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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaaccattaattaccgttttttacccttgtggacag

Basic information

species Vitis vinifera
transcript Vv00s0187g00170.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os09g32220.1 (Oryza sativa), 5'ss of exon 3
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgctat--tctttaatgtaatagatcagatgactaaccat-taattaccgttttttacccttgtggacag
 || || |   | || || || ||||||||    ||||| || |||||||||||||| ||||| ||||||||||||||||| || |||||  |||| |||||   |  |      |||    || ||    ||||   |   || | || | | ||||| ||| |   | |  | |||| |            
CCCGAAAGAGGAAGCACAGAAAGCTCAGGCTGCCATGTTTTCAGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTCTCTATGATAGTTCCTCAGgttcagtagcttacatttcaattttcttccatcttagctaccatggctctgtttactaaacatgttgcttcaatatttttcag----------

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G014313_T02 (Zea mays), 5'ss of exon 3
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgct-attctttaatgtaatagatcagatgactaaccattaat--taccgttttttacccttgtggacag-----------
||| ||||   | ||||| || |||||||||   ||||| ||||||||||||||||| ||||| ||||||||||||||||| || |||||  |||| |||||  ||   || ||    |   || ||  |  |  | | || | |   |   |  |  |  |  |   ||   | | ||| | |  |     |           
TCCAAAGGAAGACGCGCAGAAGGCTCAGGCAGCCATGTTTTCTGATCCAAACATGGCCATGGACATGATGAAGAAGAACCTATCCATGATAGTTCCTCAGgttctgtgttccgtacactgatttacttgtggtgcactatagttggctaatcgtgtggcattctaccgtatgttatattaacatcataacttgtgtttttgcag

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G08370.1 (Glycine max), 5'ss of exon 1
-TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaaccattaattaccgttttttacccttgtggacag--------------------------------
 ||| ||||| ||||  || ||| | || ||||| |||||||||||||| |||||||| ||||||||||||||||| |||||||||||||||||||| ||||||||    | || ||||     | || |   || |   | | |||||     ||    | |  || ||  || | |    | |    ||                                
TTCCAAAGGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCGAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATCATTCCTCAggtattaaaattggagtttgacagtcctctggctttagaaactggatcacgctccttgt-acttgtttccaattatcagatgtctcactagcatctacttacgttgtttcgtattttttgaca

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA08G44410.1 (Glycine max), 5'ss of exon 4
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaaccattaattaccgttttt------tacccttgtggacag-----------------------------
||| || || ||||  || ||| | || ||||| ||||||||||||||||||||||| ||||||||||||||||| |||||||||||||| ||||| ||||| ||    | || ||||     |||  |   || |  |  | |||||      |   | ||  || || || ||      | ||    |||                                 
TCCAAAAGGCCAGGGCCAGAATCCGCAAGCACAGATGTTCTCTGATCCAAACATGGCCATGGATATGATGAAGAAAAACCTTTCAATGATAATTCCTCAGgtgttaaaattggagtttgacagtgcactagctttagattttggatcatgctcttgtactttttttcccattattaggagatgcctcactggcttttacttatgttgttttctattttcccacag

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G12590.1 (Arabidopsis thaliana), 5'ss of exon 3
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgta--ttgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaacc---attaattaccgttttttacccttgtggacag
||| |||||  | || |||||| | || ||    ||||| |||||||| |||||||| ||||||||||||||||| || ||||| ||||| ||||| |||||   |||   | |   | ||   |  ||||  |||   || |  | |||  | |  |||    || | ||||| ||||  |             
TCCCAAGGGAGAAGCTCAAAATCCACAAGCTGCTATGTTTTCTGATCCTAACATGGCCATGGATATGATGAAGAAAAATCTTTCTATGATTATTCCTCAGgtgagttgtatttgaaatgtttcat--ctatgtttttgcgttactggtcatttaagaaactgatatcacttaccattttgcag------------

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ16947 (Selaginella moellendorffii), 5'ss of exon 3
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaaccattaattaccgttttttacccttgtggacag
||| ||||| ||||  || || |  ||||| |||||| | || || ||||||||||| ||||| ||||||||||||||| | || ||||||||||| ||||| |||  ||       |  |||  |  |   |  | ||      ||                                           
TCCAAAGGGCCAGGGCCAGAACGTCCAGGCTCAAATGCTTTCGGACCCAAACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgt-ttggcgttccaaaatcttgtctcggtc--tcgacgtttcttttccag----------------------------------------

upper sequence: Vv00s0187g00170.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ16068 (Selaginella moellendorffii), 5'ss of exon 3
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaaccattaattaccgttttttacccttgtggacag
||| ||||| ||||  || || |  ||||| |||||| | || || ||||||||||| ||||| ||||||||||||||| | || ||||||||||| ||||| |||  ||       |  |||  |  |   |  |   ||    || |  |  |       |                           
TCCAAAGGGCCAGGGCCAGAACGTCCAGGCTCAAATGCTTTCGGACCCAAACATGGCAATGGACATGATGAAGAAGAACTTGTCCATGATCATTCCTCAGgt-ttggcgttccaaaatcttgtctcggtc--tcgagccaacttttcgggcgtttcttttgcag--------------------------

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|30132459|gb|CB917798.1|CB917798
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|30136299|gb|CB921637.1|CB921637
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|294966792|gb|GW837811.1|GW837811
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|32250235|gb|CD716054.1|CD716054
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|30135330|gb|CB920668.1|CB920668
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|110407602|gb|EC973208.1|EC973208
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|110428045|gb|EC994506.1|EC994506
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|110417816|gb|EC983901.1|EC983901
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|110712100|gb|EE089333.1|EE089333
EST:     ACACGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|352764273|gb|FQ471253.1|FQ471253
EST:     GGATAGGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACNNNNNNNNCTCTGGATTTGTAGCAG
genomic: GGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|110429192|gb|EC995681.1|EC995681
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|27580483|gb|CB003178.1|CB003178
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|110728851|gb|EE104791.1|EE104791
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
EST: gi|30125541|gb|CB910880.1|CB910880
EST:     ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAG                         ACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG
genomic: ACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgt ... ttgtggacagACTCTTACTTTTGCTTGGGTTAACTTTTTCTTCTCTGGATTTGTAGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTAAGGGTCAGGCGCAAAATGCTCAGGCACAAATGTTCTCTGATCCAAACATGGCTATGGATATGATGAAGAAGAACCTTTCAATGATCATTCCCCAGgtattgctgtcggtgttttctgttgctattctttaatgtaatagatcagatgactaaccattaattaccgttttttacccttgtggacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC