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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagatttatcatttgactgtcagaacaatcacattaacatgctgttttcctctaatattttccctacttgctgacatcttaaggaggatatgtgggaa...

Basic information

species Vitis vinifera
transcript Vv18s0072g00770.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 5'ss of exon 6
CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgt--aagatttatcatttgactgtcagaac--aatcacattaacatgctgttttcctctaat----attttccctacttgctgacatcttaaggaggatatgtgggaa
|||||||| |||||||||| ||| || || || || ||||||||||| || |||||||||||||| || ||||| |||||||| |||||    |||| | || |  | |    |  |  |||   |||         |        |||    |||||    || || |    |  |        | ||| |   
CTTGTGTTGAGCACTGGAAATGGAGTAAACGGTTTCACCCTTGATCCTTCCCTTGGGGAGTTCATTCTGACTCATCCAAACATCAAGgtctgtgattcaacaatgcaattcttgttcttaattggattggtcatggatcaaaacaaaatggccatttttggcacctg-tactgtactcttctttttgtgtag---

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 5'ss of exon 7
CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgt----aagatt-tatcatttgactgtcaga--acaatcacattaaca-tgctgttttcctctaatattttccctacttgctgacatcttaaggagg-atatgtgggaa--------------------
|||||  | || ||||||| |||||| ||||| || || ||||||||||| || |||||||||||| | ||||| ||| |||| |||||    ||||   | |  |||||||  | |   |  |    ||||  | || |  || | |||  || | | |  |||      |     ||  |   ||||||| |                      
CTTGTTCTGAGTACTGGAAATGGTGTCAATGGCTTCACACTTGATCCATCTCTCGGGGAGTTCATATTAACTCATCCAGACATCAAGgtttataagacaattttttttgactaactgtttatgagacaattagtagtgatacttccgtcttttaatgtac--actgatgagcgggcaaaatactcatatgtgtgttctatgcttcactctgtgcag

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM5G836250_T02 (Zea mays), 5'ss of exon 6
CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagatttatcatttgactgtcagaacaatca----cattaacatgctgttttcc------tctaatattttcc--------ctacttgctgacatcttaaggaggatatgtgggaa-------
|| ||  | ||||||||||||||||| ||||| || || || || || |||||||||||||||||||| || || ||| |||| ||||| | || |     | |  | |  |  || ||     |||  || ||  |||   |         |||| || |         | |||      | ||||      |  | | | |         
CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCACTTGGGGAGTTCATACTAACCCATCCAGACATCAAGgttatatcttctcgtagcttcttcgttcagtccttgtcatgcacgtgaagttgctcgggcaacagaatacttactgatcactgccactcatctccctctttgcattgtgacgcgcgcgcgcgcag

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA16G28310.1 (Glycine max), 5'ss of exon 8
CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagatttatcatttgactgtcagaacaatcacattaacatgctgttttcctctaatat-tttccctacttgctgacatcttaaggag---gatatgtgggaa
|||||||||||||||||| | ||||||||||| || |||||||| ||||| ||||| |||||||| || |||||||| ||||||||||||   ||  || | | |||    |   | |   || ||  |  | || ||     | ||  ||  ||   |||| | |||||| | |       |  |     
CTTGTGTTAAGCACTGGAGCAGGTGTTAATGGTTTCACCCTTGACCCATCTCTTGGTGAGTTCATCCTAACTCACCCTAACATTAAGgta---ttgctcttctcacttgtgggttactattataaat-tattcttctctctggaaatgcttgtctggctgctcagatcttatgaaactcagcacctccttg

upper sequence: Vv18s0072g00770.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: PP1S385_43V6.1 (Physcomitrella patens), 5'ss of exon 7
CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagatttatcatttgactgtcagaacaatcacatta-acatgctgttttcctctaatattttccctacttgctgacatcttaaggaggatatgtgggaa------
 | ||  | ||||| ||  |||| |||||||| || ||||| ||||| |||||||||||||||||  | || |||||  |||| ||||     ||||| || ||  ||||      || |||||     | ||  ||| |   |||   ||      || |     |   | | |  | |      ||      
TTGGTACTGAGCACAGGTGCTGGGGTTAATGGCTTCACCCTCGATCCTTCACTTGGGGAGTTCATCTTGACGCACCCTGACATCAAGg-----tttat-atctgtatgtcctt-tgatgacatttcgtgttctaattttcctaaatgcatttaagtgttcccacatttgcatgaactaaaccctacaagtccgt

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|38516542|gb|CF983717.1|CF983717
EST:     CTTGATCCCATCACTTGGGGGAGTTCATACTTACTCACCCAAACATTAAG                         ATTCCAAAGAAAGGAAAAATTTACTCCAGTAAAT
genomic: CTTGATCC-ATCACTTGGGG-AGTTCATACTTACTCACCCAAACATTAAGgtaagattta ... tcctgcacagATTCCAAAGAAAGGAAAAATTTACTC-AGTAAAT
EST: gi|32247391|gb|CD713210.1|CD713210
EST:     CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG                         ATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
genomic: CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagattta ... tcctgcacagATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
EST: gi|32271549|gb|CD720708.1|CD720708
EST:     CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG                         ATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
genomic: CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagattta ... tcctgcacagATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
EST: gi|32267853|gb|CD717012.1|CD717012
EST:     CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG                         ATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
genomic: CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagattta ... tcctgcacagATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
EST: gi|32270796|gb|CD719955.1|CD719955
EST:     CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG                         ATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
genomic: CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagattta ... tcctgcacagATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
EST: gi|110361485|gb|EC924959.1|EC924959
EST:     CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG                         ATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
genomic: CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagattta ... tcctgcacagATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
EST: gi|30324923|gb|CD008185.1|CD008185
EST:     CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG                         ATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
genomic: CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagattta ... tcctgcacagATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
EST: gi|32270921|gb|CD720080.1|CD720080
EST:     CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAG                         ATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
genomic: CCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagattta ... tcctgcacagATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
EST: gi|110371021|gb|EC934722.1|EC934722
EST:     CCTTGATCCATCACTTAGGGGAGTTCATACTTACTCACCCAAACATTAAG                         ATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT
genomic: CCTTGATCCATCACTT-GGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagattta ... tcctgcacagATTCCAAAGAAAGGAAAAATTTACTCAGTAAATGAAGGAAACACAAAGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGTGTTAAGCACTGGAACTGGTGTTAATGGATTTACCCTTGATCCATCACTTGGGGAGTTCATACTTACTCACCCAAACATTAAGgtaagatttatcatttgactgtcagaacaatcacattaacatgctgttttcctctaatattttccctacttgctgacatcttaaggaggatatgtgggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggata