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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattctttttcccttagtaagtgcatggattatatgcacttgcagcctcagcattttggtggtatatgttaactgaatcttttcgtttgaatctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04410.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: 13113.m00157 (Oryza sativa), 3'ss of exon 7
cattctttttcccttagtaagtgcatggattatatgcacttgcagcctcagcattttggtggtatatgttaactg---aatcttttcgtttga-atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG
 ||   ||||||  | ||   |   | |||  |||   |||||    |  | ||||  ||     | | | | ||    ||  |   || ||  | |  ||||||| |||||||| |||||||||||||||||||||||    || || ||| | |||| ||| ||||||   ||||||| | |||||||||||
-atggattttcctatcgtttctagtttgatattat---cttgcccttttcggatttcagttcccgaagattattgtttgataataatgtatgctaccaatgcagACTAGTTATTCATACCTTGATGTTGTTGGAAGGACGACAGTTGTACTAAAGAAGAGAAACGTAGTTGGAGAGCACAATGTTCCTTTCCAG

upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G177273_T01 (Zea mays), 3'ss of exon 6
--cattctttt--tcccttagtaagtgcatggattatatgcacttgcagcctcagcattttggtggtatatgttaactgaatcttttcgtttgaatctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG
  ||  | | |  |  | ||    |   | |     |   |  |  ||  ||  ||   |  | | | ||| ||   ||| |  | |  | |  |    ||||||| |||||||| |||||||| ||||||||||||||   ||| || ||  | ||||||||||| ||    |||||||   |||||||||||
gtcagccctgtagtttcctatcttgcaaaggagcagtgc-ctttctcaaactttgctgatgagagat-tattttg--tgattactgtgttctttactgatgcagACTAGTTATTCATACCTTGACGTTGTTGGAAGGACGACGGTTGTACTGAAGAAGAAAAATGTTGTAGGGGAGCACAACGTTCCTTTCCAG

upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA20G32070.1 (Glycine max), 3'ss of exon 6
--cattctttttcccttagtaagtgcatggattatatgcacttgcagcctcagcattttggtggtatatgttaactgaatcttttcgtttgaatctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG
    ||   ||   ||    |||    |   || | || ||||  ||| | |    |||| |    |      |       |||   ||||||  | |||||| ||  ||||| |||||||||||||| || || |||||||| ||||||||||| | ||||| |||||||||||| | || ||||||||||
agagtttgattctgctcttgaagaatttcacttgt-tgtacttttagcataaagcatttgattccctgcagctaaaatggttttaaatttgaactt-tgcagATCAAGTATTCATACCTTGATGTTGTCGGCAGAACTGTGGTGGTTCTAGAAAAAAGAAATGCAGTTCCTGAGCATAATACTCCTTTCCAG

upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G35450.1 (Glycine max), 3'ss of exon 6
-cattctttttcccttagtaagtgcatggattatatgcacttgcagcctcagcattttggtggtatatgttaactgaatcttttcgtttgaatctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG
   ||   ||   ||    |||    |   || | || ||||| ||| | |    |||| |    |      |       |||   |||  | || |||||| ||  ||||| || ||||||||||| || || |||||||| ||||||||||| | ||||| |||||||||||| | |  |||||| |||
gagtttgattctgctcttgaagaatttcacttgt-tgtacttgtagcataaagcatttgattccctgcagctaaaatggttttaaattttgaactttgcagATCAAGTATTCATATCTTGATGTTGTCGGCAGAACTGTGGTGGTTCTAGAAAAAAGAAATGCAGTTCCTGAGCATAATGCTCCTTTTCAG

upper sequence: Vv13s0019g04410.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA10G35450.2 (Glycine max), 3'ss of exon 6
-cattctttttcccttagtaagtgcatggattatatgcacttgcagcctcagcattttggtggtatatgttaactgaatcttttcgtttgaatctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG----------
   ||   ||   ||    |||    |   || | || ||||| ||| | |    |||| |    |      |       |||   |||  | || |||||| ||  ||||| || ||||||||||| || || |||||||| ||||||||||| | ||||| |||||||||||| | |  |||||| |||          
gagtttgattctgctcttgaagaatttcacttgt-tgtacttgtagcataaagcatttgattccctgcagctaaaatggttttaaattttgaactttgcagATCAAGTATTCATATCTTGATGTTGTCGGCAGAACTGTGGTGGTTCTAGAAAAAAGAAATGCAGTTCCTGAGCATAATGCTCCTTTTCAGGTATTTACCA

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|71865487|gb|DT014542.1|DT014542
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|351015486|gb|FQ447315.1|FQ447315
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|71881801|gb|DT030856.1|DT030856
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|37187617|gb|CF606970.1|CF606970
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|349824067|gb|FQ417454.1|FQ417454
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|351031867|gb|FQ460124.1|FQ460124
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|352790365|gb|FQ478005.1|FQ478005
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|349812777|gb|FQ410419.1|FQ410419
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|349816667|gb|FQ404914.1|FQ404914
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|51052013|gb|CO819346.1|CO819346
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|351051855|gb|FQ455269.1|FQ455269
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|351045790|gb|FQ440975.1|FQ440975
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|349811345|gb|FQ407571.1|FQ407571
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|351048526|gb|FQ448800.1|FQ448800
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|351053182|gb|FQ455639.1|FQ455639
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|349807244|gb|FQ401236.1|FQ401236
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGCCTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
EST: gi|110414535|gb|EC980369.1|EC980369
EST:     CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAG                         ACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA
genomic: CGAAAGAACCTTCTGCTGTGGTTCCTTTCCCAGTGGACCAACATTTGGAGgtggttattt ... atctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctcagcattttggtggtatatgttaactgaatcttttcgtttgaatctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG
                     tgttaac  putative branch site (score: 2)
                 tatatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattctttttcccttagtaagtgcatggattatatgcacttgcagcctcagcattttggtggtatatgttaactgaatcttttcgtttgaatctgtgcagACCAGTTATTCTTACCTTGATGTTGTTGGAAGGACTGTGGTAGTTCTAGAAAAGAAAAATGTAGTTCCTGAGCACAGTATTCCTTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - -tccctta
- - - - - - - - - - - gcatgga
- - - - - - - - - - - - - - - - - - cacttgc
- - - - - - - - - - - - - - - - - - - - - -agcctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtggt