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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCATTTCTGTCATGTCTATGTGGACTAGAATGCAGCCAGCATATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgttctgaattcaatgtttcagtggattaattcagtattaatattgttaaaatatatatcttaaaacacttggattttctctaatgttatctt...

Basic information

species Vitis vinifera
transcript Vv01s0026g00920.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G031824_T01 (Zea mays), 5'ss of exon 5
GTCATTTCTGTCATGTCTATGTGGACTAGAATGCAGCCAGCATATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgttctgaattcaatgtttcagtggattaattcagtattaa-tattgttaaaat-atatatcttaaaac--acttggattttctctaatgttatctt
|| ||  | || ||||| |||||||||||| |||||||||  ||||||| ||| |||||||||||||| ||||| ||  | ||||  || |||||  | |  | |||   | |||  ||        | |||  |||||    |||   || || || |   || || |     |    ||     |||| |   | 
GTAATGGCAGTTATGTCAATGTGGACTAGATTGCAGCCAGTTTATGCTGCAAACATGTGGAATGAAGCCCTAAACAAACGACTTGGCACTGAGgttgtagattactg---ttaatacttattctccctcattgggtattgggcattcacaagattattttgattcaagctagtgtaaggttaaaacaatgctgaat-

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA02G03160.1 (Glycine max), 5'ss of exon 5
GTCATTTCTGTCATGTCTATGTGGACTAGAATGCAGCCAGCATATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgttctgaattcaatgtttcagtggat-taattcagtattaatattgttaaaatatatatcttaaaacacttggattttctctaat-gttatctt---
|| ||||||||||||||||||||||| |||||||||||||| ||||||| ||| |||||||||||||| || || ||| || | | ||| |||||||     |  |||  |   |  | || | ||  |  ||   |    |||||||   |  || | | |||       ||| |    | | |  || |       
GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCACTGAACAAGCGGTTAGGGACTGAGgtat----atcttgatgttggt-ctacaatagacatgcttacatgaatatattgtcctatgatttcttttactttttatgggtaacatttcacagtcaagccaag

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA01G04400.1 (Glycine max), 5'ss of exon 5
GTCATTTCTGTCATGTCTATGTGGACTAGAATGCAGCCAGCATATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgttctgaattcaatgtttcagtggat-taattcagtattaatattgttaaaatatatatcttaaaacacttggattttctctaatg-ttatctt---
|| ||||||||||||||||||||||| |||||||||||||| ||||||| ||| |||||||||||||| || || ||| || | | ||| |||||||     |  |||  |   |  | |||| ||| |  ||   |    ||| |||   |  |  | | |||       ||  |  | | | | | | |       
GTAATTTCTGTCATGTCTATGTGGACAAGAATGCAGCCAGCTTATGCTGCAAACATGTGGAATGAAGCGCTGAACAAGCGGTTAGGGACTGAGgtat----atcttgatgttggt-ctacagtagatgtgcttacatgaatatactgtcctatgacttcttttactctttatgtgtaatatttcacggtcaaaacaag

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA18G17350.1 (Glycine max), 5'ss of exon 4
-GTCATTTCTGTCATGTCTATGTGGACTAGAATGCAGCCAGCATATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgta--tttgtgttctgaattcaatgtttcagtggattaattcagtattaatattgttaaaatatatatcttaaaacacttggattttctctaatgttatctt-
 || ||||||||||||||||||||||||||| |||||||||| ||| | | ||||||||||||||||||  | |||||| || | | ||| ||||||  | |  |  |||  || ||  |||| ||||    | | |||||  || |  |  |||| |||    ||     |||   || | |    | ||  ||  
GGTAATTTCTGTCATGTCTATGTGGACTAGATTGCAGCCAGCTTATTCGGCAAATATGTGGAATGAAGCATTGAATAAGCGGTTAGGGACTGAggtaagtcttggcactggtttaaacatttctgtgggaagaat-agtatccatttgctctaaatgtat---ctagtgttctttccttcttttcctttttccctaa

upper sequence: Vv01s0026g00920.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT1G70160.1 (Arabidopsis thaliana), 5'ss of exon 5
GTCATTTCTGTCATGTCTATGTGGACTAGAATGCAGCCAGCATATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgttctgaattcaatgtttcagtggattaattcagtattaatattgttaaaatatatatcttaaaacacttggattttctctaatgttatctt
|| |||||||||||||||||||||||| |  | || || ||||||||||  ||||||||||| || || || |||||  | || |  || ||||||       ||    ||| ||  |||    |||||   | |||      |   ||| |  | |   ||  |                            
GTTATTTCTGTCATGTCTATGTGGACTCGTGTACAACCTGCATATGCTGCTAATATGTGGAACGAGGCACTTAATAAACGACTCGGTACTGAGgtac--aatatccagtttctattgttcttcagattaggac-gtacaggc-taactaataagtttccgttgtacag-------------------------

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|110721434|gb|EE098424.1|EE098424
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTGAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|27579647|gb|CB002342.1|CB002342
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|22008704|gb|BQ793738.1|BQ793738
EST:     GGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: GGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|27579589|gb|CB002284.1|CB002284
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|110425597|gb|EC991986.1|EC991986
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|32245156|gb|CD710975.1|CD710975
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|18458423|gb|BM436701.1|BM436701
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGC
EST: gi|110419714|gb|EC985963.1|EC985963
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|30322099|gb|CD005361.1|CD005361
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTANATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGANACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|27578697|gb|CB001392.1|CB001392
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|27581381|gb|CB004076.1|CB004076
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|30322426|gb|CD005688.1|CD005688
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTG
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTG
EST: gi|34545798|gb|CF514030.1|CF514030
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|34545878|gb|CF514110.1|CF514110
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|30323405|gb|CD006667.1|CD006667
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
EST: gi|28970697|gb|CB349730.1|CB349730
EST:     ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAG                         GATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC
genomic: ATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgt ... tttacttcagGATTTGGACTTGCTTGGAATTCTTGCTGAAACAGAAAAGCGTGGCTTGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCATTTCTGTCATGTCTATGTGGACTAGAATGCAGCCAGCATATGCTGAAAATATGTGGAATGAAGCTCTAAATAAGAGGCTTGAGACCGAGgtatttgtgttctgaattcaatgtttcagtggattaattcagtattaatattgttaaaatatatatcttaaaacacttggattttctctaatgttatctt

- - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaca