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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGCTTTAAAAACAGATCTCAAAGGACGGACTCAACAAAAAAAACAATTGGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccaccttgtcatcttgcatagatttctggcactcttattgattgctgcctgaaagcttgagccttttgggttgacattttcttacaccattgctc...

Basic information

species Vitis vinifera
transcript Vv18s0072g00720.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G044681_T01 (Zea mays), 5'ss of exon 4
CTTGCTTTAAAAACAGATCTCAAAGGACGGACTCAACAAAAAAAACAATTGGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccaccttgtcatcttgcatag-atttctggcactcttattgattgctgcctgaaagcttgagcct--tttgggttgacattttcttaca--ccattgctc-------
||  |||| ||||| |||||||||||  | || || || |||||||| || || || || || |||||||| |||||||| ||||||||||| |||||||||||   ||    | ||     ||   || |     |    | || ||     |||||     ||  | |       | |  ||| | |||  |   ||  | |        
CTCACTTTGAAAACTGATCTCAAAGGGAGAACACAGCAGAAAAAACAGTTAGTCAAGGAGAACTTTGATTGTTTTGTCTCGTGCAAAACTACAATAGATGgtat-ttacgcaattattagatatgccatgttgcagataaatgttcatgat--cctgagtttctggacatggacaatgattgcatctccttgtaatacacagttttatgcag

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G050647_T01 (Zea mays), 5'ss of exon 4
CTTGCTTTAAAAACAGATCTCAAAGGACGGACTCAACAAAAAAAACAATTGGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccaccttgtcatcttgcatagatttctggcactcttattgattgctgcctgaaagcttgagccttttgggttgacattttcttacaccattgctc---------
||  | || ||||| |||||||||||  | || || || |||||||| || || || || || || ||||| |||||||| ||||||||||| |||||||||||      | ||  |     | |    | | |||    | || ||     |||||   | ||  |  | |   ||  |||   ||   | ||  | |          
CTCACCTTGAAAACTGATCTCAAAGGGAGAACACAGCAGAAAAAACAGTTAGTCAAGGAGAACTTCGATTGTTTTGTCTCGTGCAAAACTACAATAGATGgtat-ttgtgtagttgttagatacatccatattgcaaaaatgttcatgat--cctgagttcatggacaatgt---tttgcatcccctcgtaacacagttttttttgcag

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G112801_T01 (Zea mays), 5'ss of exon 8
CTTGCTTTAAAAACAGATCTCAAAGGACGGACTCAACAAAAAAAACAATTGGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccaccttgtcatcttgcatagatttctggcactcttattgattgctgcctgaaagcttgagccttttgggttgacattttcttacaccattgctc--------
||  | || ||||| |||||||||||  | || ||||| |||||||  || || || || || || ||||| |||||||| ||||||||||| |||||||||||      | ||  |  |  ||| ||   |    |   ||    ||  ||      || ||  |     ||  ||| |||   | |  | ||    |         
CTCACCTTGAAAACTGATCTCAAAGGGAGAACACAACAGAAAAAACTGTTAGTCAAGGAGAACTTCGATTGTTTTGTCTCGTGCAAAACTACAATAGATGgtat-ttgtgtagttgt--tagatacatccatattgcaaataaatgttcatgatcctgagtttatggacaatgttttg-catccccgtgtaacacaatttttttgtag

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AC194296.3_FGT001 (Zea mays), 5'ss of exon 9
CTTGCTTTAAAAACAGATCTCAAAGGACGGACTCAACAAAAAAAACAATTGGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtat--gccaccttgt----------catcttgcatagatttctggcactcttattgattgctgcctgaaagcttgagccttttgggttgaca--ttttcttacaccattgctc------------------------------------------------------------
||  | || ||||| |||| ||||||  | || || || ||||||| ||| || || || || || ||||| |||||||| ||||||||||| |||||||||||  |     ||||          ||| ||||| | |  | |  ||   |  |   ||  ||    |    |||   |     |    |||  |||| ||    ||||| |                                                             
CTCACCTTGAAAACTGATCCCAAAGGGAGAACACAGCAGAAAAAACTATTAGTCAAGGAGAACTTCGATTGTTTTGTCTCGTGCAAAACTACAATAGATGgtatttgtgtagttgttagatacatccatattgcaaataaatgtt-catgatcctgagtttatggacaatgttttgcatccccgtgtaaaacaattttttttctgacattgattcgaaattgagacagatagaggaagatcctgaaggtgtaggtactgctcacttgtattcag

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA10G36120.1 (Glycine max), 5'ss of exon 4
CTTGCTTTAAAAACAGATCTCAAAGGACGGACTCAACAAAAAAAACAATTGGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccaccttgtcatcttgcatagatttctggcactcttattgat--tgctgcctgaaagcttgagccttttg-ggttgacattt-tcttacaccattgctc
|||||||| ||||| ||| ||||| | || ||| | || | ||| || |||||||| || || ||||||||||||||||| |||||||| || || |||||||||  || || |  | |||||  ||| |     || ||  || |   | |      ||   || || |||  | |  ||  |||  | | |  |    ||||
CTTGCTTTGAAAACTGATTTCAAAAGTCGTACTGAGCAGAGAAAGCAGTTGGTTAAGGACAACTTTGATTGCTTTGTCTCTTGCAAAACAACAATTGATGgtatgg-actttat--ttttgcac-gatattcaaaaccctagttaaccatacaaaagtaatcttttagtcttgggtgactggtattcctatcatgctcaagctc

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G31490.2 (Glycine max), 5'ss of exon 4
CTTGCTTTAAAAACAGATCTCAAAGGACGGACTCAACAAAAAAAACAATTGGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccaccttgtcatcttgcatagatttctggcactcttattgattgctgcctgaaagcttgagccttttgggt---tgacattt-tcttacaccattgctc
|||||||| ||||| ||| ||||| | || ||| | || | ||| || |||||||| || || ||||||||||||||||| |||||||| || || |||||||||  || || |  | |||||| |  |||     | |   || |            |   |     | ||||||   |   |||  | | || |    ||||
CTTGCTTTGAAAACTGATTTCAAAAGTCGTACTGAGCAGAGAAAGCAGTTGGTTAAGGACAACTTTGATTGCTTTGTCTCTTGCAAAACAACAATTGATGgtatga-actttat--ttttgcatggcattcaaa-gcccagtttaaccatacaaaagtaatcttttattcttgggtgtctagtattcctgtcacgctcaagctc

upper sequence: Vv18s0072g00720.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G21170.1 (Arabidopsis thaliana), 5'ss of exon 4
CTTGCTTTAAAAACAGATCTCAAAGGACGGACTCAACAAAAAAAACAATTGGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccaccttgtcatcttgcatagatttctggc---actcttattgattgctgcc-tgaaagcttgagccttttgggttgacattttcttacaccattgctc
|||||  | ||||  ||  | || || || | || |||||  ||||||||||| ||||| |||||||| ||||||||||| || ||||| || || ||||||||||    ||    ||    ||  ||||    |   |||||| |   ||| ||   ||||   |   ||||||    || |||                   
CTTGCCCTGAAAAGTGACTTAAAGGGCCGTAATCTACAAAGGAAACAATTGGTGAAAGATAATTTTGACTGCTTTGTCTCGTGTAAAACAACAATTGATGgtatgcattattacactcaattatctattttgaactttactcttctctcttgttgatgtgaacattactgcctttc---tttacag------------------

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|32248250|gb|CD714069.1|CD714069
EST:     GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATG                         ATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
genomic: GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccacc ... gtttgtatagATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
EST: gi|30327435|gb|CD010697.1|CD010697
EST:     GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATG                         ATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
genomic: GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccacc ... gtttgtatagATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
EST: gi|32248056|gb|CD713875.1|CD713875
EST:     GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATG                         ATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
genomic: GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccacc ... gtttgtatagATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
EST: gi|32272073|gb|CD721232.1|CD721232
EST:     GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATG                         ATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
genomic: GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccacc ... gtttgtatagATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
EST: gi|32272496|gb|CD721655.1|CD721655
EST:     GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATG                         ATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
genomic: GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccacc ... gtttgtatagATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
EST: gi|30326194|gb|CD009456.1|CD009456
EST:     GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATG                         ATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
genomic: GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccacc ... gtttgtatagATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
EST: gi|32248851|gb|CD714670.1|CD714670
EST:     GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATG                         ATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
genomic: GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccacc ... gtttgtatagATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
EST: gi|32249201|gb|CD715020.1|CD715020
EST:     GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATG                         ATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA
genomic: GGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccacc ... gtttgtatagATATACAGTCAAAATTGAAAAGGATTGAAGAAGACCCTGAAGGTTCAGGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGCTTTAAAAACAGATCTCAAAGGACGGACTCAACAAAAAAAACAATTGGTTAAAGAAAATTTTGATTGCTTTGTCTCATGCAAAACTACCATAGATGgtatgccaccttgtcatcttgcatagatttctggcactcttattgattgctgcctgaaagcttgagccttttgggttgacattttcttacaccattgctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA