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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgtttcacgctcattctgttttgttaatactccattttgatttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG

Basic information

species Vitis vinifera
transcript Vv19s0015g01160.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os08g25310.1 (Oryza sativa), 3'ss of exon 8
----gtttgtgtttcacgctcattctgttttgttaatactccattttgatttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
    | ||    ||||    |||| | | | |||  |    |||  ||||||    |    |    || |||  ||  |   |||| |||  |  | |    ||| ||||| ||||| || ||||||||  | ||||| |||||| |||| || || ||||| | |||||| ||||| ||||||||||||||| | || ||||||
gtaagctttccattcagaaacattttatatggtttcttgatcataatgattt----tgtcgtcatgtctttgatttaatgcacattgttttgctattta---cagCCAACTTCCTGAATTTTTGGGTGGAGCATGCACTTGTGCTGCTGAGGGAGGATGCCTCAAGTCTAACAAAGGCCCATGGAATGATCCTAACATTATGAAG

upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G014994_T03 (Zea mays), 3'ss of exon 7
gtttgtgtttcacgctcattctgttttgttaatactccattttgatttctaattctatttgttccttgcatttttcttcattttttcccc----ttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
                           |||  |  |   || |     | ||   |||||  |   || |  | | | ||  | ||   |    |   | ||||| ||| |||| || | ||| ||||| || ||||||||| |||   |||| ||||||||||||||||| |||||||| |||| |||||||  ||||||||||
---------------------------gttggtggtggcttct----ccaaagattattttattggtgaacctgtgtgcaaatcttaagcaaaatgtatcttcagCCAATTGCCGGATTACTTTGGTGGTTCATGCACATGTTCTAACCATGGAGGGTGCCTGAGGTCTAACAAAGGTCCCTGGAGTGATCCTTCAATAATGAAG

upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G010834_T01 (Zea mays), 3'ss of exon 6
---gtttgtgtttcacgctcattctgttttgttaatactccattttgatttcta-attctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
    ||| | | | ||   |||  |      | | | ||| ||  | ||   ||  | | ||| |   |||  ||| |   |  ||| ||    |  | ||  |||||||| ||||| || ||||| ||  | ||||| |||||| |||  || || ||  |||||||||| |||||||||||||||||||| || || ||||||
gtattttttctattacaaccatattaagc-ataatttctcgatcataatgattatgtcccattag---cttagattgtgtgtgttttcttttgatgttggt--agTCAACTTCCTGAATTTTTGGGGGGGACATGCACTTGTGCTGCTGTGGGAGGATGTATGAGGTCTAACAAAGGTCCATGGAATGATCCAGATATTATGAAG

upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G48060.2 (Glycine max), 3'ss of exon 4
gtttgtgtttcacgctcattc-tgttttgttaatactccattttgatttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
                ||||  ||| ||  | |||   ||||   ||||||| ||| |||| ||  ||   ||    ||  |   |    ||     | ||||||  |||| |||||  ||||||| ||||| ||||||||| | || ||||| || ||  ||||||| || |||||||||||||||||||| || ||||||
-----------gtatacatttatgtcttcatcatatggcattggaatttcta-ttcaatttattgattaatttgaattttgtaaatgaaact----atacagTCAGTTGCCAGACTTTCTGGGTGGTTCTTGTACATGTGCTGCAGAAGGTGGATGTCTTCGGTCTAACAAGGGTCCATGGAATGATCCTGACATCATGAAG

upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G12450.1 (Glycine max), 3'ss of exon 8
gtttgtgtttcacgctcat-tctgttttgttaatactccattttgatttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
                ||| | ||| ||  | ||||| |||| | ||||||| ||| || | ||  ||   ||    ||  |   |    ||     | ||||||  |||| |||||  ||||||| ||||| ||||||||| | || ||||| || ||  ||||||| || |||||||||||||||||||| || ||||||
-----------gtatacatctatgtcttcatcatactgcattgtaatttcta-ttcaatatattgattaatttggattttgtaaatgaatct----atacagTCAGTTGCCAGACTTTCTGGGTGGTTCTTGTACATGTGCTGCAGAAGGTGGATGTCTTCGGTCTAACAAGGGTCCATGGAATGATCCTGACATCATGAAG

upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 7
gtttgtgtttcacgctcattctgttttgttaatactccattttgatttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
    || |    |  | | |    ||  | | |||| | || | ||||||| | | | |||||  ||   || || ||  |   | |  ||     | ||||||  |||| ||||| ||||||||  | || |||||| ||   || ||||| || || |||||||  ||||||||||||||||||||||| || ||||| 
----gtatgaatctatgacttcaattcatca-tactgccttataatttcta-tacaaattgttgtttaatttattgtttgtaaatacatct----atacagTCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGGATGTCTAAGGTCTAGCAAAGGTCCATGGAATGATCCTGATATCATGAAA

upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G56160.1 (Arabidopsis thaliana), 3'ss of exon 8
-------gtttgtgtttcacgctcat------tctgttttgttaatactccattttgatttctaattctatt-tgttc-cttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
        ||| |   |||| |||||      | ||||||||  |||  |   ||  | || |  || |    || |  | |   | ||| ||  |||| |  |||   ||| ||||||||| || || |||||||| ||||  |||| |||| |||  || || |||||| |||||||||| ||||| || |||||||||||||||||| |  ||
gttaattttttatagctcac-ctcatagagtttttgttttgtagatagcctcattcaagttttggttatggcatgctaacattagtatttattgcttttctttcctctctgtacagTCAACTTCCAGAATTCTTGGGAGGCTTATGCAAATGTCCTAACGAGGGAGGGTGCTTGAGGTCTAACAAAGGACCCTGGAATGATCCTGAAATAGTTGAG

upper sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G55690.3 (Arabidopsis thaliana), 3'ss of exon 9
gtttgtgtttcacgctcattctgttttgttaatactccattttga---tttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGT---GGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
             |    ||   || | || | ||| ||  |  |   ||||  |    || | |  |    | || |   |  |  | | |  |  |  | |||||| |||| || ||| | || || || ||| | ||   |  ||||||    ||||| ||  | ||||||||||| || |||||||||||||||||||||   
-------------gtagctttctttctctttacactgcacctgaaaagtttcagaaatcatgtctagccaatacttatgagctctggtgctctgtgct--ttagTCAATTGCCAGAATTCCTTGGAGGTTCATGCTCTTGCTTTGGTGATGGAGGAGGGTGTCTTCGCTCTAATAAAGGACCCTGGAATGATCCTGAAATAATG---

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|110690338|gb|EE067360.1|EE067360
EST:     GTGCTGGAGCCCAAATTCTTATGTAAACTTCTGGAAGTCATTGACTCAAG                         TCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
genomic: GTGCTGGAGCCCAAATTCTTATGTAAACTTCTGGAAGTCATTGACTCAAGgtttgtgttt ... tcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
EST: gi|30328313|gb|CD011575.1|CD011575
EST:     CTTATGTAAACTTCTGGAAGTCATTGACTCAAG                         TCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
genomic: CTTATGTAAACTTCTGGAAGTCATTGACTCAAGgtttgtgttt ... tcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
EST: gi|32269703|gb|CD718862.1|CD718862
EST:     CTTATGTAAACTTCTGGAAGTCATTGACTCAAG                         TCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
genomic: CTTATGTAAACTTCTGGAAGTCATTGACTCAAGgtttgtgttt ... tcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
EST: gi|32247565|gb|CD713384.1|CD713384
EST:     CTTATGTAAACTTCTGGAAGTCATTGACTCAAG                         TCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
genomic: CTTATGTAAACTTCTGGAAGTCATTGACTCAAGgtttgtgttt ... tcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
EST: gi|32249844|gb|CD715663.1|CD715663
EST:     CTTATGTAAACTTCTGGAAGTCATTGACTCAAG                         TCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
genomic: CTTATGTAAACTTCTGGAAGTCATTGACTCAAGgtttgtgttt ... tcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
EST: gi|32247747|gb|CD713566.1|CD713566
EST:     CTTATGTAAACTTCTGGAAGTCATTGACTCAAG                         TCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG
genomic: CTTATGTAAACTTCTGGAAGTCATTGACTCAAGgtttgtgttt ... tcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
 ttctaat  putative branch site (score: 2)
           tttgttccttgcattt  putative PPT
                       atttttcttcattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgtttcacgctcattctgttttgttaatactccattttgatttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA