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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagcatacttctcattttatgttttttgtcaaattatcactttttaggtgtcaagcctaactactcaagtcttgcatttggcatag

Basic information

species Vitis vinifera
transcript Vv17s0000g01530.t01
intron # 5
splice site 5'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os07g19470.1 (Oryza sativa), 5'ss of exon 5
GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgta------tcctagcatacttct--------cattttatgtt------------ttttgtcaaattatcactttttaggtgtcaagcctaactac--tcaagtcttgcatttggcatag--------------------------------------
| |||||||| |||||||||||||| || || ||||| ||||| || || |||||||| ||||| |||||  | || ||||||||||| ||       || ||   ||| | |        ||| |||| ||            ||| ||   ||  |||  |  |  | | || |   || |    | | || |  || |  ||||                                        
GAGTGAATGCTGATGATGTTCGAGTAACAGTTGCTGCTCCTGCTGCTCGAGGGGAAGCAAACAACGAACTACTAGAGTTCATGGGCAAGgtgattttctcttatggtacctttattgggaacatgttatcttattgaattccactttcgtaggatgttcatctactttgagacatgtaaaaatgtgttaatgtttcacaataagcattctgaccctctgatgcgaacaagttcatgctatgaatcag

upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G099547_T04 (Zea mays), 5'ss of exon 5
GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcct-----agcatacttctcattttatgttttttgtcaaattatcactttttagg--tgtcaagcctaactactcaagtcttgca-tttggcatag-
| |||||||| ||||| |||||||| || |||||||| | ||| || || ||||||||||||| |||  |  | ||||| |||||||| ||    |     |       ||| || |||| | |  |||   ||| |    ||| ||   ||| ||   | |       | |  | ||   || |||   
GAGTGAATGCTGATGACGTTCGAGTAACGGTAGCTGCCCTTGCTGCTCGAGGGGAAGCTAACAGTGAGTTGCTAGAATTTATGGGCAAGgtgattttcttcaatgacactctaatcttat-tgtggtgtggtattgtgcactttgagccttgtaaaaagtgatattctgattgctccagcgtgccatcac

upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT5G63440.3 (Arabidopsis thaliana), 5'ss of exon 5
GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagca------tacttctcattttat---gttttttgtcaaattatcactttttaggtgtcaagcctaactactcaagtcttgcatttggcatag----------------------------
|||| ||||| ||||||||||| |||||||| ||||| || ||||||||||||||||||||||| || ||| ||||||||||||| |  ||| |  | ||      || |  ||| ||| |    ||| |  || | | |   | ||| |  | |      | |  | | | || ||        |                                
GGGTAAATGCTGATGATGTTCGTGTGACTGTTGCTGCACCAGCAGCCCGTGGGGAAGCTAACAACGAGCTTCTGGAATTCATGGGAAGGgtaccaaatcaatccgttattaatcactttttaagatttatactctagtcacggcgtttcatattttgtatgtgaaaa-tgaggttttttgaccaacgcgacacgacctctgtgtttttactctttcag

upper sequence: Vv17s0000g01530.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S121_20V6.1 (Physcomitrella patens), 5'ss of exon 5
GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatc--ctagcatacttctcattttatgttttttg---tcaaattatcacttt-ttaggtgtcaagcctaactactcaagtcttgcatttggcatag---
| |||||||| |||||||| || || ||||| ||||| |||||||||||||| ||||| ||||| || ||  | || | |||||| || ||| |  ||  ||||||| |||||  || |  || |   ||  |   |     | ||   |  ||    | | || |  |    | | ||   | |     
GTGTGAATGCGGATGATGTCCGGGTAACTGTGGCTGCACCTGCAGCCCGTGGTGAAGCAAACAACGAGCTGCTTGAGTACATGGGGAAGgtagcgtctcacatactt-tcattgaatttcattagaattcgtaaggtggtggtgttgtataacacatttgaataattgatggatactttactcctttgtt

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|351012338|gb|FQ430023.1|FQ430023
EST:     CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA                         GTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
genomic: CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagc ... tttggcatagGTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
EST: gi|351029663|gb|FQ427503.1|FQ427503
EST:     CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA                         GTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
genomic: CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagc ... tttggcatagGTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
EST: gi|349821093|gb|FQ404346.1|FQ404346
EST:     CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA                         GTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
genomic: CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagc ... tttggcatagGTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
EST: gi|351027269|gb|FQ444518.1|FQ444518
EST:     CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA                         GTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
genomic: CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagc ... tttggcatagGTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
EST: gi|351040562|gb|FQ438106.1|FQ438106
EST:     CTGCGGCCCGTGGGGAAGCTA-CAATGAACTTTTGGAGTTCATGGGCAAA                         GTACTGGGTCTAAGACAGAGCCAGATGACTCTTCAGAAGGGG
genomic: CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagc ... tttggcatagGTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGG
EST: gi|351027068|gb|FQ439929.1|FQ439929
EST:     CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA                         GTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
genomic: CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagc ... tttggcatagGTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
EST: gi|122691965|gb|EC985892.1|EC985892
EST:     TTTTGGAATTCATGGGCAAA                         GTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
genomic: TTTTGGAATTCATGGGCAAAgtatcctagc ... tttggcatagGTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
EST: gi|351019261|gb|FQ429421.1|FQ429421
EST:     CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA                         GTACTGGGTCTAGGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
genomic: CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagc ... tttggcatagGTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
EST: gi|122691854|gb|EC984376.1|EC984376
EST:     CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAA                         GTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC
genomic: CTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagc ... tttggcatagGTACTGGGTCTAAGACTGAGCCAGATGACTCTTCAGAGGGGGTGGAATAAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTGAATGCAGATGATGTTCGAGTGACTGTAGCTGCGCCTGCAGCCCGTGGGGAAGCTAACAATGAACTTTTGGAATTCATGGGCAAAgtatcctagcatacttctcattttatgttttttgtcaaattatcactttttaggtgtcaagcctaactactcaagtcttgcatttggcatag

- - - - - - - - - - - - - - - - - - -  CTGCAG