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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAAGGATGTCTTCAGTAAACCAGATGACATTCTAACTGCTGCGGAGAAATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagcaatcacacttgattttttttctctttgttttttgggggtgggggggcggtggggaattgtgcttatggatgctcttgagaactacaacaa...

Basic information

species Vitis vinifera
transcript Vv17s0000g05990.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os06g12220.1 (Oryza sativa), 5'ss of exon 4
GAAGAAGGATGTCTTCAGTAAACCAGATGACATTCTAACTGCTGCGGAGAAATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagcaatcacacttgattttttttctctttgttttttgggggtgggggggcggt----ggggaattgtgcttatggatgctcttgagaactacaacaa-
 |  || ||   | | |||||||| |||||  | ||| | |||||||||| ||| ||| || ||||||||||||| |||||||||||  |||| | || ||||  |  |   ||| |  | |  |  |  |   |    ||  ||   ||        ||    ||    |  |||||         | |   || |     |  
AAGAAAAGAAAACCTGAGTAAACCTGATGATGTGCTATCAGCTGCGGAGAGATATATTGAACAGAATGGACCAGAAGCATTTGAGAAACTCATCAGCAAGgtattcttgt--tcaaaactaaaatcatcacaacta---ttagggaaatgcaactctagtatatggatgttcatgctttattccatccctccaaagtgtttgagg

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA17G10730.1 (Glycine max), 5'ss of exon 4
GAAGAAGGATGTCTTCAGTAAACCAGATGACATTCTAACTGCTGCGGAGAAATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagcc-------agcaatcacacttgattttt---tttctctttgttttttgggggtgggggggcggtggggaattgtgcttatggatgctcttgagaactacaacaa
||| || || | |||  |||| | |||||| |||||||||||||| ||||| ||||| |||||||||||| |||| ||||||||||||||||| || ||||||   |       || || | || ||  || |    |||  ||||||||||             |  ||    |||  |     ||    |||||   |          
GAAAAAAGACGCCTTGGGTAAGCGAGATGATATTCTAACTGCTGCAGAGAAGTACATCCAAGAGAATGGAACAGAAGCATTTGAGAATATCATCAATAGGgtatttccatttgtagaaaacccagtttgttgtggaattttgctttgtttttgtatatccaacttgttgtact-aatactaacggtgccatctctttgcag---------

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA05G01160.1 (Glycine max), 5'ss of exon 4
GAAGAAGGATGTCTTCAGTAAACCAGATGACATTCTAACTGCTGCGGAGAAATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagcca----gcaatcacacttgattttttttctctttgttttttgggggtgggggggcggtggggaattgtgcttatggatgct-cttgagaactacaacaa
||| ||||||| |||  |||| | |||||| ||||| |||||||| ||||| ||||| |||||||||||| |||| ||||||||||||||||| || ||||||   |     |||   | |    |     ||  | |   |||||     ||      |        | ||||   ||   | ||| |        | ||    
GAAAAAGGATGCCTTGGGTAAGCGAGATGATATTCTGACTGCTGCAGAGAAGTACATCCAAGAGAATGGAACAGAAGCATTTGAGAATATCATCAATAGGgtatttctatttgcatctatagaaaacccagttgttgtggatttttgctttgtttttttgtatatccaacttgt-tgtactaacgctgccatctctttgcag---

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G33880.1 (Glycine max), 5'ss of exon 4
GAAGAAGGATGTCTTCAGTAAACCAGATGACATTCTAACTGCTGCGGAGAAATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgt-------aagccagcaatcacacttgattttttttctctttgtttt---ttgggggtgggggggcggtggggaattgtgcttatggatgc--tcttgagaactacaacaa---------------
 || |||||   ||   | || ||||| ||| |||| ||||| |||||||| |||||| ||||| ||||| | || |||||||||||| |  ||| || |||       ||  |   |   ||| ||   ||      | ||| || |   ||  |  | |        |     ||  |  || || ||     |||  | ||||                     
CAAAAAGGACTCCTCGGGCAAGCCAGAGGACGTTCTCACTGCCGCGGAGAAGTACATTGAAGAGCATGGAACTGAAGCATTTGAGAATCTGCTTAGCAAGgtgtctcctaattccatatgtacaatttggttaccaaatatttattctatcttttgttttgtttttttatcaactatgctatttttgtatctcaccttttgtactaatggtgctcatcattctgcag

upper sequence: Vv17s0000g05990.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT1G74520.1 (Arabidopsis thaliana), 5'ss of exon 4
GAAGAAGGATGTCTTCAGTAAACCAGATGACATTCTAACTGCTGCGGAGAAATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagcaatcacacttgattttttttctctttgttttttgggggtgggggggcggtggggaattgtgcttatggatgctcttgagaactacaacaa
||||| |||| ||||||| |||||||| ||  |  |||| ||||| ||||| ||||||  |||||||||||| ||||| |||||||| ||| | | | ||||| | ||    |     |  ||    |  |||||   || |    |          |         | | ||| |   |  |||||     | ||    
GAAGATGGATATCTTCAGAAAACCAGACGATGTGTTAACAGCTGCTGAGAAGTACATTGCAGAGAATGGACCTGATGCTTTTGAGAAGATCTTAAGCCGGgtatgtcatgtgttttgttctataagat--ctcttaacttctcattgacaaaaaaatgtgattcttctttacttctc--ttttcttgtatcttgcag---

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|34544790|gb|CF513022.1|CF513022
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|351016143|gb|FQ435463.1|FQ435463
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|349825153|gb|FQ415700.1|FQ415700
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|32458365|gb|CD799539.1|CD799539
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCGGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|83275253|gb|DV938404.1|DV938404
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|110696739|gb|EE073118.1|EE073118
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|349824511|gb|FQ413178.1|FQ413178
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|110696491|gb|EE072653.1|EE072653
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|71875506|gb|DT024561.1|DT024561
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|83277540|gb|DV941548.1|DV941548
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|349825152|gb|FQ415699.1|FQ415699
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|32458283|gb|CD799457.1|CD799457
EST:     TACATTCAAAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCGGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: TACATTC--AAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|351020210|gb|FQ445817.1|FQ445817
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|351018684|gb|FQ424791.1|FQ424791
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|110424630|gb|EC990997.1|EC990997
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|349829195|gb|FQ419727.1|FQ419727
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|294966237|gb|GW839460.1|GW839460
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATC-AAGTCCAGAGG
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGG
EST: gi|110412973|gb|EC978742.1|EC978742
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|349817530|gb|FQ407320.1|FQ407320
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|110702147|gb|EE080527.1|EE080527
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
EST: gi|349833130|gb|FQ416508.1|FQ416508
EST:     AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGG                         GTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA
genomic: AATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagc ... tctgatgcagGTGGATAGGGAATCCAAGTCCAGAGGTAGCAACTATGCTATTTTTTGACGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAAGGATGTCTTCAGTAAACCAGATGACATTCTAACTGCTGCGGAGAAATACATTCAAGAGAATGGACCAGATGCATTTGAGAATATCATTAACAGGgtaagccagcaatcacacttgattttttttctctttgttttttgggggtgggggggcggtggggaattgtgcttatggatgctcttgagaactacaacaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aactacaa