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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttgctgagaatgtatatgtttgatactagtgactacctgtattagtatgaactgtggtcagcatcactcttatctttggtttcttgtctgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGCTAGCATGGAGGATTTCTATGATGTAAAAATGTCCAAGATTGATGGGCAA

Basic information

species Vitis vinifera
transcript Vv16s0050g02570.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA14G31890.1 (Glycine max), 3'ss of exon 3
-tgttgctgagaatgtatatgtttgatactagtgactacctgtattagtatgaactgtggtcagcatcactcttatct--ttggtttcttgtctgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGCTAGCATGGAGGATTTCTATGATGTAAAAATGTCCAAGATTGATGGGCAA
   |||||  || ||  |   |||| |  || |   ||| | |  |  | |  | |||| | |  || | |  ||  |  ||   |   | | |  ||| |||||| || |||| ||| |||||||||||||||||||| |||||||||||||  |  ||||||||||| |||||| | || |  |  ||||||| ||| |||
gatttgctt-gactggctggatttggtg-tactttatacttttgctgatctatattgtgataaa-ataaatggtacttatttcaatgaatttttatttggcagTGACGATGGAAGACTTAGCTGTGGGTATTCAAGTTTTAGGGGAAAGAGAGTGACAATGGAGGATTTTTATGATATTAAGACATTGAAGATTGGTGGCCAA

upper sequence: Vv16s0050g02570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G08090.1 (Glycine max), 3'ss of exon 2
-tgttgctgagaatgtatatgtttgatactagtgactacctgtattagtatgaactgtggtcagcatcactcttatct--ttggtttcttgtctgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGCTAGCATGGAGGATTTCTATGATGTAAAAATGTCCAAGATTGATGGGCAA
   |||||  || ||  |   |||| |  || |   ||| | |  |  | |  | |||| |||  || | |  ||  |  ||  ||   | | |  ||| ||||||||| |||| ||| |||||||| ||||||||||| |||||||||||||  |  ||||| ||||| |||||| | || |  |  ||||||| ||| |||
gatttgctt-gactggctggatttggtg-tactttatacttttgctgatctatattgtgatcaa-ataaatggtacttatttcattgaatttttatttggcagTGAAGATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGTGACAATGGAAGATTTTTATGATATTAAGACATTGAAGATTGGTGGCCAA

upper sequence: Vv16s0050g02570.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G08090.2 (Glycine max), 3'ss of exon 2
----tgttgctgagaatgtatatgtttgatactagtgactacctgtattagtatgaactgtggtcagcatcactcttatctttggtttcttgtctgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGCTAGCATGGAGGATTTCTATGATGTAAAAATGTCCAAGATTGATGGGCAA-----
       ||    || |   | |  || |||||  ||   | || ||||   || || |      |     |||  | || |||  || || |    ||| ||||||||| |||| ||| |||||||| ||||||||||| |||||||||||||  |  ||||| ||||| |||||| | || |  |  ||||||| ||| |||     
gcttgactggctggatttggtgtactttatacttttgctgatctatattgtgatcaaata-----aatggtacttatttcattgaatttttat----ttggcagtgaagATGGAAGACTTAGCTGTGGTTATTCAAGTTTTAGGGGAAAGAGAGTGACAATGGAAGATTTTTATGATATTAAGACATTGAAGATTGGTGGCCAATCAAT

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|71858967|gb|DT008022.1|DT008022
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|351049251|gb|FQ428994.1|FQ428994
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|351026149|gb|FQ428161.1|FQ428161
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|351012838|gb|FQ430401.1|FQ430401
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|351056534|gb|FQ442362.1|FQ442362
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|351037286|gb|FQ457119.1|FQ457119
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|161714697|gb|FC064481.1|FC064481
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAATCTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|351015894|gb|FQ431849.1|FQ431849
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|351026397|gb|FQ428409.1|FQ428409
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|110392544|gb|EC958041.1|EC958041
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|351042859|gb|FQ451153.1|FQ451153
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
EST: gi|351023854|gb|FQ423277.1|FQ423277
EST:     TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAG                         TGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC
genomic: TTGCCAGAGAAAGAGGACGATGGTGGCTATGCCAGTGGAGGATGGAAAAGgtgataaatg ... tgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtatgaactgtggtcagcatcactcttatctttggtttcttgtctgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGCTAGCATGGAGGATTTCTATGATGTAAAAATGTCCAAGATTGATGGGCAA
                                          gtctgat  putative branch site (score: 4)
                                    tttcttgtct  CT-rich tract
                          ttatcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgttgctgagaatgtatatgtttgatactagtgactacctgtattagtatgaactgtggtcagcatcactcttatctttggtttcttgtctgattgacagTGAAGACGGAAAACTGAGCTGTGGGTATTCAAGTTTCAGGGGAAAGAGAGCTAGCATGGAGGATTTCTATGATGTAAAAATGTCCAAGATTGATGGGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
tgttgct
- - - -gagaatg
- - - - - - - - - - - - - - - - - -tacctgt
- - - - - - - - - - - - - - - - - - - - - - - -tatgaac