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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttaagatctgaatgaagctttaaagttttgaggtgcattaatgatatcaataatcgcccaggcgaatgttaatacattttgctctgtcattttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGATCGAGTG

Basic information

species Vitis vinifera
transcript Vv07s0005g02990.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g44930.1 (Oryza sativa), 3'ss of exon 2
----ctttaagatct-gaatgaagctttaaagttttgaggtgcattaatgatatcaataatcgcccaggcgaatgttaatacattttgctctgtcattttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGATCGAGTG
      | ||||| | | |||     | | | | |  |  | |||   || |   |   ||  |  |    | |||   |    | || | ||||  ||   ||||||||||| ||||||||||| || || |||| ||||||||| ||||||||  || ||
ttgttctcaagattttgcatgctagatcacaatgt-aatcttcatatgtgcttatagccatt-ctaaacttactgtacctttgatgtggtttgtctctt---cagTTGACAGGAGATATACATGAAGAAGTGGAGAATCATAACCGAATGCTGGACAGAATG

upper sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os08g44930.2 (Oryza sativa), 3'ss of exon 2
----ctttaagatct-gaatgaagctttaaagttttgaggtgcattaatgatatcaataatcgcccaggcgaatgttaatacattttgctctgtcattttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGATCGAGTG-------------------------------------------
      | ||||| | | |||     | | | | |  |  | |||   || |   |   ||  |  |    | |||   |    | || | ||||  ||   ||||||||||| ||||||||||| || || |||| ||||||||| ||||||||  || ||                                           
ttgttctcaagattttgcatgctagatcacaatgt-aatcttcatatgtgcttatagccatt-ctaaacttactgtacctttgatgtggtttgtctctt---cagTTGACAGGAGATATACATGAAGAAGTGGAGAATCATAACCGAATGCTGGACAGAATGGTACTAATATCCTGCAAGATGCTATCTTTCTTGTCACTACTCT

upper sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G31790.1 (Glycine max), 3'ss of exon 3
ctttaagatctgaatgaagctttaaagttttg---aggtgcattaatgatatcaataatcgcccagg----cgaatgttaatacattttgctc---tgtcattttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGATCGAGTG
         ||  |  | | |||| | |||     || || |  |   |  |  || || | | |      | |   | |||  ||||| |     | | |||  |||||||  ||||||||||| |||||||||| || || ||||||||||||||||||||| ||
---------ctaga-aagggtttagaatttcatatagatgtagcaggcagttgcatgatggtctaaaacaactagcataaatttatttttcatgggtatgattgcaacagTTATCAGGTGATATAAATGAGGAGGTGGATAGCCATAACCGCATGCTGGATCGAATG

upper sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G18170.2 (Glycine max), 3'ss of exon 3
-------ctttaagatctgaatgaagctttaaagttttgaggtgcattaatgatatcaataatcgcccaggcgaatgttaatacattttgctctgtcattttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGATCGAGTG
         | ||||| | ||    |   |  ||||||| | ||  |||||    |   || |    ||     || || |    ||        | |||  |||||||| ||||||||||| ||||||| || || ||||||||||| |||||||||||  ||
tgtatcctgtaaagatgttaacagtg---tgcagttttgtgctggtttaatatcttt--tactttatcaact--atattgaagttttgaagagcataattgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGATCGTATG

upper sequence: Vv07s0005g02990.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G04020.1 (Glycine max), 3'ss of exon 3
ctttaagatctgaatgaagctttaaagttttgaggtgcattaatgatatcaa-taatcgcccaggcgaatgttaat-acattttgctc--tgtcattttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGATCGAGTG
   | |   ||| |  |    ||||     ||  ||    | ||| | | || |  || |     | | | | | | |  ||||  |     | |||  |||||||| ||||||||||| ||||||| || || ||||||||||| |||||||||||  ||
---tgaatcctgta-aagatattaacaacgtgcagttttctgatggtttaaaattttcactttatcaactataattgaagttttaatgagcataattgcaacagTTGTCAGGTGATATAAATGAGGAAGTGGATAGTCATAACCGGATGCTGGATCGTATG

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|110368599|gb|EC932587.1|EC932587
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|34549774|gb|CF518006.1|CF518006
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|26257147|gb|CA808210.1|CA808210
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGCTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|30306129|gb|CB982923.1|CB982923
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|110371595|gb|EC935706.1|EC935706
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|29782805|gb|CB348441.2|CB348441
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|110708420|gb|EE085941.1|EE085941
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|110405426|gb|EC970967.1|EC970967
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|30306203|gb|CB982997.1|CB982997
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|34550262|gb|CF518480.1|CF518480
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|110724887|gb|EE101110.1|EE101110
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|110378284|gb|EC943408.1|EC943408
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
EST: gi|28969494|gb|CB348527.1|CB348527
EST:     ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGA                         TTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT
genomic: ATGAAAGAGCAGTGGATGGACTGCAAGATAGAGTTAATCTGCTGAAGCGAgtaagttcta ... attttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcaataatcgcccaggcgaatgttaatacattttgctctgtcattttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGATCGAGTG
                       tgttaat  putative branch site (score: 3)
                                           tcatttt  putative PPT
                     aatgttaatacatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttaagatctgaatgaagctttaaagttttgaggtgcattaatgatatcaataatcgcccaggcgaatgttaatacattttgctctgtcattttaacagTTGACAGGTGATATACATGAGGAGGTTGAGAGTCATAACCGCATGCTGGATCGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - -ctgaatg
- - - - - - - - - - - - - - - - - gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccaggc