaatttactattatggggaaatt---catactgtatttgtgctgttcaatctagggtgaataattcttgaatatggttttgatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACG
       | |  |   || |||   ||  | | |||     ||   | ||||   | |||  | ||     | | |    |   | ||||| ||||| |||||||||||||||||||| || ||||| ||||| ||||| ||||||||||| ||| |||||||||||||||||||||| || 
-tttatatagaagtgtttaactggaattagaatatttgatgtataatgtttggatt-ttctttgtataagtattgagaactctgtttggttatgatt-atcagGCAAGCAAAGGATGTTGTTAAAGGTATAAAGAAGCGGATTGGAAGTAAAAATTCAAAAGTTCAACTTCTTGCACTAACT

upper sequence: Vv04s0008g03720.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G32760.1 (Arabidopsis thaliana), 3'ss of exon 1
aacctctttgttgcaatttactattatggggaaattcatactgtatttgtgctg-ttcaatctagggtgaataattcttgaatatggttttgatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACG
 |  |  ||  |    |||   |||    | |      | | || | ||| ||   |  | | |   |   | ||   ||||  |||||    |||   ||||||||||| ||||| || |||||||| ||||| || ||||| || | ||||||||||| ||| ||||||||  | || 
-attttctttatatgctttgtgattggaagaaggagatttcagtgtgtgtactaactgcaccaatactatgtgatgtctgaaactggttcctgttttgtagGCAAGCAAAAGATGTTGTGAAAGGCATTAAAAAACGGATTGGTAGCAGGAATCCAAAAGCTCAGCTTCTTGCCTTAACT

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|352764099|gb|FQ467669.1|FQ467669
EST:     GATTGGGCGATGAACATCGAGATCTGTGATATGCTTAATCACGACCCTGG                         GCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAA
genomic: GATTGGGCGATGAACATCGAGATCTGTGATATGCTTAATCACGACCCTGGgtatatattt ... gatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAA
EST: gi|161707455|gb|FC055985.1|FC055985
EST:     GATGGGGCGATGAACATCGAGATCTGTGATATGCTTAATCACGACCCTGG                         GCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAA
genomic: GATTGGGCGATGAACATCGAGATCTGTGATATGCTTAATCACGACCCTGGgtatatattt ... gatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAA
EST: gi|18459792|gb|BM438070.1|BM438070
EST:     TGAACATCGAGATCTGTGATATGCTTAATCACGACCCTGG                         GCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAA
genomic: TGAACATCGAGATCTGTGATATGCTTAATCACGACCCTGGgtatatattt ... gatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtgctgttcaatctagggtgaataattcttgaatatggttttgatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACG
                                         ttttgat  putative branch site (score: 4)
                       aataattcttgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacctctttgttgcaatttactattatggggaaattcatactgtatttgtgctgttcaatctagggtgaataattcttgaatatggttttgatttatcagGCAAGCAAAGGATGTGGTCAAAGGCATAAAAAAGCGCATTGGAAGTAAGAATCCAAAAGTTCAACTTCTTGCACTGACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - tgttgca
- - - - - - - - - - - -ttatggg
- - - - - - - - - - - - - - - - - - catactg
- - - - - - - - - - - - - - - - - - - - - - -tttgtgc