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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagctcttaacgagtatgtatattaagatgtgagtaggcgccttcattccaggccagcttttacatttaacacaaacactctcggcctttgcttgcag

Basic information

species Vitis vinifera
transcript Vv09s0002g01800.t01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA16G00590.1 (Glycine max), 5'ss of exon 18
CCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagctcttaacgagtatgtatattaagatgtgagtaggcgccttcattccaggccagcttttacatttaa-cacaaacactctcggcct--ttgcttgcag
| || | |||||| || || ||  | ||  |||| |||||||||||||| ||||||||||| ||||| || ||||||||||||||||| || ||||||||  |    | | |   |   |||  |    | |   | |   ||   | |  | ||    ||||  |   || ||  |  ||  |   | |  |||  | |||
CTGAGAGGAGGGTCGTTCCGGGTTCGGGTGCTGAAGAATTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatcattcttaatctgctgcttattgtctatttttttttgtaaccaaaactttaagctttattttgtagcaaaacatgataacaatacactttgttgtgttcag

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA07G03930.2 (Glycine max), 5'ss of exon 18
CCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagctcttaacgagtatgtatattaagatgtgagtaggcgccttcattcc--aggccagcttttacatttaacacaaacactctcggcctttgcttgcag----------
| || | |||||| || || ||  ||||  |||| || ||||||||||| ||||||||||| ||||| || ||||||||||||||||| || ||||||||  |  ||||||   |  ||  | |||   | | |         ||  |  |  |  | |         ||| |    || |||  |   |    |     |          
CTGAGAGGAGGGTCGTTCCGGGTTCAGGTGCTGAAGAGTTCAAGTTTGCTTCCTTCATGTCTGTGACCCTCAGCTGTGATCATCGTGTTATAGATGgtaatca-ttcttaatctgc-tgcttcttattgtttaaactaatatttttgtaactgaaactactaagcttgttttatggtaaaacttgctaacaaaacaatttgttctgttcag

upper sequence: Vv09s0002g01800.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: PP1S78_56V6.1 (Physcomitrella patens), 5'ss of exon 16
CCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagctcttaacgagtatgtatattaagatgtgagtaggcgccttcattccaggccagcttttacatttaacacaaacactctcggcctttgcttgcag-----
| || ||| || | || || ||       || ||| |||   |  | | | | || ||| | || ||| | ||||||||||||||||| |||||||||||||  |  ||   ||   | || ||     | | ||| | ||     | |    |  || |  ||   | |||   |||   || ||  | ||||   |      
CTGAGAAGCGGTTGGTGCCAGGACTTACACCAGATCAATATGACGTCGGCACTTTTATGACTGTTACAATGAGCTGTGATCATCGTGTTATTGATGgtaagtt-ccgtttctgatcttttaaat----gtattagt-gccgaacgaacttagtgtgagttcataacctcaac--gaacgaacttggtgtgtgctaataagctca

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|22008294|gb|BQ793328.1|BQ793328
EST:     TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
genomic: TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
EST: gi|110407843|gb|EC973460.1|EC973460
EST:     TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTACATCGAGAACC
genomic: TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
EST: gi|22009486|gb|BQ794520.1|BQ794520
EST:     TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
genomic: TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
EST: gi|33405959|gb|CF211586.1|CF211586
EST:     TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAGATCCTACATCGAGAACC
genomic: TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
EST: gi|34363482|gb|CF405067.1|CF405067
EST:     TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
genomic: TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
EST: gi|30131621|gb|CB916960.1|CB916960
EST:     CATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
genomic: CATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
EST: gi|161714484|gb|FC064459.1|FC064459
EST:     TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG                         GGTGCA-TTGGTG
genomic: TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagG-TGCAATTGGTG
EST: gi|51052616|gb|CO819650.1|CO819650
EST:     CTAAGCTGTGATCATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTACATCGAGAACC
genomic: CTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
EST: gi|32250355|gb|CD716174.1|CD716174
EST:     TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
genomic: TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
EST: gi|22009599|gb|BQ794633.1|BQ794633
EST:     TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
genomic: TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
EST: gi|30132039|gb|CB917378.1|CB917378
EST:     TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATG                         GTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC
genomic: TGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagct ... ttgcttgcagGTGCAATTGGTGCAGAATGGCTGAAGGCGTTCAAATCCTATATCGAGAACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGACAAGAGGGTTGTACCTGGCACAGGCCCTGATGAATTCAAGTTTGCCTCCTTCATGTCAGTGACACTAAGCTGTGATCATCGTGTCATTGATGgtaagtagctcttaacgagtatgtatattaagatgtgagtaggcgccttcattccaggccagcttttacatttaacacaaacactctcggcctttgcttgcag

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