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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcattactatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag

Basic information

species Vitis vinifera
transcript Vv01s0127g00430.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00430.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: LOC_Os05g08810.1 (Oryza sativa), 5'ss of exon 15
ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcattactatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag
| |||||||| |  || ||| | ||   |||||| ||||||||||||||||||||||| || |||||||||||||||||||| |||||||| |||||||||||   |   ||    |          | | |  |   |||| || | || |  | | |   |   |    | ||                                                                                                             
ACGTTGATTTCGCTTTCATTCTGGGTAAAGATCCAAAGCCATTTCCACCACCAATGAAACTATGCAAAGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgtaaactctttaactaacttggcgggatatctgcatgatttgttcctctgctaaaagccgattgctcgttttcag-------------------------------------------------------------------------------------------------------------

upper sequence: Vv01s0127g00430.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: LOC_Os08g21590.2 (Oryza sativa), 5'ss of exon 15
----ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgta--tcattactatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag
     | |    || ||    |    |   |||     |   |||    ||||||| |||||  | |||||||||||||||||||| ||||||||  | ||||||||  |  ||  | | |      |||     |||||  |||||| || |||     || |    | |  || ||| || | |     || |||                                                                                             
TCTCGTATATGCTTGGGGAACAACC-ACATCGA---TTTGCACCACCATCACCACCGATGAAATTATGCAAAGAAATGGTTGAGGCCATGGGTGGTACTGAAAGgtaaatgctttatttagttatgtatatatagttttgcacctttgctcatttcacagatatttattct-ttgcatgtgacttcc----attttag--------------------------------------------------------------------------------------------

upper sequence: Vv01s0127g00430.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G103721_T01 (Zea mays), 5'ss of exon 15
ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcattactatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag
||||||| ||||  |||||  | || ||||| || ||||||||||| ||||| |||||| | || || |||||||||||||| |||||||| |||||||||||   |||   | | | ||       |||    || ||||| | || ||||| |    |    | ||     | | |   |    ||||                                                                                              
ATGTTGACTTTGCTTTTATCCTTGGGCGAGACCCAAAGCCATTTCCGCCACCGATGAAGTTGTGTAAGGAAATGGTTGAGGCCATGGGTGGTGCAGAAAGgta--gtta--gttgaacaa------ttttgccaagtctttgcttttatgtttcagcagatggatactctcaaaaacttgcttttgtgtttcag------------------------------------------------------------------------------------------

upper sequence: Vv01s0127g00430.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA04G10090.1 (Glycine max), 5'ss of exon 15
ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcattactatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag
||||||||||||| |||||| | |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||   ||   ||  ||  |       |   || ||  |   | || | |||  |||| | || |    | | | |||   ||| ||  | |  |    ||   |       | |                                                                     
ATGTTGATTTTGGTTTTATTCTTGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAGGAAATGGTTGAGGCTATGGGTGGAGCTGAAAGgtacagttctcattagatga------ttcactttagattcaagactgtggtt--atgtgatctgta---gcttaaatt--gtgaaatagtgatttgtttctttgttccccatgcag--------------------------------------------------------------------

upper sequence: Vv01s0127g00430.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GLYMA06G10090.1 (Glycine max), 5'ss of exon 15
ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcattactatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag
||||||||||||| |||||| | || ||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||| ||||||||   ||   || |||     | |     |||        |     ||||   || |     ||      ||| ||       ||| |     | ||  ||||                                                                                
ATGTTGATTTTGGTTTTATTCTTGGGCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAGGAAATGGTTGAGGCTATGGGTGGAGCTGAAAGgtacagttctcattgga-----tgattcactttagattcaagagtggttgtgcgatctgtagcttaaattgtgaaatagtggttgatttctttgtccctatgcag-------------------------------------------------------------------------------

upper sequence: Vv01s0127g00430.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: AT1G60490.1 (Arabidopsis thaliana), 5'ss of exon 15
ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcattactatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag
| ||||||||||  |||||| | ||  |||||||||| ||||| || ||||| ||||| || |||||||||||||| || || ||||| |||||||||||||| | |||  |||  | ||       ||   |||   ||| |   |  |  ||    ||          || ||| |  |  | |||||  |       |      | |||                                                                        
ACGTTGATTTTGCTTTTATTCTCGGTAGAGATCCTAAACCATTCCCTCCACCTATGAAACTCTGCAAAGAAATGGTGGAAGCCATGGGCGGAGCAGAAAGgtacc-ttaaaatgatataa-------ttccatgaatattttgctctgagagttgcagcat---------ataagacttga--aaatgttggctactttgtattctgtgttgcag---------------------------------------------------------------------

upper sequence: Vv01s0127g00430.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: PP1S58_188V6.1 (Physcomitrella patens), 5'ss of exon 15
ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcatta--ctatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag
|| | |||||||| || || || || || ||||| ||||| |||||||| || ||||| ||||||||||||||||| || |||||||| || || ||||||| |  |    ||  |   |    | | | | |||  || ||   |   |||||  |      |     |  ||   || |   |   | ||   |    || |||   |||  |  |    ||| |      |     | |     | |  |   | | ||  |  ||  | | |          
ATATCGATTTTGGTTTCATATTGGGGCGTGATCCCAAGCCCTTTCCACCCCCTATGAAACTTTGCAAAGAAATGGTGGAAGCTATGGGCGGTGCCGAAAGgtgtattccgcctccgatggtgtcttaacgtctttctgctttaaatggcttgttcgaacgtgtcaaacgttaatattatcctgagctttcttgcta-gtaaccgcact-tttgagagatggcattctact-tgagattgtgtagt--ttctgaccacgattgcctttttgtaatgtgacag-----

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|27584745|gb|CB007440.1|CB007440
EST:     CCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAG                         CCCATACTATACCAGGTTCAAATCCTATTGTTGTGAAGCATACAATATCCT
genomic: CCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcattac ... tcttctgcagCCCATACTATACCAGGTTCAAATCCTATTGTTGTGAAGCATACAATATCCT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTTGATTTTGGATTTATTTTAGGCCGAGATCCTAAGCCATTTCCACCACCAATGAAGCTTTGCAAAGAAATGGTTGAGGCTATGGGTGGAGCAGAAAGgtatcattactatgggagaaaataaccttttttgagcctttggtcttttgttttatgtcacctttgctggatgagattccatgagatgttaacataccactgcatgattttgggaaccttattttgtggcaatgcgatattaccatgccaaatgcaaatggttcattacacttttcttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG