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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tacagcattctggatgcacacataagaaatttctttaattgttcatgttgtttatgacattctgtaccaaattaatgcaaaatatctcttattctctcagATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCCTATGCTGGGAATAAGACAAAGGAATACGATGATATTGCCATGAAGTACT

Basic information

species Vitis vinifera
transcript Vv07s0130g00170.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 9
--tacagcattctggatgcacacataagaaatttctttaattgttcatgttgtttatgacattctgtaccaaattaatgcaaaatatctctt-attctc--tcagATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCCTATGCTGGGAATAAGACAAAGGAATACGATGATATTGCCATGAAGTACT
   |  |||| |    |     |  ||  |   | |  || | ||    |   || |||  || | |     || |||     | | ||||| | ||    |||||| ||||||| ||||||||| || | |||||||||||| ||||| || || |||||   ||||||||||||||| || || |  ||||| ||||||||  
gtgattgcatccatcttttgagctcaatga---tgtagaaatctttgcatcagttctgatgttttcttt--gatcaatttgtcacaactcttcactcctgttcagATCGATAGAAGTGGAAAGATTCCCATGTTGAGGTTCCGGGACCGTGAATCATATGCACAGAATAAGACAAAGGAGTATGACGCAATTGCAATGAAGTATC

upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G16940.1 (Glycine max), 3'ss of exon 9
tacagcattctggatgcacacataagaaatttctttaattgttcatgttgtttatgacattctgtaccaaattaatgcaaaatatctcttattctctc--agATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCCTATGCTGGGAATAAGACAAAGGAATACGATGATATTGCCATGAAGTACT
 ||| |||  || ||  | |    |    | ||    ||   |  || ||||  | |  |  | |     ||   |||||  | |    |||| | ||  |||||||||| || |||| |||||||| ||||| | |||| || || ||||| ||||   ||||||||||||||||||| ||||||||||| |||||||| |
-aca-catgttgcatttagattccatctttatcgaccatatattctgatgttccttaattatttttattgatatctgcaatctgtaatatattttttcccagATTGATAGGACAGGAAGGATACCTATGTTGAAGCTCCGCGATCGAGAGTCATATGTACGGAATAAGACAAAGGAATATGATGATATTGCTATGAAGTATT

upper sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA04G38120.1 (Glycine max), 3'ss of exon 9
tacagcattctggatgcacacataagaaatttct-ttaattgttcatgttgtttatgacattctgtaccaa-attaatgcaaaatatctcttattctctcagATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCCTATGCTGGGAATAAGACAAAGGAATACGATGATATTGCCATGAAGTACT
 | | |||  || ||  | |    |    | |||  ||  | |||   |  |  || |   | | ||   | ||          ||  |  | || || ||||||||||| || |||| |||||||| ||||| | |||| || || || || || |   ||||||||||||||||||| ||||||||||| |||||||| |
-ata-catgttgcatttatattccatctttgtctactacatattctgatgttccataattatttttattgatatccgcaatctgtaatttattttttcccagATTGATAGGACAGGAAGGATACCTATGTTGAAGCTCCGCGATCGAGAATCATACGTACGGAATAAGACAAAGGAATATGATGATATTGCTATGAAGTATT

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|33401807|gb|CF207434.1|CF207434
EST:     CCATGCACAGAGAG                         ATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCC
genomic: CCATGCACATAGAGgtataatttg ... attctctcagATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCC
EST: gi|110722903|gb|EE099605.1|EE099605
EST:     TTGGTTGCTGCATTGAGTTTTGGAAAATAGGAAAGGCCATGCACATAGAG                         ATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCC
genomic: TTGGTTGCTGCATTGAGTTTTGGAAAATAGGAAAGGCCATGCACATAGAGgtataatttg ... attctctcagATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCC
EST: gi|110712610|gb|EE087807.1|EE087807
EST:     TTGGTTGCTGCATTGAGTTTTGGAAAATAGGAAAGGCCATGCACATAGAG                         ATTGATAGAACTGGAAAGATACCTAAGTTGAAGTTCCGAGACCGGGAGTCC
genomic: TTGGTTGCTGCATTGAGTTTTGGAAAATAGGAAAGGCCATGCACATAGAGgtataatttg ... attctctcagATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCC
EST: gi|110701816|gb|EE079820.1|EE079820
EST:     TTGGTTGCTGCATTGAGTTTTGGAAAATAGGAAAGGCCATGCACATAGAG                         ATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCC
genomic: TTGGTTGCTGCATTGAGTTTTGGAAAATAGGAAAGGCCATGCACATAGAGgtataatttg ... attctctcagATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgtttatgacattctgtaccaaattaatgcaaaatatctcttattctctcagATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCCTATGCTGGGAATAAGACAAAGGAATACGATGATATTGCCATGAAGTACT
                        aattaat  putative branch site (score: 3)
                                     tatctcttattctctc  putative PPT
                       aaattaatgcaaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tacagcattctggatgcacacataagaaatttctttaattgttcatgttgtttatgacattctgtaccaaattaatgcaaaatatctcttattctctcagATTGATAGAACTGGAAAGATACCTAAGTTGAGGTTCCGAGACCGGGAGTCCTATGCTGGGAATAAGACAAAGGAATACGATGATATTGCCATGAAGTACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - gcattct
- - -cattctg
- - - - - - - - cacacat
- - - - - - - - - - - -aagaaat
- - - - - - - - - - - - - - - - - - - - gttcatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaattaa