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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtcagatttttgtctggatat...

Basic information

species Vitis vinifera
transcript Vv04s0008g01000.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g01000.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA04G05580.1 (Glycine max), 5'ss of exon 4
TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtc---agatttttgtctggatat---
 ||||||||| |||||||||||||| | ||  ||||| |||| | ||||||||| || ||||| |||||||| ||||| || |||||||||||||||||||||||  | ||    || |  |||   ||| |||  | ||||   | ||| |  |   | |    |  | || ||| ||| |   | | |  | | | |   |   
ATTTGACATGCTGCGCAGGCAATCATTGCGCTCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcatt----ttcccatgttgctctcttttatttgcttcattctattgtttgttgtgttgg--aatacgattttggcttaaaaataatatttagtgttttt

upper sequence: Vv04s0008g01000.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA06G05580.1 (Glycine max), 5'ss of exon 4
TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtcct-tcctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtc-agatttttgtctggatat---
 ||||||||| || |||| |||||  | || |||||| |||| | ||||||||| || ||||| |||||||| ||||| || ||||||||||||||||||||||| || ||| ||| ||||          |||| ||| |||   | ||| |  |         || |   |  ||  | |  || ||||| | || || |   
ATTTGACATGCTGTGCAGACAATCTTTGCGCCCTGATAACATCAGGATGTTTGTATTGGATGAGGCAGATGAGATGCTCTCTCGAGGTTTCAAGGATCAGgtcctctcattttcctatgct----gctctcttttattg-gcttcattctattgtttgtggattttggcttaaaaatactatttagttttttatttgaattttca

upper sequence: Vv04s0008g01000.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G13920.2 (Arabidopsis thaliana), 5'ss of exon 4
TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtcctt---cctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtcagatttttgtctggatat
 ||||||||||||   ||||| || |||||| ||||  |||| |||||||||||  | |||||||| ||||||||||| || || ||||||||||| |||||         |||  |  || |     |   || | ||| |   ||||      | ||||  |   |    |     | || ||||                
CTTTGACATGTTGAAGAGGCAGTCTCTTCGTGCTGACAACATCAAGATGTTTGTTCTCGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGACCAGgtatgcaaatatttctcagtgtttcaattccattctcgttata--gtttaacttgaatctcactggtttctgg----gttttttcag----------------

upper sequence: Vv04s0008g01000.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G54270.2 (Arabidopsis thaliana), 5'ss of exon 4
TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtcagatttttgtctggatat
|||||||||| |  | || ||||| || || ||||| | ||| |||||||||||  | |||||||| ||||||||||| || || |||||||||||||||||   |  | |  |||     | |  ||||      |||| |  |  ||  || |  ||     ||    | || |||| || | |   | |   |    
TTTTGACATGCTTAGAAGACAATCTCTCCGCCCTGACTGCATCAAGATGTTTGTCCTTGATGAAGCTGATGAAATGCTCTCCCGTGGTTTCAAGGATCAGgtttgttatct-tcttcaaagtttgaatctaccctctgtggttatctctgatattgact-----tggttttgtgttgttttctggtgaatttgcag----

upper sequence: Vv04s0008g01000.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G72730.1 (Arabidopsis thaliana), 5'ss of exon 4
TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtcagatttttgtctggatat
 |||||| |||| ||||| ||||| || ||| |||||   || || ||||||||  | |||||||| ||||||||||| || || |||||||||||||||||     |||      |   |  |  |  ||||  || | || | || ||  |     |  |  |||   ||| || |  |    | | |||| |     
CTTTGACTTGTTACGCAGACAATCCCTCCGTGCTGATGCAATCAAAATGTTTGTTCTTGATGAAGCTGATGAAATGCTCTCTCGTGGTTTCAAGGATCAGgtttaatcttgtttaatctcccattcacattttcttttt-ctctctgataaaatcaagt-catttgttcttataatttgatt---tctctgtcag-----

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|351016486|gb|FQ423913.1|FQ423913
EST:     TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAG                         ATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
genomic: TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctt ... catttggcagATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
EST: gi|349823870|gb|FQ415281.1|FQ415281
EST:     TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAG                         ATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
genomic: TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctt ... catttggcagATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
EST: gi|349823871|gb|FQ415282.1|FQ415282
EST:     TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAG                         ATCTATGATATTTTCCAGTTGCTGCC
genomic: TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctt ... catttggcagATCTATGATATTTTCCAGTTGCTGCC
EST: gi|351025975|gb|FQ427987.1|FQ427987
EST:     TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAG                         ATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCGGGTTGGGGTGTTC
genomic: TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctt ... catttggcagATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
EST: gi|349828337|gb|FQ416290.1|FQ416290
EST:     TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAG                         ATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
genomic: TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctt ... catttggcagATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
EST: gi|110694587|gb|EE071825.1|EE071825
EST:     TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAG                         ATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
genomic: TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctt ... catttggcagATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
EST: gi|351015540|gb|FQ447369.1|FQ447369
EST:     TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAG                         ATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC
genomic: TTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctt ... catttggcagATCTATGATATTTTCCAGTTGCTGCCATCAAAGATTCAGGTTGGGGTGTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGACATGTTGCGCAGGCAATCACTTCGTCCTGATTACATTAAGATGTTTGTGTTAGATGAAGCAGATGAAATGCTTTCACGAGGTTTCAAGGATCAGgtccttcctttgcctttgctctgtatatctttttgttgtgctgtttgctactactctctataactgtcagtatgatgttgtcagatttttgtctggatat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG