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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttaatcacagctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatttcctaaattgttgaacattcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC

Basic information

species Vitis vinifera
transcript Vv18s0041g01360.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os04g35900.1 (Oryza sativa), 3'ss of exon 7
---------------atttaatcacagctaagaataa--tttaattttgct--tgatgactctgtgtggttttttatgatggtttggtatttcctaaattgttgaac--att-catttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
               |||    ||    ||  | | |  |||| ||||  |  |  ||  ||||| |     ||| |  |  | || | ||    ||  |  | |||  |||   | |  ||| ||  ||   ||| | ||||| || ||| |  | ||||||||||||||||||||| | ||||| ||||||||||| ||
gtaagtactattatcattagcacatttttattattcacatttagtttttttatttgtgtttctgtttaaggatttttagttatctgctgttgataaatgtcctaaactgattatgtatgtagGCAATTCAGGGCCTATGTTGTCCGTTGATACAATTGAGAAAATGATGGAAGATCCAGCCGTGCAGAAGATGGTTTACCC

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AC204045.3_FGT005 (Zea mays), 3'ss of exon 3
----------------------------------atttaatcacag---ctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatttcctaaattgttgaac--attcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
                                   |||  || |||   ||    ||||  | |||| |     |  || |       |||| ||| | | |  | ||     | |||  | |||  ||||   |  |||  |  ||   ||| |  | || || ||  |  | ||||| ||||||||||||||| | ||||| ||||||||||||||
gtaagcaattgaacatacacattgcagatctctatttttgtctcagtatcttcttataaaatgatttggtagtgtaccttttatctagttttcatggttgatctgaat-----agattcctcaactgattctgctatagGTCAATCAGGACCTATGCTATCTGTTGAGACAATTGAGAAGATGATGGAAGATCCAGCTGTGCAGAAGATGGTTTATCC

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G353213_T02 (Zea mays), 3'ss of exon 8
-----------------------------------------atttaatcacagctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatttcctaaattgttgaac--attcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
                                         |||| |  |    |   |  || | | ||     || |   | | | |||||||    | || | |         || ||| || |||  ||||  ||  ||  ||| |     || |  | || || ||  |  | ||||||||||||||||||||| | ||||| |||||||| |||||
gtaagcaattgagcacacacacactgtggatctccttttgtattttagtatctttcttataaaatcatttggtagtgttccttttatctggttttcctagttgatctaaa------tagattcttcaactgattctattatagATAACTCGGCATCTATGCTATCCGTTGAGACAATTGAGAAAATGATGGAAGATCCAGCTGTGCAGAAGATGGTGTATCC

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G053019_T01 (Zea mays), 3'ss of exon 7
-----------------------------atttaatcacagctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatttcctaa---attgttgaac--attcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
                              | || |     || || ||  | | ||         ||    |||    ||| |   | |    ||||   ||  ||   |||  | |||  ||||   |  |||  |  ||   ||| |  | || || ||  |  | ||||| ||||||||||||||| | ||||| ||||||||||||||
gtaagcaattgaacatacacattgcggatctctatttgtgtctcagtatcttcttataaaatgatttggtagtgtaccttttatctagttttcatggttgatctgaattgattcctcaactgattctgctatagGTCAATCAGGACCTATGCTATCTGTTGAGACAATTGAGAAGATGATGGAAGATCCAGCTGTGCAGAAGATGGTTTATCC

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA18G05480.1 (Glycine max), 3'ss of exon 10
atttaatcacagctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatttcctaaattgttgaacattcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
     ||      ||  | || | |  |||   |   |   ||  || | |   |||||      |   || || ||||      |  ||| ||||   |  |  | |||  |  ||||||| ||||||||| |||||||||||||||| || ||||||||||| ||||||||||||||
----tataggttttacaattattgttctttcaatgtttccttcaatgagctgcattatgggttaatcaaatgtcgtaaacatgccattatttatttttggata--gAAAAATCAGTCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA11G31810.1 (Glycine max), 3'ss of exon 7
atttaatcacagctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatttcctaaattgttgaacattcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
     ||      ||  | || | |  |||   |   |   ||  || | |   |||||      |   || |||| ||      |  ||| ||||   |  |  | |||  |   |||||| ||||||||| |||||||||||||||| || ||||||||||| ||||||||||||||
----tataggttttacaattattgttctttcaatgtttccttcaatgagctgcattatgggttaatcaaatatccttaacatgccattatttatttttggata--gAAAAATCAGCCTTGTCAGTGGATGCTTTGGAGAAAATGATGGAGGACCCAACAGTGCAGAAGATGGTTTATCC

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G16620.1 (Arabidopsis thaliana), 3'ss of exon 7
-atttaatcacagctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatt---tcctaaat-----tgttgaacattcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
  | | || |    |     | || |  |   | ||  || |||| | |   || || | |   |||   | |   |||| | |     | |||   |  ||  |   || || | |   ||    || || || || ||| | |||||||||||||||||||||||||| || ||||||||||| ||
tgtgttatgattcttttttcttatatgctcacg-ttattgtctctcttttccttattctaa--atttaaaactgaatcctgagtctgtctattgtttacacagGTGGTGGGAAAGGAGGGCCGGGTTTATCTGTAGAAGCTTTAGAGAAAATGATGGAAGATCCAACAGTCCAGAAGATGGTTTACCC

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S110_13V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------------------------------------------------------------------------atttaatcacagct--aagaataatttaattttgcttgatg-actctgtgtggttttttatgatggtttggtatttcctaaattgttga--acattcatttc--cagGAAACGCAAATC---CTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
                                                                                     | ||  | || |  ||  ||      |      | || | ||  |||    ||| | |  |||| | ||  | | |   || ||| |   |||    |||  | ||||| ||||| |   || | ||    |||||     ||||||| |||||||| || |||||||| |||||||||||||||||
gtacggtttctcaattaatacgcttttgaattccctttaccttgtgtcttaaatttgtctgcgcactgtgttcatttgtgaatcctgaaagagagtttgaaacatgcaccgagagaattcgaggtaccttgtaaaatttctca-aatggatggggctgttcgttatggttaacagCATGGGATTCTGCGGGAAAAGCAAAGCAGACTGTTTTTAGTGTGGAGCAGTTGGAGAAGATGATGGAGGACCCAACAGTTCAAAAGATGGTTTATCC

upper sequence: Vv18s0041g01360.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S159_2V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------atttaatcaca-gctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatttcctaaattgttgaacattcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
                      || ||| |    || ||| || || | |||   |||       |  ||  |  ||   | | ||||| | ||  ||  |   | |||   |  |    | | ||  || |  |  ||||  | || ||     ||||||| |||||||| ||||||||||| |||||||||||||| ||
accttaaattgggaaagagggtttaaattatttacttagagtagttcattttctattgggagaatttcgtaatgatt--gggttgtttgttgttgtctctagCATGGAATTCTGCTGGAAAAGGAAAACAGA--CGGTCTTCACTGTTGACCAATTGGAGAAGATGATGGAGGATCCAACAGTTCAAAAGATGGTTTACCC

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|30137643|gb|CB922981.1|CB922981
EST:     AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTC                         GAAATGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
genomic: AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTCgtaagttaaa ... tcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
EST: gi|110699715|gb|EE076966.1|EE076966
EST:     AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTC                         GAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAA-TGATGGGAG
genomic: AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTCgtaagttaaa ... tcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
EST: gi|37183876|gb|CF603230.1|CF603230
EST:     AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTC                         GAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
genomic: AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTCgtaagttaaa ... tcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
EST: gi|30136598|gb|CB921936.1|CB921936
EST:     AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTC                         GAAATGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
genomic: AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTCgtaagttaaa ... tcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
EST: gi|32268986|gb|CD718145.1|CD718145
EST:     GTTTCTGAGGATTCTCAATCTACTC                         GAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
genomic: GTTTCTGAGGATTCTCAATCTACTCgtaagttaaa ... tcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
EST: gi|30136267|gb|CB921605.1|CB921605
EST:     AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTC                         GAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
genomic: AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTCgtaagttaaa ... tcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
EST: gi|30126394|gb|CB911733.1|CB911733
EST:     AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTC                         GAAATGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG
genomic: AACTCCTCCCAGGCCAGGCATGGGCGTTTCTGAGGATTCTCAATCTACTCgtaagttaaa ... tcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtggttttttatgatggtttggtatttcctaaattgttgaacattcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC
                           tcctaaa  putative branch site (score: 2)
                                            ttcatttcc  putative PPT
     ttttttatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttaatcacagctaagaataatttaattttgcttgatgactctgtgtggttttttatgatggtttggtatttcctaaattgttgaacattcatttccagGAAACGCAAATCCTTTCTTGTCGGTGGATGCTCTGGAGAAAATGATGGAAGATCCAACAGTGCAAAAGATGGTTTATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - aatcaca
- - - - - - - aagaata
- - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - -tgtgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttgg