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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaatcagtgactggcaacctttcttgagaagttatgctttggatgatggatattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG

Basic information

species Vitis vinifera
transcript Vv09s0002g02100.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g10050.1 (Oryza sativa), 3'ss of exon 2
aaatcagtgactggcaacctttcttgagaagttatgctttggatgatggatattttaaaattgaagttt--taattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG
 |     |||    ||  |||| ||     | | |  |||  ||  |||| || ||| | |  |  |||  | ||     | |  || |||      | ||||||||||  |||||||||||||||||||||| ||||  |||||||| || |||||  ||||||| |||||||||||  ||| ||| |||||| | |||||
-accttctgaactacattctttattattttgctctttttta-atcttggacatcttacattctatatttcctgatccaagatacttaacttccattgtgcagAATATGTTTTGCAAGAAATTACAAAAGCTGGGTTTGTAGAACCTACTCCTATCCAGTCTCAAGGTTGGCCAATGGCACTGAGGGGACGTGATCTTATTGG

upper sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G143246_T01 (Zea mays), 3'ss of exon 2
---aaatcagtgactggcaacctttcttgagaagttatgctttggatgatggatattttaaaattgaagttttaattatttaaatgt--acctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG
       |  |  |  | | | |   |||     || |||| ||     |||    || | |  || |  ||||    |||  |||   ||  |||||  | ||||||||||  ||||||| || ||||||||||| ||||  |||||||| || |||||| | ||||| ||||| ||||| ||||  ||||| ||  | |||||
agtgttccttttgcatgtagcatgcattgcacttttctgctgtg-----tgggaccttcatatctgcatatttatagctttggatgctgactgttgtggtttcagAATATGTGTTGCAAGAGATCACAAAAGCTGGTTTTGTGGAACCTACCCCTATCCAATCGCAAGGTTGGCCGATGGCATTGAGAGGCCGCGACCTTATTGG

upper sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G20670.1 (Glycine max), 3'ss of exon 2
aaatcagtg-actggcaacctttcttgagaagttatgctttggatgatgg----atattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG
  || | |  |||       | |||||  || ||     |  ||| ||||    | || ||  ||     ||  | ||| || |    |   ||    | ||||||||||||  |||||||||||||||||||||||||| |||||||||||||||| ||| ||||||| ||||| |||||||||||||| |||||| | || ||
-tatgattatactatatgattatcttgcaaaatttattatcagattatgggatgacatgtttcaaacagcgtactgatttttcagccttggttt----aatccagAATATGTACTGCAAGAAATTACAAAAGCTGGCTTTACTGAACCTACACCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG

upper sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G01260.1 (Glycine max), 3'ss of exon 2
aaatcagtg-actggcaacctttcttgagaagttatgctttggatgatgg----atattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG
 | | | |  | ||      | |||||  || ||     |  ||| ||||    | || ||  ||     ||  | ||| ||      |   ||    | |||||||||||| ||| ||||||||||||||||||||||| |||||||||| ||||| ||| ||||||| ||||| |||||||||||||| |||||| | || ||
-attgattatattgtatgattatcttgcaaaatttgttatcagattatgggatgacatgtttcaaacagtgtactgatttttcggccttggttt----aatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTGATAGG

upper sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA07G11880.1 (Glycine max), 3'ss of exon 1
----aaatcagtgactggcaacctttcttgagaagttat-gctttggatgatggatattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG
    |    | ||  ||   | ||| |   | |  ||||    ||    ||||  |  ||| |||  |  ||  | ||| ||      |   ||    | |||||||||||| ||| ||||||||||||||||||||||| |||||||||| ||||| ||| ||||||| ||||| |||||||||||||| |||||| | || ||
attgattatattgtatgattatcttgcaaaaaattttatcagattatgggatgacttgtttcaaacagt-gtactgatttttcggccttggttt----aatccagAATATGTAATGGAAGAAATTACAAAAGCTGGCTTTACTGAACCTACGCCCATTCAATCTCAAGGTTGGCCCATGGCTTTGAAGGGGCGTGATCTAATAGG

upper sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT1G55150.1 (Arabidopsis thaliana), 3'ss of exon 2
----------------------------aaatcagtgactggcaac-ctttcttg---agaagttatgctttggatgatggatattttaaaattgaagttttaattatttaaat-gtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG
                             |    |||| | |   | ||| | ||      |  |||| | | |   ||     | ||  | ||   | | ||  || | | || ||  | |  |     |||| |||||  || ||||  |||  || ||||| ||| |||||||||| || || ||| |||| || |||||||||||| ||||||| |||||| | || ||
gtaaactcttgaatttggcaatcatgtagagcttgtgattagtttcacttacatgtcttagatgtatgatgtagcatatatgcctgttttatttttggatatacctactgatatagtttcctgattggctcagATTATGTTTTGGAAGAGGTTAAGAAGGCTGGTTTTACTGAACCTACGCCTATACAATCTCAGGGGTGGCCAATGGCTATGAAGGGACGTGATCTTATCGG

upper sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ10791 (Selaginella moellendorffii), 3'ss of exon 2
aaatcagtgactggcaacctttcttgagaagttatgctttggatgatggatattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG
                                || ||   | | | |   | | |  |     | ||||| |||  |   ||||   |  ||     |||| |||||  | || ||| ||   ||||| || ||    || || ||  |||| ||||||||||||||||| ||||||||||| ||  | ||| |  | ||
-------------------------------gtaggc---gaaggtttcttctatcgaggacaaggttttgattgatcttatgtggat--gttttggcagACTATGTTCTCCAGGAAGTTCTCAAAGCCGGTTTCAAGGAGCCCACCGCCATTCAAGCTCAAGGATGGCCCATGGCTTTGAAAGGGAGGGATCTAGTAGG

upper sequence: Vv09s0002g02100.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: EFJ26152 (Selaginella moellendorffii), 3'ss of exon 2
aaatcagtgactggcaacctttcttgagaagttatgctttggatgatggatattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG
                                || ||   | | | |   | | |  |     | ||||| |||  |   ||||   | | |   |||||| |||||  | || ||| ||   ||||| || ||    || || ||  |||| ||||||||||||||||| ||||||||||| ||  | ||| |  | ||
-------------------------------gtaggc---gaaggtttcttctatcgaggacaaggttttgattgatcttatgtggatgttt---tccagACTATGTTCTCCAGGAAGTTCTCAAAGCCGGTTTCAAGGAGCCCACCGCCATTCAAGCTCAAGGATGGCCCATGGCTTTGAAAGGGAGGGATCTAGTAGG

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|161712403|gb|FC061708.1|FC061708
EST:     TCGGGATGTTCCAAAACCAGTCATGACTTTTCGCGATGTGGGCTTGCCAG                         AATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCA
genomic: CCGGGATGTTCCAAAACCAGTCATGAATTTTCGCGATGTGGGCTTGCCAGgtacttattt ... gtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atggatattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG
                     ttttaat  putative branch site (score: 3)
                                        cctttgt  putative PPT
     tattttaaaattgaag  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaatcagtgactggcaacctttcttgagaagttatgctttggatgatggatattttaaaattgaagttttaattatttaaatgtacctttgtgactccagAATATGTCATGCAAGAAATTACAAAAGCTGGCTTTGCTGAACCTACACCCATCCAAGCTCAAGGATGGCCAATGGCTTTGAAGGGCCGTGATGTCATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
aaatcag
- - - -tgactgg
- - - - - - - caacctt
- - - - - - - - - - - - - - - - - tgctttg
- - - - - - - - - - - - - - - - - - - - - -tgatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaattga