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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acccattgtatatgtcagagttcacattcataacttaaccaatgcttcaatagaaggtcaactggaacttcccctttatgcagtgttgtgatttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCTGGCATTAGCTATG

Basic information

species Vitis vinifera
transcript Vv01s0010g00950.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g02750.3 (Oryza sativa), 3'ss of exon 10
-acccattgtatatgtcagagttcacattcataacttaaccaatgcttcaatagaaggtcaactggaacttcccctttatgcagtgttgtgatttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCTGGCATTAGCTATG
   | | | |  |  | | |    |   ||||||| |     ||     |   ||    ||         |   |  | |||| | || | |    | |||  |  ||||||| || || || ||  ||||||||||||||||||||||||||||| |||| |||
aggcaactattgaatttaaataaaaatatcataacgttctttatttgatagccgataaacattcaacctatgatcaatttgcattattctaaacc-tacagCATTCACAATGTGTACAAAGTGGTCGAGGCAAGAAAAGGAAGCATGCTGCTGGCACTAGCAATG

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g02750.4 (Oryza sativa), 3'ss of exon 10
-acccattgtatatgtcagagttcacattcataacttaaccaatgcttcaatagaaggtcaactggaacttcccctttatgcagtgttgtgatttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCTGGCATTAGCTATG------------------------------------
   | | | |  |  | | |    |   ||||||| |     ||     |   ||    ||         |   |  | |||| | || | |    | |||  |  ||||||| || || || ||  ||||||||||||||||||||||||||||| |||| |||                                    
aggcaactattgaatttaaataaaaatatcataacgttctttatttgatagccgataaacattcaacctatgatcaatttgcattattctaaacc-tacagCATTCACAATGTGTACAAAGTGGTCGAGGCAAGAAAAGGAAGCATGCTGCTGGCACTAGCAATGGTAAGATCTAAATATGTCATTTTGTGATTTTATCAT

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G466281_T02 (Zea mays), 3'ss of exon 10
--------acccattgtatatgtcagagttcacattcat-aacttaaccaatgcttcaatagaaggtcaactggaacttcccctttatgcagtgttgtgatttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCTGGCATTAGCTATG
        |    |||    | | | | || | |||  | || ||    | |  || |||| ||  | |  | ||        |  |   | | |||  | |  | |||  |  ||||||| ||||| || ||| | |||||||||||||||||||| |||||| |||| |||
atttacttaatgcttgagctttttatattttatatttgtgaatttttgtattatttaaatataatataaggttga--------taaagttaattttgcaact-gtacagCATCCACAATGTATATAAAGTCGTTGAAGCAAGAAAAGGAAGCATGCTTCTGGCACTAGCCATG

upper sequence: Vv01s0010g00950.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G25585.3 (Arabidopsis thaliana), 3'ss of exon 8
-----------acccattgtatatgtcagagttcacattcataacttaaccaatgcttcaatagaaggtcaactggaacttcccctttatgcagtgttgtgatttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCTGGCATTAGCTATG
           || | |  |   | | |  | || | |||   |  | |  ||   | | |         |       ||   | | || |||   |  |   || | |||    |  |||||||| || ||||| ||  ||||||| ||||||||||| || ||||||||||||
gtgagttttccacacttcatcggtcttatcggtctc-ttctcgagctgagaaaaattgctaactttttctatgccttgctctgcttatacgcacactgcttcattctacagCACGTCTAATGTTTACAAAGTTGTACATTCAAGAAATGGAAGCATGCTTCTAGCATTAGCTATG

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|110701014|gb|EE078175.1|EE078175
EST:     GTGTTGTTTATAATGATTGCTTTTGGTGTGATACCAACAGTCTCATTCAA                         TGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCT
genomic: GTGTTGTTTATAATGATTGCTTTTGGTGTGATACCAACAGTCTCATTCAAgtaagtgatt ... atttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCT
EST: gi|33409238|gb|CF214865.1|CF214865
EST:     GTGTTGTTTATAATGATCGCTTTTGGTGTGATACCAACAGTCTCATTCAA                         TGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCT
genomic: GTGTTGTTTATAATGATTGCTTTTGGTGTGATACCAACAGTCTCATTCAAgtaagtgatt ... atttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCT
EST: gi|33409643|gb|CF215270.1|CF215270
EST:     GTGTTGTTTATAATGATCGCTTTTGGTGTGATACCAACAGTCTCATTCAA                         TGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCT
genomic: GTGTTGTTTATAATGATTGCTTTTGGTGTGATACCAACAGTCTCATTCAAgtaagtgatt ... atttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaatagaaggtcaactggaacttcccctttatgcagtgttgtgatttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCTGGCATTAGCTATG
                                           tgatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acccattgtatatgtcagagttcacattcataacttaaccaatgcttcaatagaaggtcaactggaacttcccctttatgcagtgttgtgatttatgcagTGTATACAATGTTTATAAGGTTGTTCAGGCAAGAAAAGGAAGCATGCTGCTGGCATTAGCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
-cccattg
- - - - - - - - - - - cacattc
- - - - - - - - - - - - - - - - - - - ccaatgc
- - - - - - - - - - - - - - - - - - - - - - - - aatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgtg