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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTAAAATCAATGAGGATTTCTACAGCCGCACCTTCTCCGGTGGCCTTATCACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgtttttctctcttttggactgatttttttggttctgaattctgtttgattgccgagaaacttattcggagtggaaatttcaggcctttctttgcta...

Basic information

species Vitis vinifera
transcript Vv12s0178g00020.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0178g00020.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os03g20520.1 (Oryza sativa), 5'ss of exon 1
CCTAAAATCAATGAGGATTTCTACAGCCGCACCTTCTCCGGTGGCCTTATCACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgtttt---tctctcttttggactgatttttttggttctgaattctgttt--gattgccgagaaacttattcggagtggaaatttcaggcctttctttgcta
|| ||  | || ||||| ||||||||||||||| ||||||| ||||| |||||  |   ||||||  |||  || ||| |||||||| |||| ||| || ||| ||       | |     ||  |      | |  |      || |   ||  ||||     |          |   |||   |    |  |  |        
CCCAAGGTGAACGAGGACTTCTACAGCCGCACCCTCTCCGGCGGCCTCATCACCATCGCCTCCTCGCTCGCCATCCTCCTCCTCTTCCTCTCCGAGATCCgtacgtcacgcgccacctccctgatccctccctctccgcctcagatcccccttccgatttttcgggtttccgcctgccttgggtgtgggggcgcggtggc-----

upper sequence: Vv12s0178g00020.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: AT1G36050.2 (Arabidopsis thaliana), 5'ss of exon 1
CCTAAAATCAATGAGGATTTCTACAGCCGCACCTTCTCCGGTGGCCTTATCACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgtttttctctcttttggactgatttttttggt-tctgaattctgtttgattgccgagaaacttattcggagtggaaatttcaggcctttctttgcta
||||| |||||||| ||||| |||||||| || || ||||| ||  ||||||| ||  |||||||| | |||||| || | ||||||||||| |||||| ||| || ||     |||     |  ||||| |   | ||   || | ||||  |      |||| |  ||  || |      || ||              
CCTAAGATCAATGAAGATTTTTACAGCCGTACATTATCCGGCGGAGTTATCACTCTCCTCTCCTCCGTTGTTATGTTCCTTCTCTTCTTCTCCGAGCTCCgtacgtattaacaacttcgcttccaattttgtgaatctccatatccagtttcgtaattttgaaattcttt--gattctgttgtttag--------------
















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|349830254|gb|FQ420514.1|FQ420514
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351017588|gb|FQ435941.1|FQ435941
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351032592|gb|FQ458957.1|FQ458957
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351046419|gb|FQ453035.1|FQ453035
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351032954|gb|FQ461843.1|FQ461843
EST:     CACGCTAATTTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|110712317|gb|EE089798.1|EE089798
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|352791378|gb|FQ480957.1|FQ480957
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351037083|gb|FQ465075.1|FQ465075
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351051772|gb|FQ455186.1|FQ455186
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351038305|gb|FQ460997.1|FQ460997
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351036806|gb|FQ457519.1|FQ457519
EST:     CACGCTAATCTCCTCCATCGTTGTGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351044765|gb|FQ449019.1|FQ449019
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351025136|gb|FQ433553.1|FQ433553
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351031032|gb|FQ444859.1|FQ444859
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|110711767|gb|EE088624.1|EE088624
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|349832977|gb|FQ416355.1|FQ416355
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351053700|gb|FQ440210.1|FQ440210
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351015973|gb|FQ431928.1|FQ431928
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTGGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|30296167|gb|CB972961.1|CB972961
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTGGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|352786840|gb|FQ481215.1|FQ481215
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351053378|gb|FQ455714.1|FQ455714
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351013633|gb|FQ429774.1|FQ429774
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351014796|gb|FQ437996.1|FQ437996
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351013590|gb|FQ429731.1|FQ429731
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|161718985|gb|FC068640.1|FC068640
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|349825901|gb|FQ423196.1|FQ423196
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|110689266|gb|EE065350.1|EE065350
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351034302|gb|FQ448099.1|FQ448099
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351016879|gb|FQ424306.1|FQ424306
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|294966371|gb|GW839478.1|GW839478
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTGGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|352789786|gb|FQ478601.1|FQ478601
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|110359140|gb|EC920148.1|EC920148
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTGGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA
EST: gi|351029738|gb|FQ427578.1|FQ427578
EST:     CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCA                         GACTATACCTCCACACAGTTACAGAAACAAAACTCGTGGTCGATACTTCAA
genomic: CACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgttttt ... tctattgcagGACTATACCTCCACACAGTTACAGAAACAAAACTTGTGGTCGATACTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTAAAATCAATGAGGATTTCTACAGCCGCACCTTCTCCGGTGGCCTTATCACGCTAATCTCCTCCATCGTTATGCTCTTCCTCTTCTTCTCTGAGCTCAgtatgtttttctctcttttggactgatttttttggttctgaattctgtttgattgccgagaaacttattcggagtggaaatttcaggcctttctttgcta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gagaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtggaaa