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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttcattttttttttctcatttcattgagattgattgcatttgagtgggcaaattggtgtgttaattaatggcttattgtttctgtcctatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCACTGGTGTGCTGTGCGGGGTGCAATCCAGGTTGCAGAGCTATTACTCCAAG

Basic information

species Vitis vinifera
transcript Vv11s0118g00470.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g43680.1 (Oryza sativa), 3'ss of exon 1
---tatttcattttttttttctcatttcattgagattgattgcatt-tgagtgggcaaattggtgtg-ttaattaatggcttattgtttctgtcctatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCACTGGTGTGCTGTGCGGGGTGCAATCCAGGTTGCAGAGCTATTACTCCAAG
    || |        | |    ||   ||| ||  |||  ||||| ||       || || || ||        |||  ||  |||   ||  || |   ||||||||||| |||||||||||| || || ||||||||||| ||||||||||||||| ||||||| || ||    ||||| ||||| |||||  | ||  |||
ctgcatgtagacgaagtatcactatgctattcag--tgagcgcattctgcacatataattttgtttgaccggactatgattt--tgtgcttggtctttg-aacagCATGGAGCAGATGTAAATGCTGTGGACCACACTGGGCAAACAGCACTTCACTGGAGTGCTGTACGTGGACACATCCAAGTTGCTGAGCTTCTTCTGAAAG

upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g09130.1 (Oryza sativa), 3'ss of exon 1
--tatttcattttttttttctcatttcattgagattgattgcatttgagtgggcaaattggtgtgttaat-taatggcttattgtttctgtcctatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCACTGGTGTGCTGTGCGGGGTGCAATCCAGGTTGCAGAGCTATTACTCCAAG
  |   |    |  ||||  |   | |  |    |   |   ||     |  |    ||| | || |    | | || |    | || |   ||    |||||||||||| ||||||||||||  |||| || || ||||| |||||||| |||||| |||| || || |||   || || |||||||| ||| | ||  |||
cttgagttgcatggttttctttgctgctctatagtatgtcctatccttttcagttgtttgctttggtgggatgacggttctcagcttgttgtctg---gacagCATGGAGCAGATGTAAATGCTATAGACCATACAGGGCAAACAGCACTCCACTGGAGTGCGGTACGTGGTCATATTCAAGTTGCAGAACTACTTCTGAAAG

upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G087806_T01 (Zea mays), 3'ss of exon 1
--tatttcattttttttttctcatttcattgagattgattgcatttgagtgggcaaatt--ggtgtgttaattaatggcttattgtttctgtcctatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCACTGGTGTGCTGTGCGGGGTGCAATCCAGGTTGCAGAGCTATTACTCCAAG
  | ||| |      ||||  |   |  | |    ||| ||   |||| ||       |  | |  |||   | |||  ||  |||  ||||  |    || ||||||||| |||  ||||||| || ||||||||||| || ||||||||||||||| ||||||| || |||   || || ||||| || ||| | ||  |||
tgtgtttgaaaggcattttagctacttttggttgatgactgttgttgattgaatttccttggttccgtttggtgatgattt--tgtccctgtatttg--gatagCATGGAGCAGACATAAATGCTGTGGATCACACTGGACAAACAGCACTTCACTGGAGTGCTGTACGTGGTCATATTCAAGTTGCTGAACTACTTCTGAAAG

upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G024437_T02 (Zea mays), 3'ss of exon 1
---tatttcattttttttttctcatttcattgagattgattgcatttgagtgggcaaatt--ggtgtgttaattaatggcttattgtttctgtcctatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCACTGGTGTGCTGTGCGGGGTGCAATCCAGGTTGCAGAGCTATTACTCCAAG
   | ||  |     | ||    | ||  | |    ||| ||   |||| ||       |  | | | ||   | |||  ||  || || | |   |    | ||||||||| |||   |||||| || ||||||||||| || ||||||||||||||| ||||||| || |||   || || ||||| || ||| | ||  |||
tgctgttgaaaggcatattagctacttt-tggttgatgactgttgttgattgaatttccttggttctctttggtgatgattttgtgcttgtatttga----atagCATGGAGCAGACACAAATGCTGTGGATCACACTGGACAAACAGCACTTCACTGGAGTGCTGTACGTGGTCATATTCAAGTTGCCGAACTACTTCTGAAAG

upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA17G11600.1 (Glycine max), 3'ss of exon 1
-tatttcattttttttttctc--atttcattgagattga-ttgcatttgagtgggcaaattggtgtgttaattaatggcttattgtttctgtcctatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCACTGGTGTGCTGTGCGGGGTGCAATCCAGGTTGCAGAGCTATTACTCCAAG
 | |||  |||||||    |   || |  |  | ||||  |||    | |||| | |  | |   |||  | |||    | |||| ||   |  |   || |||||||| |||||||||||||||  |||||| ||||| ||||| ||  | || ||| |||| || |||||||| || |||| ||||||||| |||||||| |
gtgttttttttttttacaattgaatgtattaaaaattggcttggcaataagtgtggagttagacatgt--actaa--attaattggttgatttgtggttggcagCATGGGGGAGATGTAAATGCAACAGATCATACTGGTCAGACGGCCTTACATTGGAGTGCGGTTCGGGGTGCTATTCAGGCTGCAGAGCTTTTACTCCAGG

upper sequence: Vv11s0118g00470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G23230.1 (Glycine max), 3'ss of exon 2
tatttcattttttttttctcatttcattgagattgattgcat-ttgagtgggcaaattggtgtgttaattaatggcttattgtttctgtcctatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCACTGGTGTGCTGTGCGGGGTGCAATCCAGGTTGCAGAGCTATTACTCCAAG
                    || |     |  |||  |  || || |||  |  |||| || |  |  | |||   | | || ||   |  |   || |||||||| |||||||||||||||   ||||| ||||| ||||||||  | || ||| |||| || |||||||| || |||||||| || || |||||||| |
------------------gtatgtagccaaatttggcttgatattaagtatg-gaattagtcttatcctaaat---taactggttgatttgtggttggcagCATGGGGGAGATGTAAATGCAACGGATCATACTGGCCAGACAGCCTTACATTGGAGTGCGGTTCGGGGTGCTATTCAGGTTGCGGAACTTTTACTCCAGG

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|161721152|gb|FC071027.1|FC071027
EST:     AGTGGGCGGCTCTGAATAATCGAACCGCGGCTGCGCAGTATATCATCGAG                         CATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCAC
genomic: AGTGGGCGGCTCTGAATAATCGAACCGCGGCTGCGCAGTATATCATCGAGgttttcattc ... tatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCAC






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtgggcaaattggtgtgttaattaatggcttattgtttctgtcctatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCACTGGTGTGCTGTGCGGGGTGCAATCCAGGTTGCAGAGCTATTACTCCAAG
                    aattaat  putative branch site (score: 3)
                                    tttctgtcct  putative PPT
                tgttaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttcattttttttttctcatttcattgagattgattgcatttgagtgggcaaattggtgtgttaattaatggcttattgtttctgtcctatatgacagCATGGAGGAGATGTAAATGCAGTAGATCACACTGGGCAGACAGCACTTCACTGGTGTGCTGTGCGGGGTGCAATCCAGGTTGCAGAGCTATTACTCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - gcatttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatggct