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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTGGCATCAGGTTTTGCTGAGGTTATTAAGTATGGGCTTATTAGGGATGCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaatattccattctcatcatattcttcttaaaaaaaatttgattttatgtgagattagcttatagttcaatacttaagatttgcattcagtgat...

Basic information

species Vitis vinifera
transcript Vv04s0023g03820.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G051129_T01 (Zea mays), 5'ss of exon 3
AGTTGGCATCAGGTTTTGCTGAGGTTATTAAGTATGGGCTTATTAGGGATGCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaa-----------atattccattctcatcatattcttcttaaaaaaaat-ttgattttatgtgagattagcttatagttcaatacttaagatttgcattcagtgat
|| | || |||||  |||| |||||  | ||||||||||| || ||||||||   |||||||||||||||||||||||| |||| |  |||  | |||||||| | ||            |   |   |   ||| |||| || || ||  |  | | ||   ||      | |   | |  ||   | ||||  | ||             
AGCTAGCTTCAGGCATTGCCGAGGTAGTAAAGTATGGGCTCATAAGGGATGCACCATTCTTTGAGTGGCAAGAGAAGAACATGCCGAAATTGTTAGCAAGgtattcaacttgtttctgtgtgcactgatgctatcgtatttttgttcaacgagttgtagaacctacacagcagtttataactgtattagacttgtggttc------------

upper sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G573867_T01 (Zea mays), 5'ss of exon 4
AGTTGGCATCAGGTTTTGCTGAGGTTATTAAGTATGGGCTTATTAGGGATGCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaatattccattctcatcatattcttctta-aaaaaaatttgattttatgt-gagattagcttatagttcaatact---taagatttgcattcagtgat
|| | || |||||  |||| |||||  | ||||||||||| || ||||||||   ||||||||||||||||||||| || ||||  | |||  | |||||||| | || |  | | |        || |  | | | |     |||  |     ||| || | ||| | | |||| |  |||   | ||| |||   ||      
AGCTAGCCTCAGGCATTGCCGAGGTAGTGAAGTATGGGCTCATAAGGGATGCACCATTCTTTGAGTGGCAAGAGAAAAACATGCCTGAATTGTTAGCAAGgtactcaacttgttcctgtgtgcattaatgctatcatatttttattctacgaattgtagacactagat-acagtttataactgtattagacttgtggtcct----

upper sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA01G36890.1 (Glycine max), 5'ss of exon 4
AGTTGGCATCAGGTTTTGCTGAGGTTATTAAGTATGGGCTTATTAGGGATGCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaa--------taaaatattccattctcatcatattcttcttaaaaaaaatttgattt---tatgtgagattagcttatagttcaatacttaagatttgcattcagtgat
|  ||||||||||  |||| |||||||| ||||||||||| ||||||||||| || || ||||||||||||||||| ||||||||   |||| |||||||||||        | || || |    | | || |  |  || |     ||| ||   ||    |||||    || |||   |    | ||    |   |||           
AACTGGCATCAGGGCTTGCAGAGGTTATAAAGTATGGGCTCATTAGGGATGCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTACTGGCAAGgtaaatttttaattaagtactgtgctgtaataagctaattttctgggaaagttatgttaaaatatgtacttttggctggaaaa--agtatcccaagcttgag---------

upper sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA11G08350.1 (Glycine max), 5'ss of exon 4
AGTTGGCATCAGGTTTTGCTGAGGTTATTAAGTATGGGCTTATTAGGGATGCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaatattccattctcatcatattcttct-taaaaaaaatttgattttatgtgagattagcttatagttcaatacttaagatttgcattcagtgat---
|  ||||||||||  | || |||||||| ||||||||||| ||||||||||| || || ||||||||||||||||| ||||||||   |||| |||||||||||   | | ||  |||    | || | || |  |||   || |||      |||| |  |||   |||   |   |   |   |     || |   | |   
AACTGGCATCAGGGCTAGCAGAGGTTATAAAGTATGGGCTCATTAGGGATGCAGAGTTTTTTGAGTGGCAAGAGAAAAATATGCACTTATTATTGGCAAGgtaa---atttttttattaat-taatgtgctgcaataatctaattttctgggaatgttatgttaaaatatgtatttttggctggaaaaaatatcctaagcttga

upper sequence: Vv04s0023g03820.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT5G66120.2 (Arabidopsis thaliana), 5'ss of exon 4
AGTTGGCATCAGGTTTTGCTGAGGTTATTAAGTATGGGCTTATTAGGGATGCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaatattccattctcatcatattcttcttaaaaaaaatttgattttatgtgagattagcttatagttcaatacttaa-gatttgcatt-cagtgat
|| ||||||||||  | ||||| || || ||||| |||||||| |||||||| || |||||||| ||||| |||||||| ||  |||||||  ||||||||||||   |  || ||         | | |     | |||||  ||||  | ||| |    |  || | |   || |   | |  || | |||  |||    
AGATGGCATCAGGCCTAGCTGAAGTGATCAAGTACGGGCTTATCAGGGATGCCGAGTTCTTTGAATGGCAGGAGAAGAACATTGAGGCATTGCTGGCAAGgtaattttacgttacaa-------gtgtgcccaaaacaaaaacattgagatcatgagtctatccctgaaaaaacattgtgtgataatattcatcgcag----

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|110715477|gb|EE093574.1|EE093574
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71879469|gb|DT028524.1|DT028524
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71878029|gb|DT027084.1|DT027084
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71880570|gb|DT029625.1|DT029625
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71879450|gb|DT028505.1|DT028505
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|294967283|gb|GW840158.1|GW840158
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCCAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71877779|gb|DT026834.1|DT026834
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71879745|gb|DT028800.1|DT028800
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|110700156|gb|EE077872.1|EE077872
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71878345|gb|DT027400.1|DT027400
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|351014558|gb|FQ437560.1|FQ437560
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|351034081|gb|FQ447999.1|FQ447999
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71877851|gb|DT026906.1|DT026906
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71877603|gb|DT026658.1|DT026658
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|110369125|gb|EC933271.1|EC933271
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|110360137|gb|EC922817.1|EC922817
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71890445|gb|DT039500.1|DT039500
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71880590|gb|DT029645.1|DT029645
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71880998|gb|DT030053.1|DT030053
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|110408342|gb|EC973977.1|EC973977
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71879800|gb|DT028855.1|DT028855
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
EST: gi|71880385|gb|DT029440.1|DT029440
EST:     GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAG                         GGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC
genomic: GCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaat ... tcctttgcagGGATCCAGGTGCACTGGCTTATGCTATCAAGCGATCATGTGAAAACAAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTGGCATCAGGTTTTGCTGAGGTTATTAAGTATGGGCTTATTAGGGATGCTGAATTCTTTGAGTGGCAAGAGAAGAATATGCAGGCATTAATGGCAAGgtaataaaatattccattctcatcatattcttcttaaaaaaaatttgattttatgtgagattagcttatagttcaatacttaagatttgcattcagtgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa