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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagactgtactggcagtagtcctttgtcagaaattttttgcatttatatttaccactcttgtaaatctttttggatgttttcctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTCGCTCGTTCAACTGATGATTTCAATGGAGCACAGCTGAAAGCCGTTTGTG

Basic information

species Vitis vinifera
transcript Vv05s0020g01180.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 8
gtgagactgtactggcagtagtcctttgtcagaaattttttgcatttatatttaccactcttgt----aaatctt--tttg---gatgttttcctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTCGCTCGTTCAACTGATGATTTCAATGGAGCACAGCTGAAAGCCGTTTGTG
||  |  |  |    | ||  |   |  ||||  | | |||     |  |||| |   | |  |    || || |  |||     || | |   | | || |||| || ||||| |||||||||||| ||||||| || |||||||| || || ||||| ||||| ||||| ||||||||||| || |||||||| |||||||
gtaggtttccagaacctgtgatgtctaatcagctaatgtttattcatccatttgcttttgtaatccacaagtcatgctttaactaatatgtggttctctgtagATTCACTCAAGAAAAATGAATGTAAACCCAGATGTGAATTTTGAAGAGCTGGCTCGCTCAACAGATGACTTCAATGGAGCGCAACTGAAAGCTGTTTGTG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 7
---------gtgagactgtact--ggcagtagtcctttgtcagaaattttttgcattta--tatttaccactcttgtaaatctttttggatgttttcctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTCGCTCGTTCAACTGATGATTTCAATGGAGCACAGCTGAAAGCCGTTTGTG
            |   | | ||      |  |   ||||||||    |||   || |     ||||| |||   |  |  | || |    || |   |||||    ||||||||||||||||||||||||| | || || || || ||||| ||| | ||||| ||||||||||| ||||| ||||||||||| || || |||||||
gtcggtctcaacaacttatgctcaaattgctgaagtttgtcagtggctttcctcagtaggccatttatcacaacta-acgtgttctgtattggtcctctgta----gATCCATTCAAGGAAAATGAATGTAAATCCTGATGTCAACTTTGAAGAATTGGCTCGCTCAACTGATGACTTCAACGGAGCACAGCTAAAGGCAGTTTGTG

upper sequence: Vv05s0020g01180.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G100873_T01 (Zea mays), 3'ss of exon 1
gtgagactgtactggcagtagtcctttgtcagaaattttt---tgcatt-tatatttaccactctt-gtaaatctttt-----tggatgttttcc------tgta-tgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTCGCTCGTTCAACTGATGATTTCAATGGAGCACAGCTGAAAGCCGTTTGTG
||  | ||  ||      |  ||  ||  | ||| ||| |   || ||  | | ||| |  | ||  |||  || |||       |||||||||        | | || ||||||||||||| |||||||| ||| | || || || || || || ||| | ||||| ||||| ||||| ||||| |||||||||||||| || || ||||
gtcggtctccacaacttatgttcaatttgctgaagtttgtcaatgaatgatgtttttgcttcactcagtaggtcatttaccaactgatgttttctgtatgtcgcactgtagATCCATTCAAGAAAAATGAACGTAAATCCGGATGTCAACTTCGAAGAATTGGCTCGCTCAACAGATGACTTCAACGGAGCACAGCTGAAGGCAGTCTGTG

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|30133923|gb|CB919262.1|CB919262
EST:     AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAG                         ATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
genomic: AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAGgtgagactgt ... ctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
EST: gi|110717892|gb|EE094156.1|EE094156
EST:     AA-TTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAG                         ATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGA
genomic: AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAGgtgagactgt ... ctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGA
EST: gi|110360884|gb|EC924326.1|EC924326
EST:     AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAG                         ATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
genomic: AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAGgtgagactgt ... ctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
EST: gi|351026518|gb|FQ428530.1|FQ428530
EST:     AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAG                         ATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
genomic: AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAGgtgagactgt ... ctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
EST: gi|351019753|gb|FQ439570.1|FQ439570
EST:     AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAG                         ATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
genomic: AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAGgtgagactgt ... ctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
EST: gi|351019480|gb|FQ429615.1|FQ429615
EST:     AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAG                         ATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
genomic: AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAGgtgagactgt ... ctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
EST: gi|351027526|gb|FQ446689.1|FQ446689
EST:     AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAG                         ATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC
genomic: AAATTGAGTTCCCTCATCCTTCTGAAGATGCAAGAGCGAGAATTTTGCAGgtgagactgt ... ctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatttatatttaccactcttgtaaatctttttggatgttttcctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTCGCTCGTTCAACTGATGATTTCAATGGAGCACAGCTGAAAGCCGTTTGTG
                                      tgttttcct  CT-rich tract
                     ttgtaaatcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagactgtactggcagtagtcctttgtcagaaattttttgcatttatatttaccactcttgtaaatctttttggatgttttcctgtatgcagATCCATTCAAGGAAAATGAATGTACACCCAGACGTAAATTTTGAGGAACTCGCTCGTTCAACTGATGATTTCAATGGAGCACAGCTGAAAGCCGTTTGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA