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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgattctccaattgatcttttcaaaattttattttttatttttgtttttaatttttatgttgattttgagctaaaagtttggttttcttatttttggtttggtctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACA

Basic information

species Vitis vinifera
transcript Vv15s0046g02280.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
----------------------------------------------------------------------gttgattctccaattgatcttttcaaaatttt-attttttatttttgtttttaatttttatgttgattttgagctaaaagt-ttggttttcttatttttggtttggtctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACA
                                                                       ||||||||    ||  ||| ||     | |  ||  | || | |  | | |  || || ||||| ||| | | |    |  ||||   | || ||  |   ||| | |    |||||||||||| || ||||||||||||||| | || ||||| ||||| |||||||  ||| | ||||  || || | ||| |
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctt--tctattggtggtctccatcgtctaatctgatgtgttgttgtt-tgttgttttgggggtggggggattggggattttcttggtttcttgttgttg--cagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA

upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 1
gttgattctccaattgatcttttcaaaattttattttttatttttgtttttaatttttatgttgattttga-gctaaaagtttggttttc-ttatttttggtt-tggtctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACA
                      | |  ||||| |    | |||  ||  ||  ||| ||||  ||||| || |   |    ||| | | | ||  |  ||| | | |   |   |||||||||||| || ||||||||||||||| | || ||||| ||||| ||||||| |||  | || | ||| || |  || |
---------------------gtgaggattttgtggcgtgtttcggtgatt--tttctatgg-gatttcgatggggattccttgatctgcgtttctactggctgttgatgcctgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
gttgattctccaattgatcttttcaaaattttattttttatttttgtttttaatttttatgttgattttgagctaaaagtttggttttcttatttttggtttggtctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACA
               |||  | |    |||   ||| || ||    ||  |    |||  |         || |     | |   |  |   |      | ||   |     |||||||||||||| |||||||| |||||| | |||||||| |||   || ||||||||| | || ||||||||  |||| |
--------------ggattgtgttgtgattacttttcttgttcgaattggtgcggtttggggaatcggcaagttgttgttgtatctgacgattcaagaatgtgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA

upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
----------------gttgattctccaattgatcttt----tcaaaattttattttttatttttgttt-ttaatttttatgttgattttgagctaaaagtttggttttcttatttttggtttggtctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACA
                 | || | || | |   ||||     || |     |||     |  | | ||| ||   |||  |  |   |   |  | |  | ||  | || ||  ||    ||     |    ||||||||||||||| ||||||||||||||| | || ||||| ||| | |||||  ||||| | |||||||||||  | || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaaaacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttc--cagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

upper sequence: Vv15s0046g02280.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
---------gttgattctccaatt--gatcttttcaaaattttattttttatttttgttt-ttaatttttatgttgattttgagctaaaagtttggttttcttatttttggtttggtctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACA
         |     |||| ||||   ||   |||     | |    |  |  | | ||| ||   |||  |  |   |   |  | |  | ||  | || ||  ||    ||     |    ||||||||||||||| ||||||||||||||| | || ||||| ||| | |||||  ||||| | |||||||||||  | || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttc--cagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

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|161706781|gb|FC055498.1|FC055498
EST:     AAAATTATGTCTTCACCAAGCAAACGCAGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
genomic: CAAATCATGTCTTCACCAAGCAAACGCAGAGAGATGGACTTGATGAAACTgttgattctc ... tctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
EST: gi|351029514|gb|FQ436908.1|FQ436908
EST:     CAAATCATGTCTTCACCAAGCAAACGCAGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
genomic: CAAATCATGTCTTCACCAAGCAAACGCAGAGAGATGGACTTGATGAAACTgttgattctc ... tctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
EST: gi|110420607|gb|EC986882.1|EC986882
EST:     GTCTTCACCAAGCAAACGCAGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
genomic: GTCTTCACCAAGCAAACGCAGAGAGATGGACTTGATGAAACTgttgattctc ... tctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
EST: gi|34550367|gb|CF518585.1|CF518585
EST:     AAAATTATGTCTTCACCAAGCAAACGCAGAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTGCAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
genomic: CAAATCATGTCTTCACCAAGCAAACGCAGAGAGATGGACTTGATGAAACTgttgattctc ... tctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
EST: gi|83274683|gb|DV938779.1|DV938779
EST:     AGCAAACGCAGAGAGAT-GACTNGATGAAACT                         GATGATGAGTGA-TACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
genomic: AGCAAACGCAGAGAGATGGACTTGATGAAACTgttgattctc ... tctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
EST: gi|351037950|gb|FQ465188.1|FQ465188
EST:     AAAATTATGTCTTCACCAAGCAAACGCAAAGAGATGGACTTGATGAAACT                         GATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT
genomic: CAAATCATGTCTTCACCAAGCAAACGCAGAGAGATGGACTTGATGAAACTgttgattctc ... tctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgattttgagctaaaagtttggttttcttatttttggtttggtctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACA
           agctaaa  putative branch site (score: 3)
                         ttttcttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgattctccaattgatcttttcaaaattttattttttatttttgtttttaatttttatgttgattttgagctaaaagtttggttttcttatttttggtttggtctcaaacagGATGATGAGTGATTACAAGGTGGAGATGATCAATGATGGCATGCAAGAGTTCTATGTGCATTTCCATGGACCCAGTGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA