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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACCCCACTGGTGTTGATCCAACTCTTGAGCAGTGGGAGCAGATCAGACAGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagacagacctgtgaacaaaacaggttgtgattgtgatggaatacctgaaaattcagagaataatgaaatatttcttcaatagccttttctatatgtacaatctgtttaatctagagaatctggtcattgtag

Basic information

species Vitis vinifera
transcript Vv11s0016g03720.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g03720.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os01g55540.1 (Oryza sativa), 5'ss of exon 7
TAACCCCACTGGTGTTGATCCAACTCTTGAGCAGTGGGAGCAGATCAGACAGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagacagacctg-tgaacaaaacaggttgtgattgtgatggaatacctgaaaattcagagaataatgaaatatttcttcaatagccttttctatatgtacaatctgtttaatctagagaatctggtcattgtag
 ||||| ||||| || || |||||| | || |||||||| |||||||| |||||||||||||||||||  ||| | || || ||||| || |||||||||||||   |  | | |  | || |       || |  || | | | |  |  ||| |  |  |  |||| | | |  | |  |   ||  |||    |||  || | |                               
CAACCCTACTGGAGTAGACCCAACTTTGGACCAGTGGGAACAGATCAGGCAGTTGATGAGATCAAAAGCATTGCTGCCATTCTTTGATAGCGCTTATCAGgtaaattattggcatccttaatacttatacttctagttcttaggaagca--tgaca--ttggttaatacttatacttctagttcttatactta---atacttatact-------------------------------

upper sequence: Vv11s0016g03720.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: EFJ08853 (Selaginella moellendorffii), 5'ss of exon 7
TAACCCCACTGGTGTTGATCCAACTCTTGAGCAGTGGGAGCAGATCAGACAGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagacagacctgtgaacaaaacaggttgtgattgtgatggaatacctgaaaattcagagaataatgaaatatttcttcaatagccttttctatatgtacaatctgtttaatctagagaatctggtcattgtag
||||||||| || || |||||||| |   ||||||||||    ||| | |||   ||  |    |  ||    ||||| |||||||||||||||||||||||| | |  | | |||  || |      | |   | |||  | |   | |                                                                                       
TAACCCCACCGGGGTGGATCCAACACCACAGCAGTGGGAAGGAATCCGGCAGGCAATCCGGAATAGGGGACATTTACCATTTTTTGACAGTGCTTATCAGgtatc-gctataactgaaaatacgtacagatagaactgtt-tcgttcatccag------------------------------------------------------------------------------------

upper sequence: Vv11s0016g03720.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: EFJ09053 (Selaginella moellendorffii), 5'ss of exon 7
TAACCCCACTGGTGTTGATCCAACTCTTGAGCAGTGGGAGCAGATCAGACAGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagacagacctgtgaacaaaacaggttgtgattgtgatggaatacctgaaaattcagagaataatgaaatatttcttcaatagccttttctatatgtacaatctgtttaatctagagaatctggtcattgtag
||||||||| || || |||||||| |   ||||||||||    ||| | |||   ||  |    | |||    ||||| |||||||||||||||||||||||| | |  | | | |  || |      | |   | |||  | |   | |                                                                                       
TAACCCCACCGGGGTGGATCCAACACCACAGCAGTGGGAAGGAATCCGGCAGGCAATCCGGAATAGAGGACATTTACCATTTTTTGACAGTGCTTATCAGgtatc-gctatagcggaaaatacgtacagatagaactgtt-tcgttcatccag------------------------------------------------------------------------------------

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|110707578|gb|EE084139.1|EE084139
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGAATTGCAAGTGGGTATTTTGAATGCAAATGCCC
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGG-TAGTTTGGATGCAGATGCCC
EST: gi|161719485|gb|FC066421.1|FC066421
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|110362755|gb|EC926307.1|EC926307
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTCTGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTGGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|110415342|gb|EC981242.1|EC981242
EST:     TTTGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: TTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|18458020|gb|BM436298.1|BM436298
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|351043366|gb|FQ451418.1|FQ451418
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAN                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|351041433|gb|FQ447560.1|FQ447560
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCCAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|37188125|gb|CF607476.1|CF607476
EST:     TTTTTTGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: TTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|351032771|gb|FQ462485.1|FQ462485
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAN                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|161716797|gb|FC067211.1|FC067211
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|30128545|gb|CB913884.1|CB913884
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|161719920|gb|FC069024.1|FC069024
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|110732365|gb|EE107590.1|EE107590
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|351036480|gb|FQ457193.1|FQ457193
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|349816215|gb|FQ403711.1|FQ403711
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAATCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
EST: gi|27586682|gb|CB009377.1|CB009377
EST:     AGTTGATGAGATCAAAAGGGTTGTTACCNNNNNNNGACAGTGCTTATCAG                         GGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT
genomic: AGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagaca ... gtcattgtagGGATTTGCAAGTGGTAGTTTGGATGCAGATGCCCAGTCTGTTCGAATGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACCCCACTGGTGTTGATCCAACTCTTGAGCAGTGGGAGCAGATCAGACAGTTGATGAGATCAAAAGGGTTGTTACCTTTTTTTGACAGTGCTTATCAGgtaacagacagacctgtgaacaaaacaggttgtgattgtgatggaatacctgaaaattcagagaataatgaaatatttcttcaatagccttttctatatgtacaatctgtttaatctagagaatctggtcattgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA