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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacttcctttgctcactttcttgaatttctgtcaaaagataaaagtattataatgattttaataatgttgaagtattataatgtctaatgatctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGAGTGCCAGTGGCTTTCATGTGTATGAAG

Basic information

species Vitis vinifera
transcript Vv01s0146g00120.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0146g00120.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S568_5V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------tacttcctttgctcactttcttgaa---tttctgtcaaaagataaaagtattataatgattttaataa-----tgttgaagtattataatgtctaatgatctctg--cagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGAGTGCCAGTGGCTTTCATGTGTATGAAG
                                 |    | |     |    | ||||   ||| ||| || |||| ||  | ||       |||| ||||     | || |   | ||   |   |  |  | | ||   ||||||| |||||| | || |||||||||||| | ||||| || |||||||| || ||||| | |||||||||  | |||
gtacactcacatcgttcaacgctctaaattgagatccacatgatatatggccatgaaaattttatgtaaatagatgaacttcttgacggacttttgataactcactatttactaactactgtaaatctttgtttatgagtagATGACGAATGAATTGGGCAAGGCTATGTTCGCCAAAGCTGGAGAGCTTGGTGTTCCAGTTGGTTTCATGTGCTTCAAG
















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|351039710|gb|FQ464748.1|FQ464748
EST:     GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCGG                         ATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCGGGGGAGCTTGGA
genomic: GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAGgtatctaatt ... atctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
EST: gi|33407684|gb|CF213311.1|CF213311
EST:     GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAG                         ATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
genomic: GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAGgtatctaatt ... atctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
EST: gi|351056524|gb|FQ455176.1|FQ455176
EST:     GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAG                         ATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
genomic: GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAGgtatctaatt ... atctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
EST: gi|110382591|gb|EC946898.1|EC946898
EST:     GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAG                         ATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
genomic: GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAGgtatctaatt ... atctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
EST: gi|110724885|gb|EE101102.1|EE101102
EST:     GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAG                         ATGACCAATGAAATTGGGAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
genomic: GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAGgtatctaatt ... atctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
EST: gi|351032774|gb|FQ462488.1|FQ462488
EST:     GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAG                         ATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
genomic: GTTATCGTGCAGTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAGgtatctaatt ... atctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
EST: gi|110367255|gb|EC931182.1|EC931182
EST:     GTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAG                         ATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA
genomic: GTTCGCTTCAATCCATATTTATGGCCATCTGGTCAGCAGgtatctaatt ... atctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattataatgattttaataatgttgaagtattataatgtctaatgatctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGAGTGCCAGTGGCTTTCATGTGTATGAAG
                                     gtctaat  putative branch site (score: 3)
                                              tctctgc  putative PPT
     taatgattttaataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacttcctttgctcactttcttgaatttctgtcaaaagataaaagtattataatgattttaataatgttgaagtattataatgtctaatgatctctgcagATGACCAATGAAATTGGAAAGGCTATGTTCTCAAAAGCAGGGGAGCTTGGAGTGCCAGTGGCTTTCATGTGTATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
tacttcc
- - - - -tgctcac
- - - - - - - - - - - - - - ctgtcaa
- - - - - - - - - - - - - - - - - - -gataaaa