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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAACCAGCTCGATGGATTGCAGATCAAAGAAGTGGGCGACGGCAATCTCAACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattttgattcataacggcacctcacaaattcagattcttactgaaaaaaaatggcttcactgtggaagaattttaagtgcttgtgaaggttaggtcaaagtgactgttgtaagatgtggttgtgttgagagtgcag

Basic information

species Vitis vinifera
transcript Vv03s0091g00080.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os04g57400.1 (Oryza sativa), 5'ss of exon 1
AAACCAGCTCGATGGATTGCAGATCAAAGAAGTGGGCGACGGCAATCTCAACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattttgatt-cataacggcacc-tcacaaattcagattcttactgaaaaaaaatggcttcactgtggaagaattttaagtgcttgtgaaggttaggtcaaagtgactgttgtaagatgtggttgtgttgagagtgcag
   |   ||||| |   |    ||||| || || ||||||||||| ||||||||||||||||||||| |||||  |   || ||| |||||||||| ||||| |  || |      |    || | ||  |||| ||  |      | ||           | | | | |  || ||   |  | | |                                                        
CGGCAGCCTCGACGCCCTCACCATCAAGGAGGTCGGCGACGGCAACCTCAACTTCGTCTACATCGTCCTCTCCGACGCCGGCTCCGTCGTCATCAAGCAGgtccctatctcctccacgcgccgccgccgccacacatgtacgcatcttctctct-----ccgttcctccgctgacgacgctgcaatccag------------------------------------------------------

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os04g57410.1 (Oryza sativa), 5'ss of exon 1
AAACCAGCTCGATGGATTGCAGATCAAAGAAGTGGGCGACGGCAATCTCAACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattttgattcataacggcacctcacaaattcagattcttactgaaaaaaaatggcttcactgtggaagaattttaagtgcttgtgaaggttaggtcaaagtgactgttgtaagatgtggttgtgttgagagtgcag
   ||  ||||| |   |    ||||| || || ||||||||||| ||||||||||||||||||||| |||||  |   || ||| |||||||||| ||||| |  || |    ||    || | || |     |      |   ||  |   |  | |  |   ||||    |   |||    |||   || | |    || |                                      
CGGCCGCCTCGACGCCCTCACCATCAAGGAGGTCGGCGACGGCAACCTCAACTTCGTCTACATCGTCCTCTCCGACGCCGGCTCCCTCGTCATCAAGCAGgtccctatctc--ctccacgcgccgccacc---gtcgccgctgccacacatgtagtacgcatcttctgtctccgttcttt---cgctgacgacgctgcaatccag-------------------------------------

upper sequence: Vv03s0091g00080.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G464137_T01 (Zea mays), 5'ss of exon 1
AAACCAGCTCGATGGATTGCAGATCAAAGAAGTGGGCGACGGCAATCTCAACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattttgattcataacggcacctcacaaattcagattcttactgaaaaaaaatggcttcactgtggaagaattttaagtgcttgtgaaggttaggtcaaagtgactgttgtaagatgtggttgtgttgagagtgcag
   |   || ||     |  ||||||| || || ||||||||||| ||||||||||||||||||||    |||      ||  || ||||| |||| ||||| |   |      ||  | |  |||| |   |   | | | |   | |       ||   ||| |  |   |         |  |  | | |     |  ||    |                                  
TGGCAGTCTAGACTCCATCGAGATCAAGGAGGTCGGCGACGGCAACCTCAACTTCGTCTACATCGTGCAGTCCGAGGCCGGCGCCATCGTCGTCAAGCAGgtccgtgtccg---tccgaccctcacccccacaggcccgctccgctccgcgtccttatcatttctcactctgacggcgccgcgctcgggcggaaaacggaacacgcag----------------------------------

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|161714716|gb|FC064488.1|FC064488
EST:     ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|161720482|gb|FC070594.1|FC070594
EST:     ACTTCGTCTACATCGTCATCTCCTCCACTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|46917662|gb|CN546991.1|CN546991
EST:     ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|71863664|gb|DT012719.1|DT012719
EST:     ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGGA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|161712718|gb|FC062290.1|FC062290
EST:     ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|161705568|gb|FC056173.1|FC056173
EST:     ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|161710003|gb|FC058085.1|FC058085
EST:     ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|37184887|gb|CF604240.1|CF604240
EST:     ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|46917661|gb|CN546990.1|CN546990
EST:     ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|161705684|gb|FC056612.1|FC056612
EST:     ACTTCGTCTACATCGTCATCTCCTCCACTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
EST: gi|110727897|gb|EE105184.1|EE105184
EST:     ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAG                         GCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA
genomic: ACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattt ... gagagtgcagGCGTTGCCGTACATACGTTGTATAGGGGAATCGTGGCCGATGACGAAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAACCAGCTCGATGGATTGCAGATCAAAGAAGTGGGCGACGGCAATCTCAACTTCGTCTACATCGTCATCTCCTCCAGTGGATCCTTCGTCATCAAACAGgtacaaattttgattcataacggcacctcacaaattcagattcttactgaaaaaaaatggcttcactgtggaagaattttaagtgcttgtgaaggttaggtcaaagtgactgttgtaagatgtggttgtgttgagagtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA