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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgctgttttacctttaaaaatgctacttaaaccatcttcattttttgcttggctcttgtgatgcag

Basic information

species Vitis vinifera
transcript Vv05s0077g01210.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 5'ss of exon 10
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgt-tagtggtaactacctcatattttgctgttttacctt-taaaaatgctacttaaaccatcttcattttttgcttggctcttgtg---atgcag
|||||  |||| |||||||| || ||||| ||||||||| | |||||||||||||| || |||||||| ||||| || |||  | ||  ||     | | ||||     | ||   |       ||| | ||||    ||  |    |  |   |   || | ||   ||| ||
GTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTGgtacattgcaaatctgtttagatttcatcttcttctatcgctcctatgttgcttatcgtatagttgcctgataagtaattcctatgaaaatgtag

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 5'ss of exon 10
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtg----gtaactacctca-tattttgctgtttt-------acctttaaaaatgctacttaaaccatcttcattttttg----cttggctcttgt---gatgcag
|||||  | |||||||| || || ||||| ||||| ||| | ||||| |||||||| || |||||||||||||| ||||||   |      ||| |   ||| | ||||  |||  |       |  |||     |     || ||| |   |  || ||||    ||    ||||||    ||  ||
GTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAGgtagatacagaataatttgttcactgttttattgtacttcagcgcatatttcgggttttgctttgaactagtgtagttctttgataactaatttcttgtctgaatatag

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G145595_T01 (Zea mays), 5'ss of exon 10
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgctgttttacctttaaaaatgctacttaaaccatcttcattttttgcttggctcttgtgatgcag----
|||||| | || ||||| || || ||||| ||||||||  | ||||||||||||||||| || ||||||||||| |||||| | || |      ||||  | || || || | || |     |||||  | |  | ||  |  || |  |      | |||   || |     
GTTCCTAATTTATATTGTATCGGAGATGCCAATGGTAAGCTCATGCTTGCTCATGCAGCCAGCGCACAAGGAATCTCAGgtaaatgttgtg---ctcacctgtttcttttat-ccatgctcgatgctgatca--ctatagttcttatacgagcaaatgttggtctgaatatag

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM2G152958_T02 (Zea mays), 5'ss of exon 10
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgctgttttacctttaaaaatgctacttaaaccatct-tcattttttgcttggctcttgtgatgcag
|| ||  | || |||||||| || ||||| ||||| ||  | |||||||| ||||| || |||||||||||||||||||||   ||  |  | | |  | | |||  ||||   |||  |  |||||  ||     |  | ||   | |||  |  || ||   ||| ||
GTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAGgtacttgagagttcctt--tttcttgtggttt---cttggagcatgcttattggtgtacttgtctgatgttgacttcctattcaaatgtag

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 5'ss of exon 10
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgctgttttacctttaaaaatgctacttaaaccatcttcattttttgcttggctcttgtgatgcag-----------------------------------------
|| || || ||||| ||||| |||||||||||||| || ||||||||||||||||||||||| || ||||| ||||| ||| | |  |  ||||    |   | |   |    | |||| |   | | |||   ||||  |   || |||  || |      |   | |                                         
GTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTGgtgaatcatt-ctactgtgttcctcgaattgaagcatttacattagatcctt--gccattgttggttattgagtgtcgtactcggcactgttccttatgtcgataaatttgcgttaccttttcatgaacag

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 5'ss of exon 10
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgctgttttacctttaaaaatg--ctacttaaaccatcttcattttttgcttggctcttgtgatgcag---------------------------------------------------------
|| || |||||||||||||| || ||||||||||| || ||||||||||||||||||||||| || ||||| ||||| |||  ||  || | |||   |   | |   ||  | |  ||| | ||   |  | | |  || ||||| |||   ||     || ||  |||                                                          
GTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGGgtgggtcata-cgaccctgttcctcgggattgaagcgctaacattggattcataacattatattcatatttattttattgattatgg-gcaatctcactcgtcccagtttctcacataaaatcgatatgcgttggttttttatgaacag

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ06739 (Selaginella moellendorffii), 5'ss of exon 10
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgc-tgttttacctttaaaaatgctacttaaaccatcttcattttttgcttggctcttgtgatgcag
|| ||||| ||||| ||||| || ||||||||||| ||| ||||||||||||| || || ||||| || || ||||||||| | |    |      ||| |||||  || | |  |  | |   ||   |||   |                                  
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgt-aatctcgagagagacatgttttgtgtgatgtgaccgtgatcgtgtctcttttgcag--------------------------------

upper sequence: Vv05s0077g01210.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: EFJ16882 (Selaginella moellendorffii), 5'ss of exon 10
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgc-tgttttacctttaaaaatgctacttaaaccatcttcattttttgcttggctcttgtgatgcag
|| ||||| ||||| ||||| || ||||||||||| ||| ||||||||||||| || || ||||| || || ||||||||| | |    |      ||| |||||  || | |  |  | |   ||   |||   |                                  
GTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAGgt-aatctcgagagaaacatgttttgtatgatgtgaccgtgatcgtgtctcttttgcag--------------------------------

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|110398357|gb|EC964660.1|EC964660
EST:     AAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAG                         TTGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCC
genomic: AAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggta ... tgtgatgcagTTGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCC
EST: gi|34544811|gb|CF513043.1|CF513043
EST:     AAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAG                         TTGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCC
genomic: AAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggta ... tgtgatgcagTTGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCC
EST: gi|110381634|gb|EC934980.1|EC934980
EST:     GCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAG                         TTGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCC
genomic: GCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggta ... tgtgatgcagTTGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCC
EST: gi|34549728|gb|CF517960.1|CF517960
EST:     AAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAG                         TTGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCC
genomic: AAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggta ... tgtgatgcagTTGTTGAGCAAGTTACCGGAAAGGATCATGTGCTCAATCATTTGAGCATCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAGgttagtggtaactacctcatattttgctgttttacctttaaaaatgctacttaaaccatcttcattttttgcttggctcttgtgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA