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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatttgaaaaccatgccagcaggataacatgctatagttactgtacttttaacatgctaatgaatgccttttaaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC

Basic information

species Vitis vinifera
transcript Vv11s0103g00550.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os06g48650.2 (Oryza sativa), 3'ss of exon 8
---------------------------------------------------------------------gaatttgaaaaccatgccagcaggataacatgctatagttactgt--acttttaacatgctaatgaat-gccttttaaacatctttgtttt-----ttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC
                                                                      |||||      ||||   | |   |   |||   || ||  | |  || |||  ||  |   ||  |  |||   | | || | | || |     | | |    |||| ||||| ||||||||| | ||||||||||| ||||||||||||||||| ||||| || || || ||  |||| |||||  ||||  | ||||| ||  |
gtaagctttgctgtacttttatatcccttgaagcatacaaagctttttaagcatgttatggttgcattgaaattttccttgcatgtttg-attgttctatgtggtaattcatatggacgtttgtcaatcatgtggcttacctaaaatatatttctcttgtggcaatgcatattccagGGGAAGGATTTGCAATGGTTTCTGGAACTAGTATGGCTGCACCACATATTGCTGGTATCGCGGCACTAATAAAACAGAAGAACCCCAAGTGGAGTCCCTC

upper sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G099452_T02 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------gaatttgaaaaccatgccagcaggata-acatgctatag-ttactgtacttttaacatgctaatgaatgcctt------ttaaacatctttgttttt-tcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC
                                                                 | ||         ||||  |    |  | ||  | | |  || ||    || |  ||     |   ||| |       || || ||  ||||  |  | ||   ||||| ||||| ||||||||| | |||||||||||||||||||| || ||||| ||||| || || || ||  ||||||||||  ||||  | ||||||||  |
gtaagctttgtatgtagatctctttttcctcaaggaagcacccatgtgattatcgccagcattttagttctgcgcttttgccgtccttttgcatattttgtggactagtgattcttgaggatatctttctgtgcttgaaccaattcaaaattgttgtggtaatattttcgcagGTGAAGGATTTGCAATGGTTTCTGGAACTAGCATGGCTGCGCCGCATATTGCTGGCATTGCAGCACTGATAAAGCAGAAGAACCCAAAGTGGAGCCCCTC

upper sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G114394_T02 (Zea mays), 3'ss of exon 9
-----------------------------------------------------------gaatttgaaaaccatgccagcaggataacatgctatagttactgtacttttaac--atgctaatgaatgccttt------------taaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC
                                                           | |||| |  ||   ||                 |||  | ||| | |  | |    || | ||   |  || |            | |||||   |||  |    |    |||| ||||| ||||||||| | ||||||||||||||||| ||||| ||||| ||||| || || || ||  ||||||||||  ||||  | ||||||||  |
gtaagcgtgcgttgtctgtagacctcttcccctcgaggaagcacccatgattaccatcagtattttactactgcgctcttgccgcccttgtgcatatcttctggattagtgatcggtggtgatatttttctgtgctcgaaccaactcaacattgctgtggtaatatttctcagGTGAAGGATTTGCAATGGTTTCTGGAACTAGCATGGCCGCACCGCATATCGCTGGCATTGCGGCACTGATAAAGCAGAAGAACCCAAAGTGGAGCCCCTC

upper sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA15G17830.1 (Glycine max), 3'ss of exon 8
gaatttgaaaacca-tgccagcaggataacatgctatagttactgt-acttttaacatgctaatgaatgccttttaaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC
||||  | |    | |   || || | ||||    |||     | | |   | || || |||  ||||    ||||   |       |||||  | |||||||||| |||||||||||||| ||||| ||||| |||||||||||||||||||||||||| ||||| ||  ||||||||||||| || ||||||||||||||
gaataagcacggaacttatagaagaaaaacacttgataaaagatatcatcatcaaaatactatagaatttgatttatttaagc--agtttttgcttgagcagGAGAGGGGTTTGCAATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC

upper sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA17G06740.1 (Glycine max), 3'ss of exon 8
----gaatttgaaaaccatgccagcaggataacatgctata-gttactgtactttta-acatgc-taatgaatgccttttaaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC
     ||||     |  | |   ||  |  |  | | || | |  |   ||||  || |  | | ||||  || | |||||| |   |||| || |       ||||| |||| |||||| ||||| |||||||| ||||||||||||||||||||||||||||| ||||| ||| |||||||||| || |||||||||||||||||
agaataattgcttgattaaggacgcgagggaggaaggtagaagaaaacttactaatatatttacataattgattcattttaagctattttgcttgt-------gcagGTGAAGCGTTTGCCATGATATCTGGAACCAGCATGGCTGCACCACATATAGCTGGAATTGCTGCTCTTATAAAGCAGAAGCATCCTCATTGGAGCCCTGC

upper sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA13G00580.1 (Glycine max), 3'ss of exon 8
---gaatttgaaaaccatgccagcaggataacatgctatagttac-tgtacttttaacatgc-taatgaatgccttttaaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC
    ||||  |  |  | |   | |||   | | |    ||  |    ||||  ||   |   || |  || | |||||| ||     |||||||  | | ||||| || |||||||| ||||| |||||||||||||||||||||||||||||||||||||| ||||| ||  |||||||||| || |||||||||||||||||
gaataattgcatgattaaggagggagggacaaaggtagaagaaaaacttactgatatgttatatagttgattcattttaagca-----gttttttgcttgtgcagGTGAGGGGTTTGCCATGATATCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATTGCTGCTCTCATAAAGCAGAAGCATCCTCATTGGAGCCCTGC

upper sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G06640.1 (Glycine max), 3'ss of exon 9
-gaatttgaaaaccatgccagcaggataacatgctatagttactgt-acttttaacatgctaatgaatgccttttaaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC
   |||        | |  || || | ||||    |||     | | |   | |  || |||   |||    ||||   |       |||||| | | |||||||| |||||||| ||||| ||||| ||||| |||||||||||||||||||||||||| ||||| ||  ||||||||||||| || ||||||||||||||
atgattaagcgtggaagatagaagaaaaacacttgataaaagatatcatcatcagtatactataaaatttgatttatttaagc--agtttttccttgtgcagGAGAGGGGTTTGCGATGATATCTGGGACTAGTATGGCTGCACCACATATAGCTGGAATTGCTGCTCTGATAAAGCAGAAACATCCACATTGGAGCCCTGC

upper sequence: Vv11s0103g00550.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G19170.1 (Arabidopsis thaliana), 3'ss of exon 9
gaatttgaaaaccatgccagcaggataacatgctatagttactgtacttttaacatgctaatgaatgccttttaaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC
      | || |  ||  || |    | |  ||   |  | | | |  |||   ||   |||    | || |||     |||||   | |    ||||||| ||||| |||||  | || || ||||| ||||||||||||||||| ||||| || |||||||| ||||| |||||||| || ||||| |||||||| ||
------gtaagcattgatagtactgaagctagc---atgtgccgaatcttttgaatcagaattgtggtctctta-----ctttgggatatt---gagcagGTGAAGGATTTGCGCTAATATCAGGAACCAGCATGGCTGCACCACACATAGCCGGGATAGCTGCGCTTGTGAAGCAGAAGCATCCTCAATGGAGCCCAGC

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|33404257|gb|CF209884.1|CF209884
EST:     CATTTGGGCTGCCTGGTTTCCAAATGGAACAGATGAGGCCAATTATGTTG                         GAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAG
genomic: CATTTGGGCTGCCTGGTCTCCAAATGGAACAGATGAGGCCAATTATGTTGgtaaatatca ... cttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAG
EST: gi|30254462|gb|CB971207.1|CB971207
EST:     CATTTGGGCTGCCTGGTCTCCAAATGGAACAGATGAGGCCAATTATGTTA                         GAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAG
genomic: CATTTGGGCTGCCTGGTCTCCAAATGGAACAGATGAGGCCAATTATGTTGgtaaatatca ... cttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttaacatgctaatgaatgccttttaaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC
          tgctaat  putative branch site (score: 2)
                               catctttgttttttct  putative PPT
                        ttttaaacatctttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatttgaaaaccatgccagcaggataacatgctatagttactgtacttttaacatgctaatgaatgccttttaaacatctttgttttttcttcgagcagGAGAAGGGTTTGCAATGATCTCTGGAACTAGCATGGCTGCACCACATATAGCTGGAATAGCTGCCCTTGTAAAGCAGAAACACCCTCATTGGAGCCCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - ttgaaaa
- - - - - -ccatgcc
- - - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatgcc