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'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ataaaattagcttggattttacatttgattttgtaacctcattcttactatgataataatgtgaggggtgcacagtactcaccaagggaacttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATCAGCTAACATATTACTAGACACAGAGCTCAATCCACACCTTACAGACTGT

Basic information

species Vitis vinifera
transcript Vv09s0002g00150.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA03G42360.1 (Glycine max), 3'ss of exon 14
ataaaattagcttggattttacatttgattttgtaacctcattcttactatgataataatgtga--ggggtgcacagtactcaccaagggaactttt--atcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATCAGCTAACATATTACTAGACACAGAGCTCAATCCACACCTTACAGACTGT
  |  | |    ||  |     | | |||||| |  ||| ||| |||  ||| ||    || ||      ||  |||   | | | |      ||||     |||||||||||||||||| | || |||||| |||||||||| ||| | || ||||| ||||||||||| || |||||||| ||||| || ||| ||||  ||
--atgactcaaatgactgacttact-gattttttttcctgatttttaa-atgttatccttgagactaaaatgaccagactttatccacaatttttttttgctagGTACCTACATGAAGTTAGTTCGCCATCAGTTGTTCATAAGAATATTAAGTCAGCCAACATATTACTGGATACAGAGCTTAATCCTCATCTTTCAGATAGT

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA19G45130.1 (Glycine max), 3'ss of exon 12
-ataaaatta---gcttggattttacatttgattttgtaacctcattcttactatgataataatgtgaggg-gtgcacagtactcaccaagggaacttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATCAGCTAACATATTACTAGACACAGAGCTCAATCCACACCTTACAGACTGT
 |  || |||     ||   ||||   | |||||||  ||  | ||  |    |    ||| |   ||     | |||| |  |            ||||   |||||||||||||||||| | || |||||| |||||||||| ||| | || ||||| ||||||||||| || ||||| || ||||| || ||| ||||  ||
gaccaacttatggattttttttttctttctgatttttaaatgttatcttcgagactcaaatgaccagactttatccacaatctttttttt-----tttttgctagGTACCTACATGAAGTTAGTTCGCCATCAGTTGTTCATAAGAATATTAAGTCAGCCAACATATTACTTGATACAGAACTTAATCCTCATCTTTCAGATAGT

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA16G01790.1 (Glycine max), 3'ss of exon 12
ataaaattagcttggattttacatttgattttgtaacctcattcttactatga-taataatgtgaggggtgcacagtact-caccaagggaacttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATCAGCTAACATATTACTAGACACAGAGCTCAATCCACACCTTACAGACTGT
  | |  ||   |  |    | |  |  ||||| |     |   | | | | | |  |        |  |  |||      | | |   |   || |  ||||||||||||||||||||| ||||||||  |||||||||| ||| | || || || |||||||| || || |||||  | ||||| || ||| | ||| ||
-cagatctaatgtacaagaca-acatagttttggacttcaagcatcaatgtaaattttcgccctgagaatcaacaacctaactctacttgtttttctcccagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTCGGCCAACATATTGCTTGATACAGATTTTAATCCTCATCTTTCTGACAGT

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G05230.1 (Glycine max), 3'ss of exon 12
-ataaaattagcttggattttacatttgattttgtaacctcattcttactatga--taataatgtgaggggtgcacagtactcaccaagggaacttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATCAGCTAACATATTACTAGACACAGAGCTCAATCCACACCTTACAGACTGT
 | | |  ||  | | |    ||||    ||||| |     |   | | | | |  |  |    ||||        |     | | |   |   || |   |||||||||||||||||||| ||||||||  |||||||||| ||| | || || || |||||||| || || |||||  | ||||| || ||| | ||| ||
gacagatctaa-tagaagacaacat--agttttggacttcaagcatcaatgtaaatttttgccctgagaatcaacaacctaactctacttgtttttctcctagGTACCTACATGAAGTTTGTTCACCATCTGTTGTTCATAAGAATATAAAGTCGGCCAACATATTGCTTGATACAGATTTTAATCCTCATCTTTCCGACAGT

upper sequence: Vv09s0002g00150.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT3G14350.3 (Arabidopsis thaliana), 3'ss of exon 13
ataaaattagcttggattttacatttgattttgtaacctcattcttact-atgataataatgtgaggggtgcacagtactcaccaagggaacttttat-----cagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATCAGCTAACATATTACTAGACACAGAGCTCAATCCACACCTTACAGACTGT
                |    | ||  |  |   || | |||| || || |  ||||||   ||  |    || ||| ||||   |  | | | || |     ||||||| | |||||||||||||||||||| || || || || ||  | |||||||| || || ||||| ||| ||||||| |||||||||||  ||||||  
---------------gtaagtctttaaacatctcaatcacattattgctcaatataatagcatgcag----cagagt-ctcatggaaagtattgttgttgttgcagGTACTTGCATGAAGTTTGCTCACCATCTATAGTCCACAAGAACATTAAATCAGCAAATATTTTACTTGACTCAGAGCTGAATCCACACCTCTCAGACTCA

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|110701239|gb|EE078596.1|EE078596
EST:     ACATGGAACACCCGCGTCAAGATTGCTTTAGGGACTGCCCGTGCATTAGA                         GTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC
genomic: ACATGGAACACCCGCGTCAAGATTGCTTTAGGGACTGCCCGTGCATTAGAgtaagtcgat ... cttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC
EST: gi|349830454|gb|FQ416752.1|FQ416752
EST:     ACATGGAACACCCGCGTCAAGATTGCTTTAGGGACTGCCCGTGCATTAGA                         GTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC
genomic: ACATGGAACACCCGCGTCAAGATTGCTTTAGGGACTGCCCGTGCATTAGAgtaagtcgat ... cttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC
EST: gi|110363514|gb|EC927108.1|EC927108
EST:     TCAAGATTGCTTTAGGGACTGCCCGTGCATTAGA                         GTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC
genomic: TCAAGATTGCTTTAGGGACTGCCCGTGCATTAGAgtaagtcgat ... cttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC
EST: gi|110360391|gb|EC923453.1|EC923453
EST:     TGCCCGTGCATTAGA                         GTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC
genomic: TGCCCGTGCATTAGAgtaagtcgat ... cttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC
EST: gi|110379506|gb|EC944705.1|EC944705
EST:     ACATGGAACACCCGCGTCAAGATTGCTTTAGGGACTGCCCGTGCATTAGA                         GTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC
genomic: ACATGGAACACCCGCGTCAAGATTGCTTTAGGGACTGCCCGTGCATTAGAgtaagtcgat ... cttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactatgataataatgtgaggggtgcacagtactcaccaagggaacttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATCAGCTAACATATTACTAGACACAGAGCTCAATCCACACCTTACAGACTGT
                              tactcac  putative branch site (score: 1)
                                             cttttatc  putative PPT
     tgataataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ataaaattagcttggattttacatttgattttgtaacctcattcttactatgataataatgtgaggggtgcacagtactcaccaagggaacttttatcagGTACCTACATGAAGTTTGCTCACCATCAATTGTTCATAAAAATTTCAAATCAGCTAACATATTACTAGACACAGAGCTCAATCCACACCTTACAGACTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- aaaatta
- - - - - - - - - - - - - - - - - aacctca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgaggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcaccaa