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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgcctgccactgttgtctggttacaagtgttaggtaaatgcaaatatattcctgttcggagaaattcaacagagtttaatgaagtggcatctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 12
-tattgcctgccactgttg--tctggttacaagtgttaggtaaatgcaaatatattcctgttcggagaaattcaacagagtttaatgaagtggcatctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG
  |   |||   | |  ||  | |||  |  | |   |  | |       |       | |    |     ||  | |  || |||||      ||    ||||| ||||  | | | || || |||||||||||||| | ||||||||| ||||  |||||||| ||||| || | |||||| ||||| || ||||||||||
taaggaccttttattaatgaatttggcaaagaattgcacatcatattctgttggcatttatcaatattgtatcttctggtttgaatgatccaatatg---cagGAGAAGAAAACTATTCGCCCTACATTTTCAGCTGAACGTATTTTTGGTGGAATATTATTGGCGATGTGTTCCAGTGATTTCATTTGCTTTTATGACTGGG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 12
--tattgcctgccactgttgtctggttacaagtgttaggtaaatgcaaatatattcctgttcggagaaattcaacagagtttaatgaagtggcatctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG
  |      |  || | |  | | |||  |  |||  |  ||||| |||||  ||     | ||  |  || ||  |    |    |  | | || ||||||||||||| |||| |||||||||| |||||||||||||  || ||||| || ||| ||||||||||||||||||||||||| || || || || || ||||
tctcaaaaataacattctcttattgttttagatgtctgccaaatg-aaataagttgtctctagggaagttttaaatggaaatgg-aattttgtatatttcagGAAAAGAAGAGTATCCGACCAACTTTTTCAGCTGAGCGAATATTTGGCGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTACGATTGGG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G03890.2 (Glycine max), 3'ss of exon 1
tattgcctgccactgttgtctggttacaagtgttaggtaaatgcaa-atatattcctgttcggagaaattcaacagagtttaatgaagtggcatctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG
 |     |  || | |  | | |||  |  |||     ||||| |  |||  ||     | ||  |  || ||  |    | |  |  | | || ||||||||||||| |||| |||||||||| ||||||||||| |  || ||||| || ||| ||||||||||||||||||||||||| || || || ||||| ||||
caaaaaataacattctcttattgttttagatgtcttccaaatgaactataagttgtctctagggaagttttaattggaaatga-aattttgtatatttcagGAAAAGAAGAGTATCCGACCAACTTTTTCAGCTGAACGAATATTTGGTGGCACTGTATTGGCAATGTGCTCAAATGATTTCATCTGCTTTTATGATTGGG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 12
tattgcctgccactgttgtctggttacaagtgttaggtaaatgcaaatatattcctgttcggagaaattcaacagagtttaa--tgaagtggca--tctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG
 |     |    || |  |   |||| |  |||     || || ||||| |||     | ||  | | | |    ||||  |  | ||        | |||||||||||||||||||||||||||||||||||||||||    || || || || |||||| |||| |||||||| || ||||| || || || ||||||||||
-aaaatttaatcctatcatt--gttatagctgtcttcgaattg-aaataaatttgctctagggaatacttagtttagttggaatttaaacaatgggtatttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAAAGAATATTCGGTGGCACTTTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 12
tattgcctgccactgttgtctggttacaagtgttaggtaaatgcaaatatattcctgttcggagaaattcaac------agagtttaatgaagtggcatctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG
     |||  || |||| |  | ||| |  |||      | || ||||| |||     | ||  | | |           || |||||  || ||| ||  ||||||||||||||||||||||||||||||||||||||||    || ||||| || ||| || |||| |||||||| || ||||| || || || ||||||||||
---atcctctcattgttataggcttatagctgtcttcgtattg-aaataaatttgctctagggaatacttggtttagttggaatttaaacaattggtat--ttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAAAGAATATTTGGTGGCACTCTACTGGCGATGTGCTCCAACGATTTCATCTGCTTTTATGACTGGG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 16
---------------tattgcctgccactgttgtctggttac-----aagtgttaggtaaatgcaaat-atattcctgttcggagaaattcaacagagtttaatgaagtggcat--ctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG
               |    | | ||  |   | ||| |||      |||  || | |   ||    | ||  |  | |  | |  |    |||  |   | ||    | |  |   || |||||||||| || |||  |||| || || ||||| ||||| |||||||| || || |||||| |||||||||||| ||||||||| || |||||||| ||||
gtttgtaattccttttggcacgttccttttccgactgattaactctaaagcttttgttttttgtgtcttattctgttatctgaaatacactaacctatgctgatacccttgtttaatttgcagGAAAAGAAGACTGTGAGACCCACCTTCTCAGCAGAGCACATTTTTGGTGGGACGTTATTGACAATGTGCTCAAGTGATTTTATATGCTTCTATGATTGGG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 12
---------------------tattgcctgccactgttgtctggttacaagtgttaggtaaatgcaaatatattc----ctgttcggagaaat---------tcaacagagtttaatgaagtggcat-ctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG
                     |  |    |||  |  |||           | |  |||   || || |||  |     ||| ||   || ||            |    | | | | |      |   |||||||||||||||||| |||| || || |||||||||||| | || ||||||||||| || || || ||||| |||| |||||| || || || ||||| ||||
gtttctaaatctttttctctctgatctaagccgtt-ctgttcaaccctgtatctatggttgttggaagtattattgatactggtcatggagatagctatattcggatctggctcattcagaaaatacattttcagGAAAAGAGGAGTATCCGCCCTACTTTTTCAGCTGAGAAGATCTTTGGAGGAACCTTGTTAGCTATGTGTTCAAGTGATTTCATCTGCTTTTATGATTGGG

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 12
---------------------------tattgcctgccactgttgtctggttacaagtgttaggtaaatgcaaatatattcctgttcggagaaattcaacagagtt-------taatgaa--gtggcatctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG
                            ||    |     ||  || || ||  | |  | | | || |||| ||   || |  |   || |  |   || |  ||       |||| ||  ||||  | |||||||||| || |||| |||| || || || ||||||||| | |||||||||||||| || || |||||||| || |||||||| || || |||||||| ||||
gtttgctattctcattatggccttactcatactattttgttggagtatgattctagggttgaagaaattgcagatgc-ttgcaatagagacagctattactggcttattatattaataaaaggtggtgt-tttcagGAAAGGAAGAGTATCCGGCCTACTTTCTCAGCTGAGAAGATTTTTGGAGGAACCTTGTTAGCAATGTGTTCGAATGATTTCATCTGCTTCTATGATTGGG

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|351030017|gb|FQ430759.1|FQ430759
EST:     CTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAG                         GAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGA
genomic: CTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcc ... catctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatattcctgttcggagaaattcaacagagtttaatgaagtggcatctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG
                               gtttaat  putative branch site (score: 4)
                                             catctttc  putative PPT
                                tttaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattgcctgccactgttgtctggttacaagtgttaggtaaatgcaaatatattcctgttcggagaaattcaacagagtttaatgaagtggcatctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGAACTTTATTGGCAATGTGCTCAAATGATTTTATTTGTTTCTATGACTGGG

- - gcctgcc
- - - - - - - - tgtctgg
- - - - - - - - - - - - - caagtgt
- - - - - - - - - - - - - - - - - aggtaaa
- - - - - - - - - - - - - - - - - - - - - - aaatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caacaga