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

...tcaaggatgcttttgtactaaatcattgtctcctttggattatatgctagagattatgatagtgataagaaaccttatgtttgttgcattccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG

Basic information

species Vitis vinifera
transcript Vv09s0002g00880.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 9
--------------------------------------------------tcaaggatgcttttgtactaaatcattgtctcctttggatta--tatgctagagattatgatagtgataagaaaccttatgtttgttgca-ttccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG
                                                  |  | |||  |  | |   |  | |   ||  ||  | |  |  | || || |      || |||  | |         | ||   ||   ||  || |||||||| ||| || || |  |||| | | || | |||||| |||||||| ||||| || ||||||||||| ||||||||| |||  || 
gtgaatatacatgccttttgtcctggcccacttgttttggtttaagtcaatacatgattgtaatatgtaatgtaacaatcaactgagcaagagctctgttaaatggctagaaagtactgaactgtaaagtattccatgttcttttttatgcagAAGGTGGAAAGGATAATGCAAATGAAGATGGTCCTGAAAACAACCCACAGTACACGACTGTTTATGTTGGCAATCTTCCTCATGAT

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM5G835213_T02 (Zea mays), 3'ss of exon 9
tcaaggatgcttttgtactaaatcattgtctcctttggattatatgctagagatta--tgatagtgataagaaaccttatgtttgttgcattccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG
|  | |  |   ||      || |  |   |      | ||||  ||| || |||       | ||     | ||||| |  |  ||       || |||||||  ||| |||||||   ||| | | || | |||||| || |||||||||| ||| ||||||||||| ||||||||| |||  |||
tagaagccggaatttggtagaagccgtacatgtcacag-ttatg-gcttgaaattgaccagcattgcagcaacaccttttaatcttttataatgttctgcagAATCTGGAAAAGAGAATCCAAATGAAGATGGTCCTGAAAATAACCCTCAGTTTACTACTGTTTATGTTGGCAATCTTCCTCACGAG

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA07G04640.1 (Glycine max), 3'ss of exon 9
tcaaggatgcttttgtactaaatcattgtctcctttggattatatgctagagattatgatagtgataagaa-accttatgtttgttgcattccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG
|     |   | ||||  |     | | |    |||      |   |||  |   ||| |||  || | |  | |  |  | | ||    |  |||| |||||||||||||||||||| | |  | ||| |||||||| ||||| ||||||||||| |||||||||||||| || ||||||||||||
ttgtaaaaattattgtgtttgtgaagtattctgttttcccagtgaactaatgga-atgctagccatgaaattaaccaacatgttttattctatttgtacagAAGATGGTAAAGAGACATCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATACTACTGTTTATGTGGGTAACCTTGCTCCAGAG

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 9
tcaaggatgcttttgtac-taaatcattgtctcctttggattatatgctagagattatgatagtgataagaaaccttatgtttgttgcattccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG
  ||  ||  ||   | | | ||  ||| | |  |     | |  |  | ||    ||| |||  || |   | || |  | | ||    |  ||||||   |||||||||||||||  | |  | ||| |||||||| ||||| ||||||||||| || ||||||||||| || |||||||| |||
gtaaaaattattgcattcatgaagtattctgttttcccagtgaactaatgga----atgctaggcatgaattaactaacatgttttatcctatttgtgctttagATGGTAAAGAGACCTCTAACAGTGATGCTCCTGAGAACAATCCTCAGTATACTACGGTTTATGTGGGTAACCTTGCTCCGGAG

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 9
------tcaaggatgcttttgtactaaatcattgtctcctttggattatat----gctagagattatgatagtgataagaaaccttatgtttgt----tgcattccttgt----gcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG
      | ||  ||    |   |  ||||           | | | || |     ||   | || |   || |  | |      | |||||| |    ||  ||  ||||    ||||| ||||||||||| ||  | | |  ||| |||||||| |||||  ||||||| ||||||||||| || || |||||||||||||||
gtatgtttaactattacctatcatgaaatagaaaatcaaatggaaatagagaaaagcctcaaataaacttaattcttaaccctttgatgtttatacattggcttatttgttcctgcagAGGATGGTAAAGATACTACTAATGGTGAAGCTCCTGAGAACAATGCTCAGTACACAACTGTTTACGTCGGTAATCTTGCTCCAGAG

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G17370.2 (Arabidopsis thaliana), 3'ss of exon 9
-------------tcaaggatgcttttgtactaaatcattgtctcctttggattatat----gctagagattatgatagtgataagaaaccttatgtttgt----tgcattccttgt----gcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG
             | ||  ||    |   |  ||||           | | | || |     ||   | || |   || |  | |      | |||||| |    ||  ||  ||||    ||||| ||||||||||| ||  | | |  ||| |||||||| |||||  ||||||| ||||||||||| || || |||||||||||||||
gtctcgggtatgtttaactattacctatcatgaaatagaaaatcaaatggaaatagagaaaagcctcaaataaacttaattcttaaccctttgatgtttatacattggcttatttgttcctgcagagGATGGTAAAGATACTACTAATGGTGAAGCTCCTGAGAACAATGCTCAGTACACAACTGTTTACGTCGGTAATCTTGCTCCAGAG

upper sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------------------------------------------tcaaggatgcttttgtactaaatcattgtctcctttggattatatgctagagattatgatagtgataagaaaccttatgtttgttgcattccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG
                                                 ||||      |||   |    |   |  | | |  ||  | |||||  | | | | | |    | ||| ||| |  || || || |  ||  ||||||||| |||||||||||||||  || | | ||  | ||||| || ||  |||||| ||| |||||||||||||| || ||||||||||||
gttgtctttctattactgtgcaaattcttatgtttttttctccttctcctcaaatggaatttacgaacctacattgattttccctgagtaatatg--aaaaactttaa----gttaacaaagcc-atattggtcgt-ttgattgtgcagAGGATGGTAAAGAGACATTAAATGAGGAAACACCTGAAAATAATTCTCAGTTTACCACTGTTTATGTGGGAAACCTTGCTCCAGAG

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|71890328|gb|DT039383.1|DT039383
EST:     ACAAAGTTCAGATGCCAAGAGTGTGGTAGAGCTGACCAATGGTTCATCAG                         AAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
genomic: ACAAAGTTCAGATGCCAAGAGTGTGGTAGAGCTGACCAATGGTTCATCAGgtgagttgga ... ccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
EST: gi|110409533|gb|EC975197.1|EC975197
EST:     ACAAAGTTCAGATGCCAAGAGTGTGGTAGAGCTGACCAATGGTTCATCAG                         AAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
genomic: ACAAAGTTCAGATGCCAAGAGTGTGGTAGAGCTGACCAATGGTTCATCAGgtgagttgga ... ccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
EST: gi|33409957|gb|CF215584.1|CF215584
EST:     ACAAAGTTCAGATGCCAAGAGTGTGGTNCAGCTGACCAATGGTTCATCAG                         AAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
genomic: ACAAAGTTCAGATGCCAAGAGTGTGGTAGAGCTGACCAATGGTTCATCAGgtgagttgga ... ccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
EST: gi|30253103|gb|CB970654.1|CB970654
EST:     ACAAAGTTCAGATGCCAAGAGTGTGGTAGAGCTGACCAATGGTTCATCAG                         AAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
genomic: ACAAAGTTCAGATGCCAAGAGTGTGGTAGAGCTGACCAATGGTTCATCAGgtgagttgga ... ccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
EST: gi|110696392|gb|EE072470.1|EE072470
EST:     ACAAAGTTCAGATGCCAAGAGTGTGGTAGAGCTGACCAATGGTTCATCAG                         AAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
genomic: ACAAAGTTCAGATGCCAAGAGTGTGGTAGAGCTGACCAATGGTTCATCAGgtgagttgga ... ccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
EST: gi|71872494|gb|DT021549.1|DT021549
EST:     GCTGACCAATGGTTCATCAG                         AAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
genomic: GCTGACCAATGGTTCATCAGgtgagttgga ... ccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
EST: gi|71876949|gb|DT026004.1|DT026004
EST:     GCTGACCAATGGTTCATCAG                         AAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT
genomic: GCTGACCAATGGTTCATCAGgtgagttgga ... ccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagagattatgatagtgataagaaaccttatgtttgttgcattccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG
                                         cattcctt  CT-rich tract
       attatgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaggatgcttttgtactaaatcattgtctcctttggattatatgctagagattatgatagtgataagaaaccttatgtttgttgcattccttgtgcagAAGATGGTAAAGAGACAGCAACTAATGAGGCTCCTGACAACAACCCTCAGTATACAACTGTTTATGTGGGCAATCTTGCTCCAGAG

- - ggatgct
- - - - - - - - - -aaatcat
- - - - - - - - - - - - - tgtctcc
- - - - - - - - - - - - - - - - - - - - - -atgctag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaacc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttgca