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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgtttgaacagaatcaaacatatatgttttggttccagcagtccttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA

Basic information

species Vitis vinifera
transcript Vv14s0108g00140.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g08960.1 (Oryza sativa), 3'ss of exon 5
------gatgtttgaacagaatcaaacatatatgttttggttccagcagtccttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA
       || ||| |   || ||||  | || ||   |  | |  ||| |    ||||| | ||| | |   |       | |    | |||| || ||  | ||||| |||||||| ||||| |||||||| || || || || || |||||||| ||  | || |||||||||||||| || |||||| ||| ||| ||||| |
acaatgcatatttca-tggactcaag-acat-tgacatattacaggcaatttcattgatttaact-gttcagtacttctatttcctgctttgtattatt--tccagTCGCTGCTTTGCGATCCAAACCCAAATTCACCTGCCAACTCTGAAGCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGA

upper sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os05g08960.2 (Oryza sativa), 3'ss of exon 5
gatgtttgaacagaatcaaacatatatgttttggttccagcagtccttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA----------------------------------------------
                                           |    ||||| | ||| | |   |       | |    | |||| || ||  | ||||| |||||||| ||||| |||||||| || || || || || |||||||| ||  | || |||||||||||||| || |||||| ||| ||| ||||| |                                              
-------------------------------------------tttcattgatttaact-gttcagtacttctatttcctgctttgtattatt--tccagtcgctgctttgcgatccaaacccaaattcacctgccaactctgaagCTGCCCGCCTATTCAGTGAGAACAAGCGGGAATACAACCGAAAAGTTCGTGAGATAGTGGAGCAGAGCTGGACCGCGGACTGATCCACTCCATCTAACCA

upper sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G110983_T03 (Zea mays), 3'ss of exon 3
---gatgtttgaacagaatcaaacatatatgttttggttccagcagtccttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA
    ||   ||   |  |   |  ||  ||||| |    ||| | || ||  ||     | |   |   ||||     |   |   ||||    ||  | |||||| || | || ||||| ||||| || ||||||||||| || ||||| || || ||||| || ||||||||||| ||||||||| | | ||| || ||  
tgccatcgctgtttatgaattattatg-atgttcttaaaccatctgtgctgatggctacagtgcgtgtgtgtgactaacctgaggtttgtgccatt--tgcagTCATTGTTGTGCGATCCAAACCCGAATTCGCCCGCTAACTCTGAAGCCGCCCGCATGTTCAGCGAGAACAAGCGAGAGTACAACCGCAAAGTTCGGGAGG

upper sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ16328 (Selaginella moellendorffii), 3'ss of exon 4
gatgtttgaacagaatcaaacatatatgttttggttccagcagtccttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA
                                 |||      ||  ||||| |     | | | ||   |   |||| |        ||    ||  |||||||||||||||||||| |||||||||||||| || || || ||||| || ||||||| ||||||||||   || ||||||||| | |||||||| || |
---------------------------------gttt----ggtttttttgctcgcctttgttggaatagactttctta-----cacttacccatcgcagTCACTGCTTTGTGATCCTAACCCAAACTCGCCGGCGAACTCCGAAGCAGCGCGGATGTATAGTGAGAACCGTCGAGAGTACAACCGGAGAGTCCGCGACA

upper sequence: Vv14s0108g00140.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ17802 (Selaginella moellendorffii), 3'ss of exon 4
gatgtttgaacagaatcaaacatatatgttttggttccagcagtccttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA
                             |||||||       |  | | |   ||      |||   | | |||    |  ||| |      ||  |||||||||||||||||||| |||||||||||||| || || || ||||| |||||||||| ||| ||||||   || ||||||||| | |||||||| || |
----------------------------gtttggtttt-----ttttctcgcctttg-----ttggaatagactttcttacacttatcc----atcgcagTCACTGCTTTGTGATCCTAACCCAAACTCGCCGGCAAACTCCGAAGCAGCACGGATGTATAGCGAGAACCGTCGAGAGTACAACCGGAGAGTCCGCGACA

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|18458409|gb|BM436687.1|BM436687
EST:     ACCAGTGGAGTCCCATATATGATGTCGCTGCTATTCTTACTTCTATCCAG                         TCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
genomic: ACCAGTGGAGTCCCATATATGATGTTGCTGCTATTCTTACTTCTATCCAGgtattatggg ... gttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
EST: gi|110695924|gb|EE074493.1|EE074493
EST:     ACCAGTGGAGTCCCATATATGATGTTGCTGCTATTCTTACTTCTATCCAG                         TCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
genomic: ACCAGTGGAGTCCCATATATGATGTTGCTGCTATTCTTACTTCTATCCAGgtattatggg ... gttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
EST: gi|32459632|gb|CD800806.1|CD800806
EST:     CAGTGGAGTCCCATATATGAGATGTTGCTGCTATTCTTACTTCTATCCAG                         TCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
genomic: CAGTGGAGTCCCATATAT--GATGTTGCTGCTATTCTTACTTCTATCCAGgtattatggg ... gttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
EST: gi|30296124|gb|CB972918.1|CB972918
EST:     ACCAGTGGAGTCCCATATATGATGTTGCTGCTATTCTTACTTCTATCCAG                         TCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
genomic: ACCAGTGGAGTCCCATATATGATGTTGCTGCTATTCTTACTTCTATCCAGgtattatggg ... gttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
EST: gi|110372214|gb|EC936367.1|EC936367
EST:     ACCAGTGGAGTCCCATATATGATGTTGCTGCTATTCTTACTTCTATCCAG                         TCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
genomic: ACCAGTGGAGTCCCATATATGATGTTGCTGCTATTCTTACTTCTATCCAGgtattatggg ... gttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
EST: gi|110715525|gb|EE093678.1|EE093678
EST:     ACCAGTGGAGTCCCATATATGATGTCGCTGCTATTCTTACTTCTATCCAG                         TCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA
genomic: ACCAGTGGAGTCCCATATATGATGTTGCTGCTATTCTTACTTCTATCCAGgtattatggg ... gttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA
                                         ttttgtt  CT-rich tract
                                      ttgttttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgtttgaacagaatcaaacatatatgttttggttccagcagtccttttgatattactagcttgatgtggtcttctgaatccttgttttgttatttcagTCACTGCTTTGTGATCCCAACCCAAACTCGCCCGCTAATTCAGAAGCTGCACGGATGTTTAGTGAGAACAAGCGCGAGTACAACAGAAGAGTCCGTGAAA

- - - - - - -aatcaaa
- - - - - - - - - - - - - - - - - ttccagc
- - - - - - - - - - - - - - - - - - - - - - ccttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctga