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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttcacaaatgatactgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT

Basic information

species Vitis vinifera
transcript Vv04s0023g01040.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os12g40490.1 (Oryza sativa), 3'ss of exon 8
cattttgaagaaactagatgtgcaatgtatatttgtttctttt-gtatgtttttcacaaatgatactgtagcattaatgtaattctttcccttt-tgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
     ||||  || |  |||  ||   | |   ||    | || ||  |  || ||    |||| ||||      | ||  | | || |  ||  |  |||||||||| | ||      |||    |  || ||  |||||||||| |||||||||||| |||||||||| || |||||  ||||||| |||||| ||||||
gtaagtgaatgaattccatgctcagaatgtgcatggacgtgttagttggagttacattcctgat-ctgtcttga-attgagactgttgcatttcatacacagATTCCAACGAACAGGAATGGGCTGATCGAATACCGAGCACATCCATTCTGGATGCAAAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTAGGTGTT

upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os06g08400.1 (Oryza sativa), 3'ss of exon 6
---------cattttgaagaaactag-atgtgcaatgta-tatttgtttcttttgtatgtttttcacaaatgatactgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
         ||| |  |||    ||  |||||  | |||  |   |    |||  | |  ||||   |||||     |     |||  ||       ||| | || | ||||||||  |||||     |||    |  || ||||||||||||||||||||| | ||| | |||||||| |||||||||   || || |||||  | || |
aataattgacatgtgaaagttgttaacatgtgttaagtaacagccgacaatttctttttgtttttttaaatg----cgccatcttacagt-------tccttcttattcagATTCCTACAAATATGAATGGCCTGATTGAATATAGAGCACATCCTTTCTGGTTACAAAAATACTGTCCATCACATGAGGTGGACGGTACTCCAAGATGCT

upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G099328_T04 (Zea mays), 3'ss of exon 7
--cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttcacaaatgatactgtagcattaatgtaattctttc--ccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
   | |    | || | |  | |      ||    ||    | |||       |  |    |||| |    | || | || |||| ||    | | ||   ||||||||| |||||  || |||    |  || ||  ||||||||||||||||||||||  |||||||||| || |||||  ||||||| ||||||||||| |
gtaagtgccgacaatccaagtttatgg-atacgcatgaaggtattgatcagaatatatttctgatccgtctgtataactgcaattattatgtcttcttccccagATTCCAACAAATAGAGATGGCCTCATTGAATACCGAGCACATCCTTTCTGGATGCAGAAGTACTGTCCTTCCCATGAAGATGATGGCACTCCTCGGTGCT

upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA01G38640.3 (Glycine max), 3'ss of exon 3
cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttca-caaatgatactgtagcattaa-tgtaattctt--tcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
   ||   ||||   | |  |  | | |   |||           |    |  ||  ||   | | |||    | || |  |||| ||  | | ||   |  |||| ||| | ||| || ||||    |  ||||||||||| |||||||||||| | ||| | ||||| || |||||||||| |||||| |||||||| ||||
--cttcatagaa--caaaccttaagtttgccttttcaaaaaagaaaaaaatggcagtaagatacattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGTCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTCCTCGTTGTT

upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA12G19010.1 (Glycine max), 3'ss of exon 5
cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttt--tcacaaatgatactgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
| ||||    |    |  ||| || | ||| ||||||  ||     | || |  | | | || |||  |||  ||| |   | |  |||   ||   | ||||||||| ||||| |||||||    |  |||||||||||||||||||||||| | ||| | || ||||| || ||||||| |||||| |||||||| ||||
ccttttttgaattagaattgtccactttat-tttgttctttcaactttttctagttatagat-ataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT

upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA02G06720.2 (Glycine max), 3'ss of exon 6
cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttcacaaatgatac--tgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
   |||   |||  ||||  |||    | |||||  ||||||    | ||| |    |  ||||    |||  ||| |   | |  |||   ||   | ||||||||| ||||| |||||||    |  |||||||||||||||||||||||| | ||| | || ||||| || ||||||| |||||| |||||||| ||||
--cttttttgaatttagaattgcccactttattttgttctttcaattttttctagttatagatataaagtacaattgaatgattgatttttgttcattgcagATTCCACCAAATTCAGCTGGTCTCATTGAGTATAGAGCACATCCTTTCTGGCTACAAAAATATTGTCCATCGCATGAGCGTGATGGTACTCCTCGCTGTT

upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA11G06650.2 (Glycine max), 3'ss of exon 2
cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttca-caaatgatactgtagcattaa-tgtaattctt--tcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
  | || | |||   |||  |  | | |   ||| ||| ||    |    |  ||  ||   ||| |||    | || |  |||| ||  | | ||   |  |||| ||| | ||| || ||||    |  ||||||||||| |||||||||||| | ||| | ||||| || |||||||||| |||||| ||| |||| ||||
--tcttcatgaa--cagaccttaagtttgcgttttttttttaaaaaaaaatggcagtaagatatattgttcagtaaactagaattattggttctttccttgtagATCCCAACTAATTCATCTGGCCTCATTGAGTATAGAGCTCATCCTTTCTGGCTACAAAAATACTGCCCATCACATGAGCTTGATGGCACTTCTCGTTGTT

upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA16G25750.1 (Glycine max), 3'ss of exon 6
-cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttcacaaatgatactgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
 | ||||  |   || |  ||| |  | ||| ||  | | |    | || |  | | | || |||| |    ||| |   |    |||   ||   | ||||| ||| ||||| |||||||    |  ||||||||||||||||||||||||   ||| | || ||||| || ||||||  |||||| |||||||| ||||
tcctttttgaattacaaattgtccgctttattttgttctttcaattttgctagttatagat-atacagcgcaattgaatgatcaatttttgttcaattcagATCCCACCAAATTCAGCTGGCCTCATTGAGTATAGAGCACATCCTTTCTGGCGACAAAAATATTGTCCATCGCATGAGGGTGATGGTACTCCTCGTTGTT

upper sequence: Vv04s0023g01040.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT4G36860.1 (Arabidopsis thaliana), 3'ss of exon 6
cattttgaagaaactagatgtgcaatg-tatatttgtttcttttgtatgtttttcacaaatgatactg----tagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
    |    || |    |  |    || | | | | |||       |  || ||| ||  |  ||||     ||   |  |||||    | |  ||  | ||  ||||||  ||||| |||||||    |  |||||||| |||||||| || ||||||||| |||| ||||| |||||||||| ||||||||||||||||||||
---gtgagtgatagccaacttctgttgatctctatattttacccaaaatttgttcccaggttgtactaagcttaatgtgtatgtataaatgtaactcctcta--gATTCCGACAAATCCAGCTGGTCTTATTGAGTATAGGGCACATCCCTTTTGGATGCAAAAGTATTGTCCTTCACATGAGCGTGATGGAACTCCTCGGTGTT

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|110731744|gb|EE106423.1|EE106423
EST:     CATGCTACAAGGATCAAAATCATCCAAGATGTAACGTTTGCAAGAACTTT                         ATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGG
genomic: CATGCTACAAGGATCAAAATCATCCAAGATGTAACGTTTGCAAGAACTTTgtaagtgtca ... ttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgtttttcacaaatgatactgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT
                         cattaat  putative branch site (score: 3)
                                    ttctttcccttttgta  putative PPT
                          attaatgtaattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattttgaagaaactagatgtgcaatgtatatttgtttcttttgtatgtttttcacaaatgatactgtagcattaatgtaattctttcccttttgtacagATTCCATCAAATGCAGCTGGAGAAACAGAGTATAGAGCACATCCTTTCTGGATGCAAGAGTACTGTCCCTCACATGAGCATGATGGAACTCCTCGGTGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - gaagaaa
- - - - - - - - - - - caatgta
- - - - - - - - - - - - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - -cacaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtagca