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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaatggtgtagatggagattaaatgattatttttacttgatgtcacagatttaacctccaagcatgttttgacattagtttttggctcttctcttttagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAGTCGAAGGGGTGGACGAACTGCTTTTATCTGAAAGTAAGTGCTTTTTATC

Basic information

species Vitis vinifera
transcript Vv19s0015g01950.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G47850.1 (Glycine max), 3'ss of exon 8
acaatggtgtagatggagattaaatgattatttttacttgatgtcacagatttaacctccaagcatgttttgacatta---gtttttggctcttctctt---ttagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAGTCGAAGGGGTGGACGAACTGCTTTTATCTGAAAGTAAGT--GCTTTTTATC
       | |  | | |   | ||   || |||      || ||   |  || ||   |  |  || ||   |  ||     |||||  || || ||||    |||  |||||||||||||||| |||||||| || |  || || || ||||| ||  ||||||||||||||||||||||||| ||| ||    |  | |  | |  
------tttttcaagaaatgtgaacacttttttagttcagaagtgtaaccttgaaatgcttatgatattaatatttttttcttttttatcttttgtcttggtgtagCTCAATGAATGAGCTGGTGGACAAATTTAATATCGCGTACGATAGGCATAGCAGAAGGGGTGGACGAACTGCTTTTATGTGAGAGCTGCTTGGTTGCTCA--

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA04G12890.1 (Glycine max), 3'ss of exon 8
acaatggtgtagatggagattaaatgattatttttacttgatgtcacagatttaacctccaagcatgttttgacattagtttttggctcttctctt---ttagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAGTCGAAGGGGTGGACGAACTGCTTTTATCTGAAAGTAAGT--GCTTTTTATC
 |||      | |||   |    ||| |  ||   |  ||    |    | |   | |   |   || | | | |||  |||||| || || ||||    |||| | |||||||| ||||| |||||||| || |  || ||||| ||||| ||  ||||||||||||||||||||||||| ||| ||    |  | |  |||  
tcaagaaaagaaatgtgaacactatgttagttcagaagtgtaaccttgaaat--gcttatgatattgatat-atattcttttttgtcttttgtcttggtgtagTGCTATGAATGAACTGGTGGACAAATTTAATATTGCGTATGATAGGCATAGCAGAAGGGGTGGACGAACTGCTTTTATGTGAGAGCTGCTTGGTTGCTTA--

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G56280.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------acaatggtgtagatggagattaaatgattatt-tttacttgatgtcacagatttaacctcca-------agcatgttttg--acattagtt------tttggctcttctcttt-tagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAGTCGAAGGGGTGGACGAACTGCTTTTATCTGAAAGTAAGTGCTTTTTATC---
                                            | |     |   |||    |||| |  |  || ||||     ||| | ||||      | ||        |    || ||  | || ||||      ||||  |  ||  | |  || |  ||||| ||| ||||||||||||||||||| |||||||||||  ||| |||||| |||||| ||||||| || || | ||||    | ||||  | |   
gtttgtacctaatgcaacattctaaagtatttgaaagcaagtatataggctagcgaatgctctttaactagtggttctttaggaactgtgaaagatacggttttcaccgggctggtggattctgttatatcagttaataattttgtttgctcaatctgcagCAACATGAACGAGATGGTCGACAAATTCAACACCGCATATGACAGAAACACTCGAAGAGGTGGAAGAACTGCATTCATGTAAAAG---ATCCTTTCCAGCGAT

upper sequence: Vv19s0015g01950.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S34_439V6.1 (Physcomitrella patens), 3'ss of exon 8
acaatggtgtagatggagattaaatgattatttttacttgatgtcaca--gatttaacctccaagcatgttttgacattagtttttggctcttctcttttagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAGTCGAAGGGGTGGACGAACTGCTTTTATCTGAAAG-TAAGTGCTTTTTATC
  ||||| |           | | |  | | || |  |  |  ||        ||   ||     |   ||   | || |  | ||     ||||  |  ||||| ||||||||| |||| ||||||||||||||||| ||||||| ||| | |||  |||||||||| ||| |||| || |||    | | |  |  | |  
ttaatggcggcttcattttctcattattcaattctggtgaagttcgtgtcacgttggtcttacgtcgacttacaaaatgaaatcttaatatttct--tgcagTACTATGAATGAGTTGGTGGACAAATTCAACACAGCTTATGACAAGCAAAATCGGCGGGGTGGACGTACTACTTTCATTTGAGTTCTCAATAGTGGTCAG-

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|110713432|gb|EE089350.1|EE089350
EST:     AATGATACATTATTGATTAGTTACCTTGCCATGTTCACCAACTGCTCAAG                         TACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAG
genomic: AATGATACATTATTGATTAGTTACCTTGCCATGTTCACCAACTGCTCAAGgtatatgcta ... tctcttttagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAG
EST: gi|110363635|gb|EC927237.1|EC927237
EST:     AATGATACATTATTGATTAGTTACCTTGCCATGTTCACCAACTGCTCAAG                         TACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAG
genomic: AATGATACATTATTGATTAGTTACCTTGCCATGTTCACCAACTGCTCAAGgtatatgcta ... tctcttttagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAG
EST: gi|110428349|gb|EC994818.1|EC994818
EST:     AATGATACATTATTGATTAGTTACCTTGCCATGTTCACCAACTGCTCAAG                         TACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAG
genomic: AATGATACATTATTGATTAGTTACCTTGCCATGTTCACCAACTGCTCAAGgtatatgcta ... tctcttttagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagatttaacctccaagcatgttttgacattagtttttggctcttctcttttagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAGTCGAAGGGGTGGACGAACTGCTTTTATCTGAAAGTAAGTGCTTTTTATC
                      ttttgac  putative branch site (score: 3)
                                  tttttggctcttctct  putative PPT
                             attagttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaatggtgtagatggagattaaatgattatttttacttgatgtcacagatttaacctccaagcatgttttgacattagtttttggctcttctcttttagTACAATGAATGAGCTGGTCGACAAATTCAACACAGCATATGACAGGCACAGTCGAAGGGGTGGACGAACTGCTTTTATCTGAAAGTAAGTGCTTTTTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - tggtgta
- - - - - - - - - - - - - - - - - - - tgatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcatgtt