Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccatttgtcttctattaagcattccatcaagagtgaccttgtaattctccaaaataatggctgaaatattgctttgctcctcaaaacgatatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGAGTATTGGCATTGATCCTTATGAAGTGTTCCAAGATGTAGAATGGGCCCT

Basic information

species Vitis vinifera
transcript Vv13s0019g05250.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G34150.3 (Glycine max), 3'ss of exon 4
tccatttgtcttctattaagcattccatcaagagtgacct-tgtaattctccaaaataatggctgaaa--tattgctttgctcctcaaaacgatatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGAGTATTGGCATTGATCCTTATGAAGTGTTCCAAGATGTAGAATGGGCCCT
  | |||  ||   |  |   || || | ||   |||    ||||  | |  | || |    ||||    | ||| | |     | | ||    | |||||||| ||||| |||||| |||| || || || |||||||||||||||||||| |||||||| || ||||||||||||||||||||||||| |||||||||  |
--cttttaactaaaacaagatatacctttaatgttgagtaatgtaggtataaataacacgtactgatgtttgttgttctaaatgttataattgaa-catgcagGTGTTGCAATGGAATTGGAGGACTCTTTGTTTCCTTTGTTGAGGGAGGTTAGTATTGGTATCGATCCTTATGAAGTGTTCCAAGATGCAGAATGGGCTTT

upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G33380.1 (Glycine max), 3'ss of exon 6
tccatttgtcttctattaagcattccatcaagagtgaccttgtaattctccaaaataatggctgaaatattgctttgctcctcaaaacgatatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGAGTATTGGCATTGATCCTTATGAAGTGTTCCAAGATGTAGAATGGGCCCT
                      |      |    |     || | |  ||||| ||   |  ||       ||||||||  |  |   |  | | |  ||||  ||  |||||||  | ||| |  |||   | |   | |   ||  |  | |  |                                           
---------------------gtattggtatcgatccttatgaagtgttccaagATGCAGAATGG------GCTTTGCTAAT--AGGTGCAAGCCTCGAGGACCTGGAATGGAACGAGCAGACTTGTTAGA-CATAAATGGGCAGATTTATGCAGCGCAG----------------------------------------

upper sequence: Vv13s0019g05250.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G33380.1 (Glycine max), 3'ss of exon 5
--tccatttgtcttctattaagcattccatc-----aagagtgaccttgtaattctccaaaata-------atggctgaaatattgctttgctcctcaaa----acgat--atcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGAGTATTGGCATTGATCCTTATGAAGTGTTCCAAGATGTAGAATGGGCCCT
  |   | | | || ||||  || ||  | |     ||||   |||||    ||  | || |||       ||  |  | ||  |||||| |     |||    |  ||  | |||||||| ||||| ||||||||||| || || || |||||||||||||||||||| |                                                 
gttatgtattttttttattgtgcttttaaccgaaacaagatacacctttatgttgactaatataggtataaataacacacatgatgcttttcattctaaatgttataattcaacatgcagGTGTTGCAATGGAACTGGAGGACTCTTTGTTTCCTTTGTTGAGGGAGGTCA-------------------------------------------------

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|110728729|gb|EE104550.1|EE104550
EST:     TATTGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
EST: gi|351028003|gb|FQ425904.1|FQ425904
EST:     TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
EST: gi|32249928|gb|CD715747.1|CD715747
EST:     TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
EST: gi|110382693|gb|EC947010.1|EC947010
EST:     TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
EST: gi|110389983|gb|EC954863.1|EC954863
EST:     TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
EST: gi|27578522|gb|CB001217.1|CB001217
EST:     TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
EST: gi|37190333|gb|CF609682.1|CF609682
EST:     TATTGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
EST: gi|110392317|gb|EC957652.1|EC957652
EST:     GAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: GAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
EST: gi|110383344|gb|EC947710.1|EC947710
EST:     TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
EST: gi|18458011|gb|BM436289.1|BM436289
EST:     TATTGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAG                         GAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA
genomic: TATAGCATTTAAGCTATTGGGATCAGAACGGTCCTTTCAAGCCCTTGAAGgtatgattct ... tatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctccaaaataatggctgaaatattgctttgctcctcaaaacgatatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGAGTATTGGCATTGATCCTTATGAAGTGTTCCAAGATGTAGAATGGGCCCT
      aaaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccatttgtcttctattaagcattccatcaagagtgaccttgtaattctccaaaataatggctgaaatattgctttgctcctcaaaacgatatcatgcagGAGTTGCTATGGAACTGGAAGATTCCTTATTTCCTTTGTTGAGGGAGGTGAGTATTGGCATTGATCCTTATGAAGTGTTCCAAGATGTAGAATGGGCCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
-ccatttg
- - - - - - - -ttaagca
- - - - - - - - - - - - ccatcaa
- - - - - - - - - - - - - - - - - - -ccttgta
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacga