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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttactcatgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactttcacttgttaaggctgttttgacatctcatgt...

Basic information

species Vitis vinifera
transcript Vv02s0012g02660.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g32800.1 (Oryza sativa), 5'ss of exon 2
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttactcatgtgcttta-attatttcaaaaaatt--caagtcat--ttataatgattcacattatactttcac-ttgttaaggctgttt----tgacatctcatgt---------------------
|||  ||||  || | ||||||||||| ||||||||||| | ||||||||| |||||||| |||||  | |||||||| ||||||||  |||| ||||||||||  ||   |||    ||| || |    |||||| |  ||  || |  |   | |  ||    | |||    ||   |||  |   |||||    ||| |  | |                        
GTACCATAAGGCTTGCCAAGAATTCGCTGAATTCTATAAGAATGCTCTTCTTTATCTGGCCTACACTACTGTGGAGTCGCTCTCTGAGTCATTCAAGCTGgtat--taacaatgccaattacataacagaaaaaaaatagcatttcctcctctcattagttagtttaataacaacatactgtgcatattgtttgtattgataatttaccctttgacactgtcatgtgtcag

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM5G868757_T04 (Zea mays), 5'ss of exon 3
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttactcatgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactttcacttgttaaggctgttttgacatctcatgt
 ||  | ||  |  | |||||||| ||||| |||||||| | ||||||||| |||||||| |||||| | ||||||||||| |||||  |||| ||||| |||||||  ||||   | | | | |  |   ||   | ||   |  |  | |   | | ||  |  | | | || || |   | || |  | | |||   
ATACCACAAGGCCTGCCAAGAATTTGCAGAGTTCTATAAGAATGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtt--tcat---catcagtaacatttgaactctaaatagaacttcagt---ttaaatgttcatctgatttattgactgttttctatcttttcag--

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G083076_T03 (Zea mays), 5'ss of exon 3
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttac-tcatgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactttcacttgttaaggctgttttgacatctcatgt
 ||  | || ||  | |||||||| ||||| |||||||| |  |||||||| |||||||| |||||| | ||||||||||| |||||  |||| ||||| ||||||| |  |||       | ||       ||||   || |    | |||   ||||  | |    || |||  |  |   | | ||| ||        
ATACCACAAGTCATGCCAAGAATTTGCAGAGTTCTATAAGAACGCTCTTCTCTATCTGGCCTACACAACTGTGGAGTCTCTATCTGAGTCATTCAAGCTAgtatgtttcaccatcaataacatttgaactgtaaaacaaaacttcagtttaaaagttcatctgacttattgactattcta---tatcttgtcag-------

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 2
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgtta-ctcatgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactt--tcacttgttaaggctgttttgacatctcatgt
|| | ||||  | ||||||||||| || || ||||| |||||||| ||||| ||| ||||||||||||||||||| |||||||||||  |||| |||||||||||| | |  |  ||  |||| | |||      |||   | | ||| |  ||  ||| || ||   |  | ||||||  |   |  | |||  | |  |||
GTTTCATAAGACACGTCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCTGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattgttgccttttttgttgtctcaaatcatggctatttacttgt--actttactctgat-tatggtgt

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G34310.1 (Glycine max), 5'ss of exon 2
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgtta-ctcatgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactttcacttgttaaggctgtttt---gacatctcatgt
|| | ||||  |  | |||||||| || || ||||| |||||||| ||||| ||| ||||||||||||||||||| |||||||| ||  |||| |||||||||||| | |  |  ||  |||| | |||      |||     | | | || ||  ||| || ||   |  | ||  | |  ||||  |   |  ||  |||  
GTTTCATAAGACATGCCAAGAATTTGCTGAGTTCTACAAAAGTGCCCTTCTCTATTTGGCATACACATCAGTGGAATCTCTCTCAGATTCATTCAAGCTGgtatgtcatcagaattgtcttaaatgtttttgttgattggttccttctttattgtctcaaatcatggct--atttacttacactgtactctggttatggcat--

upper sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT4G19006.1 (Arabidopsis thaliana), 5'ss of exon 2
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttactc-atgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactttcacttgttaaggct--gttttgacatctcatgt-------------------------------------------------------------------------------------------
|||  |||||   |||||||| ||| | || |||||||||| ||||||||| || || || || || || ||||| || ||||| ||| |||||||||||||| ||  |||    || | |||| |||   | |   |  |   | |  | | | | |  | |   |||| |    ||  || |  || ||  ||    |||                                                                                            
GTACCATAAAGTCCGTCAAGAGTTCTCTGAGTTCTATAAAAATGCTCTTCTTTACCTCGCTTATACGTCTGTGGACTCACTCTCGGAATCATTTAAGCTGgtacgtccctctgaatgttctaatcattcatatatgatatatgtagtcgttacgttaccaaatggtcttttagcaattttggataagtattagcactctatgaaaggaaacttacagtgaaaaatgctttatctctgtaaattgctttgtgttccaatcaaaatgttaatatcatatactttcgtttctttcag

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|349823515|gb|FQ414925.1|FQ414925
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|351014718|gb|FQ437918.1|FQ437918
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|110711237|gb|EE087522.1|EE087522
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGA-AATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|110712189|gb|EE089526.1|EE089526
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAAGATA-TATCTA
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGA-GATAATATCTA
EST: gi|110719329|gb|EE097178.1|EE097178
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTC
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTC
EST: gi|110713457|gb|EE089396.1|EE089396
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGGAACATTTAAGCTG                         GGATT-GGCATTTGATTTATCGCTTTCCGCGCCGCTGGGAGATAA-ATCCT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagG-ATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATC-T
EST: gi|110712232|gb|EE089617.1|EE089617
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|351030871|gb|FQ438907.1|FQ438907
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|110713832|gb|EE090100.1|EE090100
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGA-AATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|110702107|gb|EE080439.1|EE080439
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|110711790|gb|EE088671.1|EE088671
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|351027874|gb|FQ448444.1|FQ448444
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|110729815|gb|EE106179.1|EE106179
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATA-TATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|110711621|gb|EE088310.1|EE088310
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATA-TATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|351043427|gb|FQ451479.1|FQ451479
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|110712204|gb|EE089557.1|EE089557
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGA-AATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|110711432|gb|EE087905.1|EE087905
EST:     ATAACTGGCATACACATCCA-TGGAGTCTCTCCCTGAAACATTTAAGCTG                         GATTTGGCATTTGATT-ATTCGCTTTCTGCGCTGCT
genomic: ATATCTGGCATACACATC-AGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTAT-CGCTTTCTGCGCTGCT
EST: gi|349825445|gb|FQ419362.1|FQ419362
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|349825607|gb|FQ421706.1|FQ421706
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTTGGCATTTGATTTTATCGCTTTCTGCGCTGCTGGGAGA-AATATCT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTT-GGCATTTGATTT-ATCGCTTTCTGCGCTGCTGGGAGATAATATCT
EST: gi|351019814|gb|FQ439631.1|FQ439631
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
EST: gi|161718279|gb|FC066030.1|FC066030
EST:     TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTG                         GATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT
genomic: TATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttact ... gatattttagGATTTGGCATTTGATTTATCGCTTTCTGCGCTGCTGGGAGATAATATCTAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATTATAAATCTCGTCAAGAATTCGCAGAATTCTATAAAAGTGCTCTTCTATATCTGGCATACACATCAGTGGAGTCTCTCTCTGAAACATTTAAGCTGgtatgttactcatgtgctttaattatttcaaaaaattcaagtcatttataatgattcacattatactttcacttgttaaggctgttttgacatctcatgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat