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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttcatcacatgctgaagttcatgttttaaacaataggatcaaaagtgcctttcaactttcaagaatttgtttcttttctggtagaaaatggtgt...

Basic information

species Vitis vinifera
transcript Vv00s0220g00030.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G058252_T02 (Zea mays), 5'ss of exon 4
CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttcatcacatgctg-----aagttcatgtttta-aacaata----ggatcaaaagtgcctttca-actttcaagaatttgtttcttttctggtagaaaatggtgt
|| ||||||| ||| || ||||||||||| || ||| |||||||||| ||||||||| ||||||||||   || ||      ||      ||| | || |     |||  |     | |  ||| ||   | | | ||||  || |  |||  |   |  ||  |           
CTTGCCAACACTGAGGAGTACATTGATGGTCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAGgtaatgtttattgttcccttctttcaagcttatatcaagtaacgttgttttgtaataaaggtagatataatacttggaaaagcttgcatacatcgtgtca-----------

upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G168252_T01 (Zea mays), 5'ss of exon 4
CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagc---tttcatcacatgctga--agttcatgttttaaacaataggatcaaaagtgcctttcaactttcaa--gaatttgtttcttttctggtagaaaatggtgt
|| ||||| | ||| || ||||||||||| || ||| |||||||||| ||||||||| ||||||||||     | |  |  | | ||    || | ||||  |  |     |  | | || |   | |  |  |  ||  |      | |   | ||| |     |      
CTTGCCAATACTGAGGAGTACATTGATGGGCAATTCTCTGGAAACCTGGGAGAGATTCTGATCAGgtaatgtttcttgttcctttctttctagcttatgtcatgtagtgctgttttataa-taaatctagatataaaacggggaacatcttcatcctgctgcccta------

upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA20G21250.1 (Glycine max), 5'ss of exon 4
CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttc--atcacatgctgaagttcatgtt--ttaaacaataggatcaaaagtgcctttcaactttcaagaatttgtttcttttctggtagaaaatggtgt
|||||||||| |||||| |||||||| |||||||| ||||||||  | ||||||||||| ||||||||  || |  ||||  |  |  | ||  |  |  |       || | |   |   | | |   |  ||  | ||| |  | |    ||   ||  |       
CTGGCCAACACTGAAGAGTACATTGAGGGACAGTTTACTGGAAATTTGGGAGAGATTTTAATCAGgtaaattccacatcaactattctatttgttagtagtggttttttatgttttgataaggcataggaggttttaaaatctaatccaagcctttaagtcagaa----

upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G14285.1 (Arabidopsis thaliana), 5'ss of exon 4
CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttcatcacatgctgaagttcatgttttaaacaataggatcaaaagtgcctttcaac--------tttcaagaatt-----tgtttcttttctggtagaaaatggtgt----------------------------------------------------------
|| |  ||||  || |||||||||||||| || || || |||||||||||||||||||||||||||||       ||  |        |  | |||||  ||  |   |  |   ||| |||| |||        | ||  ||| |     |  ||  |||    ||  || |||  |                                                          
CTAGGAAACACCGAGGAATACATTGATGGGCAATTGACAGGAAACCTTGGAGAGATTTTGATCAGgtaaaacctttcttactgcattctgaaagttttttactgttacagtatttgtgtctttgaacgaaatagttctcgtgaagtgacattacttgatttaacttaagaattggacttacttggccattagatacacattcatcatcttgtctctgttacttggtgtgctcacag

upper sequence: Vv00s0220g00030.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT4G30220.2 (Arabidopsis thaliana), 5'ss of exon 4
CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttcatcacatgctgaagttcatgt-tttaaacaataggatcaaaagtgcctttcaactttcaagaatt-tgtttcttttctggtagaaaatggtgt
||||  ||||  |||||||| ||||||||||| || || || |||||||||||||| |||||||||||    | || || |  |    |  |  | |||   |  |  |||  |   |   |||| |  |  | || |     |    |     ||    ||     
CTGGGAAACACCGAAGAATATATTGATGGACAATTGACAGGGAACCTTGGAGAGATCTTGATCAGgtaataat-attacttcattgtctctacttattttctccttgtgattcagtttatgtttccaactatatgattcacagtgaagtgtcattacttgataaaa-

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|27585892|gb|CB008587.1|CB008587
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|34319677|gb|CF372431.1|CF372431
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|27580636|gb|CB003331.1|CB003331
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|32246334|gb|CD712153.1|CD712153
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|110730178|gb|EE106958.1|EE106958
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|110383296|gb|EC947661.1|EC947661
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|110419842|gb|EC986096.1|EC986096
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|77578909|gb|DV218261.1|DV218261
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|110426527|gb|EC992940.1|EC992940
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|110686902|gb|EE063845.1|EE063845
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|110380052|gb|EC945289.1|EC945289
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|27579125|gb|CB001820.1|CB001820
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|110731217|gb|EE109189.1|EE109189
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|27580948|gb|CB003643.1|CB003643
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|30125982|gb|CB911321.1|CB911321
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|34549721|gb|CF517953.1|CF517953
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|34544804|gb|CF513036.1|CF513036
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|27586320|gb|CB009015.1|CB009015
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
EST: gi|34544882|gb|CF513114.1|CF513114
EST:     GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAG                         ATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA
genomic: GAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttca ... tcttctacagATGTAACAATGTTCTCTATCTTCGTGGGGTACCGGAGGATGAAGAAATAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGCCAACAGTGAAGAATACATTGATGGACAGTTCACTGGAAACCTTGGAGAGATTTTGATCAGgtagctttcatcacatgctgaagttcatgttttaaacaataggatcaaaagtgcctttcaactttcaagaatttgtttcttttctggtagaaaatggtgt

- - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatagga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tagaaaa