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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttgaccttctataggtcttgttttgttttgttgtgttgtttggcctttctgtttttcttcctctttctttctttcttattcaagtgagaaatctggta...

Basic information

species Vitis vinifera
transcript Vv09s0018g02130.t01
intron # 26
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: LOC_Os02g08010.1 (Oryza sativa), 5'ss of exon 8
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttgaccttctatagg--tcttgttttgttttgttgtgttgtttggcctttctgtttttcttcc---------------tctttctttctttcttattca-agtgagaaatctggta--------------------
||| | ||| ||||||||||| ||  |||| ||    |||   ||  | |||||||| || || |||||||| || ||||||||||||||| | ||||||||     | |   | ||  | ||||||||      |     | |   | |    |||||  |||                ||  || | | |  | || || | |   || | || |                     
TCCAAGTGACAAACTTCTCCTAGTAAAAGCACTGAAAAAGAAAGGCAATGTTGTTGCTGTTACTGGAGATGGAACGAATGATGCTCCTGCATTGCATGAGgtacatacataattgggaattttgttttgaacaaataaaaggataaacataatggttttatttcaatcagatgaagacaatcgatcatgcatgttgatgcacatttctaattttgatctcttattcctcctaatttag

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GRMZM2G391042_T01 (Zea mays), 5'ss of exon 25
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttg--------accttctataggtcttgttttgttttgttgtgttgtttggcctttctgtttttcttcctctttctttctttcttattcaagtgagaaatctggta------------------------------------------------------
 || |||||||||||| | |||||  | || ||  |       ||| | |||||||| || || ||||||||||| |||||||| || ||||| |||||||||||        |   |||||   | ||   ||  ||||       |  | |  ||     |   ||| ||  ||| |  | | | ||| ||   || |   |   |                                                      
ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCACGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggactgtagtctctatgaatttttaattactttgaaac-cagcctcgttttggacatgaactttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtacttgagaaactctgaaacttgcag

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GRMZM2G140328_T03 (Zea mays), 5'ss of exon 25
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttg---------accttctataggtcttgttttgttttgttgtgttgtttggcct-ttctgttttt---cttcctctttctttctttcttattcaagtgagaaatctggta------------------------------------------------------
 || |||||||||||| | |||||  | || ||  |       ||| | |||||||| || || ||||||||||| |||||||| || ||||| |||||||||||         |    |||||    || |  ||||||  | ||      | |   || |     |   |||||   ||| |  | | | ||| |    || |   |   |                                                      
ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCATGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggactactagtccctataaaatttctaatgttttactatgaaacgagcctcattttaaacatgaacttccaagttcctaatatgtaatttacacaagcatctttccacagatgttcaagaagcatctttcggtagtagttaatgaactctgaaacttgcag

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GRMZM2G138195_T01 (Zea mays), 5'ss of exon 1
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttg--------accttctataggtcttgttttgttttgttgtgttgtttggcctttctgtttttcttcctctttctttctttcttattcaagtgagaaatctggta------------------------------------------------------
 || |||||||||||| | |||||  | || ||  |       ||| | |||||||| || || ||||||||||| |||||||| || ||||| |||||||||||        |   |||||   | ||   ||  ||||         | ||  |     |    ||| ||  ||| |  | | | ||| ||   || |   |   |                                                      
ACCAAATGATAAACTTTTACTTGTTAAGGCACTGAGGGCAAGAGGTCACGTTGTTGCTGTTACTGGAGATGGCACAAATGATGCCCCAGCACTGCATGAGgtttgtggactgtagtctctatgaatttttaattactttgaaaccagcatcggtttggacatgaa-ctttctagttcctaatatgtaatttaaacaagcatctttccatagatgttcaagaaacatcttttgttagtactcgacaaactctgaaacttgcag

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GLYMA13G44990.1 (Glycine max), 5'ss of exon 26
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttgaccttctataggtcttgttttgttttgttgtgttgtttggcctttctgtttttcttcctctttctttctttcttattcaagtgagaaatctggta--
||||| ||| || ||  |  | |||||||| ||||| |  | |||||| ||||||||||| |||||||||||||| |||||||||||||||||||||||||| ||    | | | |  | |||   | | |   |   ||      ||||    ||||  | |  ||| ||  || |||  | |||         ||| |  
TCCTACTGACAAGCTGTTGATCGTGCAAGCACTACGTACAGGTGGTGAAGTTGTTGCCGTCACAGGAGATGGCACCAATGATGCTCCTGCACTTCATGAGgtctgtatatttcttg--catgtacaggtcttgggccctgaaaatactttgaagtttttcttcgtttttttagttactttcttaagaatactgcatggaaat

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GLYMA15G00340.1 (Glycine max), 5'ss of exon 26
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttg-accttctataggtcttgttttgttttgttgtgttgtttggcctttctgtttttcttcctctttctttctttcttattcaagtgagaaatctggta
||||| ||| || ||  | || |||||||| ||||| |  | |||||| |||||||| || |||||||||||||| |||||||||||||||||||||||||| || |  ||   | | | | |    || ||   |  |       | ||   ||||||  | || ||| ||  ||||||    |||         |||  
TCCTACTGACAAGCTGTTGCTCGTGCAAGCACTACGTACAGGTGGTGAAGTTGTTGCTGTCACAGGAGATGGCACCAATGATGCTCCTGCACTTCATGAGgtctgtatatttcttggatgtagagaggtctttaggcctgaaaatactttgaagttttttcttcttttttttagtttctttcataagaatactgcatgga-

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GLYMA08G23760.1 (Glycine max), 5'ss of exon 27
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttgaccttctataggt-cttgttttgttttgttgtgttgtttggcctttctgtttttcttcctctttctttctttcttattcaagtgagaa-atctggta
||||||||| || ||| | ||||||||||| ||||| || |  || || |||||||| || |||||||||||||| |||||||||||||| || |||||||| || | |||| |   | | |  |||    ||||| |   | ||   |  ||      |||    | || |    | ||  | |||   ||| | |   ||
TCCTAATGACAAGCTTTTGCTTGTGCAAGCTCTACGTAAAGGAGGGGAAGTTGTTGCGGTCACAGGAGATGGCACCAATGATGCTCCTGCCCTACATGAGgtctgtcattctttgaatgcatccttttgactgttgagaaatatg--ttagctacaaaacttttcatctcctgaaattttgcttaagaatgaacagcatata

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: GLYMA07G00630.2 (Glycine max), 5'ss of exon 24
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttgacct--tctataggt-cttgttttgttttgttgtgt--tgtttggcctttctgtttttcttcctctttctttctttcttattcaagtgagaaatctggta
||||||||| || ||| | ||||||||||| ||||| || |  || || |||||||| || |||||||| ||||| |||||||||||||| || |||||||| || |||  ||| | | | | |  |||    ||||| |   |   |   ||       ||| |  ||| |    |||| |||||  | |     |||      
TCCTAATGACAAGCTTTTGCTTGTGCAAGCTCTACGTAAAGGAGGGGAAGTTGTTGCGGTCACAGGAGACGGCACCAATGATGCTCCTGCCCTACATGAGgtctgtcctattctttggatgcatccttttgactgttgagaaataaattagctacaaaactttttatctcctgaaatcttgcttatgaatgaacagaata-----

upper sequence: Vv09s0018g02130.t01 (Vitis vinifera), 5'ss of exon 26
lower sequence: AT3G21180.1 (Arabidopsis thaliana), 5'ss of exon 24
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtt---tgacc-ttctataggtcttgttttgttttgttgtgttgtttggcctttctgt-ttttcttcctctttctttctttcttattcaagtgagaaatctggta
|||||| || || ||  | ||||| ||||| ||||| ||   ||| || |||||||| || || || ||||| ||||||||||||||||| || |||||||||   | ||  ||||| ||||  ||| || |      ||||||| || | | ||    | |  ||  |||||  ||  ||   | |  ||              
TCCTAACGACAAGCTCTTACTTGTTCAAGCACTACGGAAAAATGGAGATGTTGTTGCAGTCACTGGTGATGGTACTAATGATGCTCCTGCCCTCCATGAGgttctctaacaattctacaggttatgtattat------gtgttgtgtgtcatctccaaatctgatttttcttttgttgctttggactatag--------------

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|71860621|gb|DT009676.1|DT009676
EST:     TTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAG                         GCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAA
genomic: TTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttgacctt ... tctattgtagGCAGATATAGGTCTCTCTATGGGCATTCAAGGAACTGAAGTTGCAAAAGAA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTAATGATAAACTTCTCCTTGTGCAAGCGCTACGCAAGGCTGGTGAGGTTGTTGCCGTAACAGGAGATGGCACTAATGATGCTCCTGCACTTCATGAGgtttgaccttctataggtcttgttttgttttgttgtgttgtttggcctttctgtttttcttcctctttctttctttcttattcaagtgagaaatctggta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttcctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagaaa