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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagaagcaatttgtcatctaagtaaggttttgcataagcatacaaatctctgaattttctgactggcgtgtttccatttgctgactttccaactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT

Basic information

species Vitis vinifera
transcript Vv05s0049g01520.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os10g33270.1 (Oryza sativa), 3'ss of exon 1
-cagaagcaatttg--tcatctaagtaaggttttgcataagcatacaaatctctgaatt--ttctgactggcgtgtttccatttgctgactttccaactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT
  || |     |||  | |  | | |  |||  ||||     | |  | |||   ||    ||||   ||   | |||   ||   |   | |    ||    |||||||||||||| || ||||||||||| ||||||||||||||||||||||||||||||||||| ||||| ||
ttagtacacggttgatttaaattattgtggtaatgcacttttacaacactctagaaaaggattcttgttgatatttttt--ttaattatatattgcgctc---agATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAAT

upper sequence: Vv05s0049g01520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G134747_T01 (Zea mays), 3'ss of exon 1
--------cagaagcaatttgtcatctaagtaaggttttgcataagcatacaaatctctgaat----tttctgactggcgtgtttccatttgctgactttccaactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT
        |   |||  ||||| |  | | |   ||||  ||  |  |   | || |  ||||    ||| || |     |||| | || || ||           |   |||||||||||||| || ||||||||||| ||||||||||||||||| ||||||||||||||||| ||||| ||
gcttttatccagagc--tttgttagtttatttcagtttatcagcactaacaagatattagaataacctttttgtcaacattgttactatatgttg----------ctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAAT

upper sequence: Vv05s0049g01520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G134747_T02 (Zea mays), 3'ss of exon 1
--------cagaagcaatttgtcatctaagtaaggttttgcataagcatacaaatctctgaat----tttctgactggcgtgtttccatttgctgactttccaactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT----------------------------
        |   |||  ||||| |  | | |   ||||  ||  |  |   | || |  ||||    ||| || |     |||| | || || ||           |   |||||||||||||| || ||||||||||| ||||||||||||||||| ||||||||||||||||| ||||| ||                            
gcttttatccagagc--tttgttagtttatttcagtttatcagcactaacaagatattagaataacctttttgtcaacattgttactatatgttg----------ctcacagATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATGTAAGAGATACCAGTGCTTCATTTATGC

upper sequence: Vv05s0049g01520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA10G00790.1 (Glycine max), 3'ss of exon 1
cagaagcaatttgtcatctaagtaaggttttgcataa-gcata-caaatctctgaattttctgactggcgtgtttccatttgctgactttccaactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT
    || | | |    |   |   | ||   |  ||| ||||| ||| |  ||    | | |   |    ||||    | ||||||  ||| |  ||   || ||||||||||| || ||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||| ||
-ttgaggattctaatgttggaaatatgtcaagtgtaatgcatatcaacttccttttatatatatttaatttgttgggttatgctgatcttcta-tttcatagGTTGAATGAAGCTGTTATGCATTTTGGGGAGAGCATCAAAGAAATAATCAATGAGGAGTTTGGTGATGGGAT

upper sequence: Vv05s0049g01520.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G23490.1 (Arabidopsis thaliana), 3'ss of exon 1
cagaagcaatttgtcatctaagtaaggttttgcataagcatacaaatctctgaattttctgactggcgtgtttccatttgctgactttccaactttga---agATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT
                                  |  ||     ||  | |  ||||| ||  |||| |  ||    |  |||  |||   | |||||   || ||||||||||| |||||||||||||||||||| || ||||| ||||||||||| || ||||| ||||||||
---------------------------------gtttgctctggaaagtttacatttt-tgggtggcttagttttgatgtctgggttt--gattttgatttagGTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT

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|30125734|gb|CB911073.1|CB911073
EST:     CTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|351031752|gb|FQ460009.1|FQ460009
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|30297048|gb|CB973842.1|CB973842
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|351018751|gb|FQ425653.1|FQ425653
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|110399295|gb|EC965794.1|EC965794
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|22014889|gb|BQ799923.1|BQ799923
EST:     CCACTGAGGTCATACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|26263703|gb|CA814766.1|CA814766
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|30132704|gb|CB918043.1|CB918043
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|34549238|gb|CF517470.1|CF517470
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|110382071|gb|EC938407.1|EC938407
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|30297110|gb|CB973904.1|CB973904
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|26265678|gb|CA816741.1|CA816741
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|26265061|gb|CA816124.1|CA816124
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|351036307|gb|FQ458682.1|FQ458682
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|110389318|gb|EC954146.1|EC954146
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|110421844|gb|EC988147.1|EC988147
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|26263686|gb|CA814749.1|CA814749
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|18458542|gb|BM436820.1|BM436820
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|26265694|gb|CA816757.1|CA816757
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|32244959|gb|CD710778.1|CD710778
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|351023724|gb|FQ448275.1|FQ448275
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|26265153|gb|CA816216.1|CA816216
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|77581866|gb|DV219897.1|DV219897
EST:     CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCACTGAGGTCCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
EST: gi|349829185|gb|FQ419679.1|FQ419679
EST:     CCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAG                         ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA
genomic: CCTACGACCCCCATTTGATCCAGGAACCCACTGTTTACAGgtccctctcc ... aactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctctgaattttctgactggcgtgtttccatttgctgactttccaactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT
                                 tgctgac  putative branch site (score: 2)
                                       ctttcca  CT-rich tract
     tgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagaagcaatttgtcatctaagtaaggttttgcataagcatacaaatctctgaattttctgactggcgtgtttccatttgctgactttccaactttgaagATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- gaagcaa
- - - - - - - - - - - - - -ttttgca
- - - - - - - - - - - - - - - - - - -gcataca
- - - - - - - - - - - - - - - - - - - - - - - -ctctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgg