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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcttatatatatatatatcgagttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA

Basic information

species Vitis vinifera
transcript Vv08s0040g02630.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G10550.1 (Glycine max), 3'ss of exon 2
-tttcttatatatatatatatcgagttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA-----
  | |||| |  || || |||  |  | |    |  |  | | |  ||   ||||  | |      |||| | | |  |  | | || | ||||||  |||||| ||||||||||||||||| |||||||||||||| |||||||||||||| |||||||| || |||||||||||||| || |||  | |||  |      
tgtccttagaattagatttattaatattgcatagaatattatattaagcagtatatttctttgtttttttttaccaacttgcttattttgttttatg-cagGCCGGATGGGACAAAGAAAGCCTATGTTAGGTTGACTCCAGATTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGTT-GTACTCTTGATT

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA18G52310.1 (Glycine max), 3'ss of exon 3
tttcttatatatatatatatcgagt-tggtggtgttttctttttccagttttatacctttcctaaattttgtt--ctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA----
    |    |   |   ||  |||| |       | |  | | |  ||   ||||  | |  |   |||| ||  | |  |    |||| | |||| || |||||||||||| ||||||||||| |||||||||||||| ||||| |||||||| |||||||| || |||||||||||||| || |||  | |||  |     
-acttggagtgcttcattaatgagtatcacataatatattatattaagcagtatatttctt-tgttttttattaccaacttggttttttttttttttttgcaGGCCTGATGGAACAAAGAAAGCCTATGTTAGGTTGACTCCAGACTATGATGCCTTGGATGTAGCTAACAAGATTGGTATCATCTAAGTT-GTACTCTTGAT

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA12G07160.2 (Glycine max), 3'ss of exon 3
---tttcttatatatatatatatcgagttggtggtgttttctttt-tccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA----
    || | | ||     | | |    |||||||  || | |||  |  |||   |      |  ||  |||| | | || | |   ||||  || | || |||||||||||| || ||||| |||||||| |||||||| || ||||| ||||| ||||||||||||||||||||||| ||||| ||   |||||        
ttggttttgagatgccgtttttttacattggtggcattgtatttagtttagtccaacg----tggtattttttctccaatttctgaatttgaattctgttgcagGCCTGATGGCACCAAGAAGGCATATGTCAGGTTGACACCTGATTACGATGCATTGGATGTGGCAAACAAGATTGGGATTATCTAGGGTAGTACTAGTACT

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G15230.1 (Glycine max), 3'ss of exon 3
--tttcttatatatatatatatcga-gttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA----
  |||   ||     | || |  || ||||  |   | |   |  |  ||||  ||    |   |   | |  | | || | |   ||||  || | || |||||||||||| || ||||| || |||||  ||||||| || ||||| ||||| ||||||||||||||||||||||| ||||| |||  ||||| | |    
ggtttgagatgccgctttacagtgaagttgtagaaatatatatggtttagttcaatgaggtattt---tctgctgcaatttctaaatttgaattctgttgcagGCCTGATGGAACCAAGAAGGCTTATGTCCGGTTGACCCCTGATTACGATGCATTGGATGTGGCAAACAAGATTGGGATTATCTAAGGTAGTACCTAGGCA

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA11G15230.2 (Glycine max), 3'ss of exon 3
--tttcttatatatatatata-tcgagttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA
  |||   ||     | || | |  |||||  |   | |   |  |  ||||  ||    |   |   | |  | | || | |   ||||  || | || |||||||||||| || ||||| || |||||  ||||||| || ||||| ||||| ||||||||||||||||||||||| ||||| |||           
ggtttgagatgccgctttacagtgaagttgtagaaatatatatggtttagttcaatgaggtattt---tctgctgcaatttctaaatttgaattctgttgcagGCCTGATGGAACCAAGAAGGCTTATGTCCGGTTGACCCCTGATTACGATGCATTGGATGTGGCAAACAAGATTGGGATTATCTAAG----------

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA13G40780.2 (Glycine max), 3'ss of exon 2
tttcttatatatatatatatcgagttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttt-tatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA----
 |   ||||   |   | ||  |        | | |            || | || |     | ||    ||   | |    |||  | ||| | || |||||||||||| || ||||| || ||||| |||||||| || |||||||| ||  |||||||||| ||||||||||| ||||| |||| || ||        
-taggtataacaaggcaaatgaaacaacaaatttatgaaaaacttgcattcaaacttacaacagatgccatttcttctgaattttaatttttctgttgcagGCCTGATGGAACCAAGAAGGCCTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATATATGGCCT

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA15G04670.2 (Glycine max), 3'ss of exon 3
---tttcttatatatatatatatcgagttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA----
       | | ||  | ||  | | |     | || |       || ||  || |||| |     ||||  | |  | |  ||     | | || | || |||||| || || || ||||| || ||||| |||||||| || |||||||| ||  |||||||||| ||||||||||| ||||| |||| || |  |      
gttgccataacatgcaaatgaaacaacaaatttgtatgaaaaacttgca--ttgatacttacaacaaatcatttcttctgaatttagat-ttttctgttgcagGCCCGACGGCACCAAGAAGGCTTATGTCAGGTTGACACCTGATTATGACGCCCTGGATGTGGCCAACAAGATTGGAATTATCTAAACTAATTCCTGGCCT

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G55280.1 (Arabidopsis thaliana), 3'ss of exon 3
tttcttatatatatatatatcgagttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA----
                          |       |     ||  | |   |||   |||    ||   ||   |    ||   | | | |||   | |||||| ||||| |||||||| || ||||| |||||||| || ||||||||||||||||||||||| ||||| || || || || |||  |  | |       
--------------------------gtaaacactaaaacttcactgagatatgggtttatgtaaacatggagtg---atgagtgtatgtttgtatgcagGCCCGATGGAACAAAGAAGGCGTATGTGAGGTTGACTCCTGATTATGATGCTTTGGATGTGGCTAACAAAATCGGGATCATCTAATCTGATCATTGTCGC

upper sequence: Vv08s0040g02630.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G39460.1 (Arabidopsis thaliana), 3'ss of exon 2
tttcttatatatatatatatcgagttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAA-TAGTAACCA---
 | |||  |    ||| | || |     ||  |  || || |   | |  | ||  ||   || ||||    ||||      ||| ||  ||| || |||||||||||| || ||||| || || || ||| | || ||||| ||||||||||||||||| || |||||||| || || || |||   ||   | |    
gtactttaaagagtatttttcta-----tgaagccttgttgtgagattgat-tatgttcaatatatttgacactatgg----tttggt--tttgttacagGCCTGATGGAACCAAGAAGGCTTACGTGAGGCTTACACCAGACTATGATGCTTTGGATGTTGCTAACAAGATCGGCATCATCTAAGTCTATCTATCTCTG

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|37187636|gb|CF606989.1|CF606989
EST:     ATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAG                         GCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGC
genomic: ATGAAGAAAATGTATGACATTCAGACCAAGAAAGTGAATACCTTGATCAGgtaaagactt ... tttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA
             tcctaaa  putative branch site (score: 2)
                                tatccttttgtctttt  putative PPT
                taaattttgttctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcttatatatatatatatcgagttggtggtgttttctttttccagttttatacctttcctaaattttgttctatatatccttttgtcttttatttcagGCCTGATGGGACAAAGAAAGCATATGTTAGGTTGACGCCAGATTATGATGCTTTGGATGTGGCAAACAAGATTGGTATTATTTAAAATAGTAACCA

- - - - - - - - - - - - - ggtggtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccttttg