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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtcctagataatgcatttatgtcaaacgtcttaattggttgattagtttctcagttagtttacttatttcttctttcag

Basic information

species Vitis vinifera
transcript Vv16s0039g02240.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os02g47110.3 (Oryza sativa), 5'ss of exon 3
----------------------------------------ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtcctagat-aatgcatttatgtcaaacgtcttaattggttgattagtttctcagttagtttacttatttcttctttcag
                                        |||||||| |||||||| |||||| ||||||| || |||||||| || || ||||||||||||   |   |||  | ||   ||     ||| |   |||   | |||  | |   |     || ||    || || |         
CTTATTCCTATATGTTATTTTTGCACGTTCTGATTTGCAGATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAGgtttaataagctattttaagttatgctcatcagatagcttgccttgttagtgaagctaaggtttggtggctttgttgcag-------

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os02g47110.1 (Oryza sativa), 5'ss of exon 4
ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtcctagat-aatgcatttatgtcaaacgtcttaattggttgattagtttctcagttagtttacttatttcttctttcag
|||||||| |||||||| |||||| ||||||| || |||||||| || || ||||||||||||   |   |||  | ||   ||     ||| |   |||   | |||  | |   |     || ||    || || |         
ATCTATGTAGTTGATTCATTGGATAGAGAGAGAATCGGAAAAGCGAAAGCGGAGTTTCAGgtttaataagctattttaagttatgctcatcagatagcttgccttgttagtgaagctaaggtttggtggctttgttgcag-------

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G106795_T02 (Zea mays), 5'ss of exon 4
ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgt-tgggtgtcctagataatgcatttatgtcaaacgtcttaattggtt-gattagtttctcagttagtttacttatttcttctttcag------------
|||||||| |||||||| |||||||| ||||||||||||||||| || || || |||||||| ||    |  |   | |    |   | ||       ||||||  ||  |  |  ||   | | |       | || |       |             
ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagattgtcagtcagagctgcttatcgctgaatttaatttcttcaaccaagttaatattgaacaattctgttgcaggcaataatcaatgatcctt

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G106795_T03 (Zea mays), 5'ss of exon 4
ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgt-tgggtgtcctagataatgcatttatgtcaaacgtcttaattggttgattagtttctcagttagt-ttacttatttcttctttcag
|||||||| |||||||| |||||||| ||||||||||||||||| || || || |||||||| ||    |  |   | |    |   | ||       ||||||  || |       |  ||||| | ||    | ||||  || |||
ATCTATGTAGTTGATTCATTGGATCGGGAGAGGATTGGAAAAGCTAAAGCTGAATTTCAGgtctgtagattgtcagtcagagctgcttatcgctgaatttaatttcttcaa------ccaagttaatattgaacaattctg-ttgcag

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G113995_T01 (Zea mays), 5'ss of exon 4
ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtcctagataatgcatttatgtcaaacgtcttaattggttgattagtttc--tcagttagtttacttatt-----tcttctttcag
||||| || |||||||| |||||||| ||||| ||||||||||| || || || ||||||||  |          |||    |    ||||    |  |||||| |  ||| ||||   |||   || ||| |         |  | || |||
ATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctg----------taaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcag

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G113995_T03 (Zea mays), 5'ss of exon 3
----------------------------------------ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtcctagataatgcatttatgtcaaacgtcttaattggttgattagttt--ctcagttagtttacttat-----ttcttctttcag
                                        ||||| || |||||||| |||||||| ||||| ||||||||||| || || || ||||||||  |          |||    |    ||||    |  |||||| |  ||| ||||   |||   || ||| |         |  | || |||
GTTATACATGGTAACTCTTTATGCACGTTTCGAGTTGTAGATCTACGTAGTTGATTCGTTGGATCGGGAGAGAATTGGAAAAGCCAAAGCTGAATTTCAGgtctg----------taaattgtcacagtcagggcttctaattgctgaattcgttttcttcaaccaggttaatatcgagcaattctgttgcag

upper sequence: Vv16s0039g02240.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G17060.1 (Arabidopsis thaliana), 5'ss of exon 4
ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtcctagataatgcatttatgtcaaacgtcttaattggttgattagtttctcagttagtttacttatttcttctttcag
|| || || || |||||||| |||||||||||||| || |||||||||  ||| ||||||||    |  |  |||      | ||     | || | ||  |    |   | | || |   |||   | ||      ||    |||
ATATACGTGGTGGATTCCTTAGATCGAGAGAGGATCGGGAAAGCAAAGCAAGAATTTCAGgtataatacctcaga------acttgcaaaagac-ttttcgtaaactctctggattataccttaccctgctctcggattgccacag

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|26264563|gb|CA815626.1|CA815626
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|30296696|gb|CB973490.1|CB973490
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71879757|gb|DT028812.1|DT028812
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71880432|gb|DT029487.1|DT029487
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71880733|gb|DT029788.1|DT029788
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71878380|gb|DT027435.1|DT027435
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71880637|gb|DT029692.1|DT029692
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|30296765|gb|CB973559.1|CB973559
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71877999|gb|DT027054.1|DT027054
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|110430069|gb|EC996597.1|EC996597
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|110716367|gb|EE091287.1|EE091287
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71880723|gb|DT029778.1|DT029778
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|33409512|gb|CF215139.1|CF215139
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|110729888|gb|EE106340.1|EE106340
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71878000|gb|DT027055.1|DT027055
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71879446|gb|DT028501.1|DT028501
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|71879383|gb|DT028438.1|DT028438
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|351036486|gb|FQ457199.1|FQ457199
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
EST: gi|110375930|gb|EC940960.1|EC940960
EST:     TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAG                         GCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA
genomic: TTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtc ... cttctttcagGCCATCATTCGAGATCCATTTATGCTGAACAGCGTCATCTTGATTTTTGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCTATGTTGTTGATTCCTTGGATCGAGAGAGGATTGGAAAAGCAAAGGCAGAGTTTCAGgttgggtgtcctagataatgcatttatgtcaaacgtcttaattggttgattagtttctcagttagtttacttatttcttctttcag

- - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - GCAAAG