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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT

Basic information

species Vitis vinifera
transcript Vv08s0007g06710.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os08g36150.1 (Oryza sativa), 3'ss of exon 2
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgactt--gtggctgtttgtgattgctttggtatttcatta-tgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
               |    | | |  ||  |      ||  ||||  | |  |    | ||| || ||   |   ||   |     ||  | |  || || | | | ||||||||| ||| |||| ||||| |||||||| ||  |||| ||||| || ||||| ||||| | |||| | | ||||||||||||||| || | ||    |
--------------gtattctatctc-atcctacgaacttcctgttaattaaacc--ataattttggctcaggcacctaactaaatatgtgtggtcatctcttgacttcagATATGGAAATTCAACTGTGGTGGAGAACACGGAGCGAGGCTGGAGAGAACTCATCTTCCAGAGGATACGCGGAGTGTTTGGTTTTGGGATCTAAAGCAGT

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G021816_T01 (Zea mays), 3'ss of exon 2
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcat-tatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
                    | | ||||| ||  | || ||      | ||  || | |||| ||    | | | |  ||  |||   |||| | ||   |   ||||| ||||| ||| |||| |||||||||||||| || ||||| ||||| || ||||| |||||   |||| | | |||||| |||||||| || | ||   | 
-------------------gtatgttgatattcctatgcttcgaacaccaaatctgt-tgatgcttgtctcttg-tacttacgatctgtttgcttttgagtacttgcagGTATGGAAATTCAACTGTGGTAGAGAACACCGAGAGAGGCTGGAGAGAACTCATATTCCAGCGGATACGCGGAGTGTTCGGTTTTGGGATCTAAAGAATC

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA09G16680.1 (Glycine max), 3'ss of exon 3
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
             |   |   || || | |   ||| ||||  |||   ||   | |||  | ||   | | |     ||    ||   | | || ||    |||||||||||| |||||||| ||||| |||||||| || || || ||| |||||||||||||||| | |||| || | | ||||||||||||||| |||  ||||
-------------gtgagtcagtgtttaatcaattcagtttgggtttgaaa---tttgttttgctcgatcgag-----ttaccgttatgtggttacttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGTTGGCGGGATCTCATTTTCCAAAGGATACGAACTGCGTTTGGTTTTGGAATTTGAGATTTT

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G30230.1 (Glycine max), 3'ss of exon 2
gttggtttctg-ttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtt-tgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
||  || | || ||||    |||       ||||      |||||||  |       | ||  | ||  ||||    ||  |||||||  ||    | |   |  | ||| ||||||||||| || ||||| |||||||| ||||| |||||| ||||||| |||||||| | |||| | || || |||||||||||||| |||  ||||
gtgagtgtttgattgagaatttgggaatggtttggggaagttttgtttttgttttcttttg--tttggtttgttaaggtggtgtgatttgttcttgaatctgtattacagGTATGGGAATGCTACTGTGGTGGAGAACACGGAAAGGGGGTGGCGGGATCTTATTTTCCAGAGGATACGTGCTGTTTTTGGTTTTGGAATTTGAGATTTT

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G28830.2 (Glycine max), 3'ss of exon 2
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
||  ||   |||| |    | |||| | ||| | | ||   ||| |  |   ||||    | ||    |  ||    | |||| ||||||   |  ||    |||||||||||| |||||||| ||||| |||||||| || || || ||| |||||||||||||||| | |||| |  | | ||||||||||||||| |||  ||||
gtgagtcggtgtttaa---tcgtttcggtttgggtttggaattggtttt---gctc----aatcgagttactgaggatatgtggttgcttgcttgcttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGATGGCGGGATCTCATTTTCCAAAGGATACGGACTGCGTTTGGTTTTGGAATTTGAGCTTTT

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G28830.3 (Glycine max), 3'ss of exon 2
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
||  ||   |||| |    | |||| | ||| | | ||   ||| |  |   ||||    | ||    |  ||    | |||| ||||||   |  ||    |||||||||||| |||||||| ||||| |||||||| || || || ||| |||||||||||||||| | |||| |  | | |||||                    
gtgagtcggtgtttaa---tcgtttcggtttgggtttggaattggtttt---gctc----aatcgagttactgaggatatgtggttgcttgcttgcttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGATGGCGGGATCTCATTTTCCAAAGGATACGGACTGCGTTTG--------------------

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G28830.1 (Glycine max), 3'ss of exon 2
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
||  ||   |||| |    | |||| | ||| | | ||   ||| |  |   ||||    | ||    |  ||    | |||| ||||||   |  ||    |||||||||||| |||||||| ||||| |||||||| || || || ||| |||||||||||||||| | |||| |  | |                          
gtgagtcggtgtttaa---tcgtttcggtttgggtttggaattggtttt---gctc----aatcgagttactgaggatatgtggttgcttgcttgcttgcaaatgcagATATGGAAATGCAACTGTGGTGGAGAACACAGAGAGGGGATGGCGGGATCTCATTTTCCAAAGGATACGGACTGC-------------------------

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G33140.1 (Glycine max), 3'ss of exon 2
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
       |  || | ||  | || ||| ||||||     |||||||  |  |  | |||     ||  ||||    ||  ||  ||| ||||    ||| | || ||| ||||||||||| || ||||| |||||||| ||||| || ||| ||||||| |||||||| | |||| | || || |||||||||||||| |||  ||||
------gtgagtggttgattggtattggttttgtggaagttttgttttt--gtttttgt----ttggtttgttaaggtgggt--ttgatttg----ttcttgatacagGTATGGGAATGCTACCGTGGTGGAGAACACGGAAAGGGGATGGCGGGATCTTATTTTCCAGAGGATACGTGCGGTTTTTGGTTTTGGAATTTGATATTTT

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G12050.1 (Arabidopsis thaliana), 3'ss of exon 2
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttg-tggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
          |    || |||    ||| |  ||  | |   |||| ||||   |  | ||   |||  |     |||||      || ||    | |   | ||||||||| |||||||| || ||||| || |||||||| ||||| ||||| ||||| || ||||| | |||  | ||||| || || ||||||||||||| || |
-------atggcctgtgtcttaagatgagtgagtgat-tcaatgttgctaaatgtgag-gacattgatgtaactactgttatctgatgtttatccaatggttgatgcagATACGGGAATGCGACTGTGGTGGAAAACACTGAGAGAGGATGGAGAGATCTTATATTCCATAGGATCCGTGCAGTTTTCGGATTTGGAATATGAACTTAT

upper sequence: Vv08s0007g06710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S454_1V6.1 (Physcomitrella patens), 3'ss of exon 4
----gttggtttctgttga-tggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
    ||   ||||| |  | | | |  |||| |  | ||    | | ||||    ||   |||     |  ||| |       | ||||||    || ||| |     | ||||||||| |||||||||||||| || ||||| ||||| || ||| | ||||| || ||||| |||||  | || || |||||||||||  | | | ||  |
ttttgtcattttctttcaaatcggtcattttcagatagt---atctgtgtttggcagtacctg-----cctactaggactgaatcgtgattttcctgttatct-----ttcagATATGGCAATGCAACAGTGGTGGAAAACACGGAAAGGGGATGGCGAGATCTGATCTTCCATAAGATTCGTGCTGTTTTTGGTTTTGGGCTGTAACTTCGT

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|110362161|gb|EC925677.1|EC925677
EST:     GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAG                         ATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
genomic: GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAGgttggtttct ... cattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
EST: gi|33403213|gb|CF208840.1|CF208840
EST:     GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAG                         ATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
genomic: GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAGgttggtttct ... cattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
EST: gi|71874177|gb|DT023232.1|DT023232
EST:     GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAG                         ATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
genomic: GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAGgttggtttct ... cattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
EST: gi|30328084|gb|CD011346.1|CD011346
EST:     GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAG                         ATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAG
genomic: GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAGgttggtttct ... cattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAG
EST: gi|32268165|gb|CD717324.1|CD717324
EST:     GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAG                         ATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
genomic: GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAGgttggtttct ... cattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
EST: gi|71887065|gb|DT036120.1|DT036120
EST:     GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAG                         ATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
genomic: GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAGgttggtttct ... cattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
EST: gi|110383599|gb|EC947981.1|EC947981
EST:     GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAG                         ATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
genomic: GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAGgttggtttct ... cattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
EST: gi|30323537|gb|CD006799.1|CD006799
EST:     GGGTTGACTGTTGTTANACTGACGCAGACTGGTATTCCTGAGGAAGATAG                         ATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
genomic: GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAGgttggtttct ... cattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
EST: gi|110373892|gb|EC938322.1|EC938322
EST:     GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAG                         ATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT
genomic: GGGTTGACTGTTGTTAAACTGACGCAGACTGGTATTCCTGAGGAAGATAGgttggtttct ... cattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT
        ttctgac  putative branch site (score: 2)
                                          tttcatt  putative PPT
                                        tatttcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtttctgttgatggcttgttttgattttgttctgtttttgttcctaaggctctgtgattctgacttgtggctgtttgtgattgctttggtatttcattatgcagATATGGGAATGCAACAGTGGTAGAGAACACTGAAAGAGGGTGGAGGGATCTCATTTTCCACAAGATAAGAGCAGTGTTTGGTTTTGGAATATGAATTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG