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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcag

Basic information

species Vitis vinifera
transcript Vv05s0049g01180.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G067764_T02 (Zea mays), 5'ss of exon 3
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctc---ttcccttgcag--------------------
  ||||||||||| |     |||||||||||||||| || ||||||||||  ||||| ||||| |  |||||||||||||||||||||   || || ||||| |  |      |||   |  |   ||   |    || |       |   ||||||   ||| |    |||     | |                    
GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactgatttaaatcttctctcaaagtgttcttttattccaattaggttttgtacttgttttgagttcatggactgagcattgcacctgttttgag

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G107629_T03 (Zea mays), 5'ss of exon 4
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtg---tgtctcttcccttgcag--------------------
  ||||||||||| |     |||||||||||||||| || ||||||||||  ||||| ||||| |  |||||||||||||||||||||   || || ||||| |  |      |||   |  |   ||   |    || |       |   | |||  ||   | | ||||| ||||                       
GCTGAAGCTGGATTTAAACCTGATGGAGCACTATGAGAGGCATTGCCCTCCACCTGAAAGGCGTTTTAATTGCTTGATTCCTCCACCACATGGCTATAAGgtcactactgatctaactcttctctcaaagtgttcttttattccaattagatcttgcatgagatatatcttcgcttgacttgagttcatagactgactat

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA20G35120.4 (Glycine max), 5'ss of exon 3
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgtgcgtaagcttaatagtaacaagggtgt----tgaagttttcttatttttgtgtgtgtctcttcccttgcag
  |||||||||| || ||| ||||||||||||||||||||||||| |||| | | || |||||||||||||||||||||||||| ||| |||| |||||||||| ||| |||  |   |  ||   | |     | |    |    |  |  | |  |||| ||| | | |    ||||||
GATGAAGCTGGACCTGTCTGTGATGGAGCACTATGAAAGACATTGTCCTCCTGCGGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCAGGATACAAGgtgaaaatttgctaagagtatatgtgatcttcaatatactctctgatactgatgtaattgt-tgtttatataatgttgcag

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G32470.1 (Glycine max), 5'ss of exon 3
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgtgc-----gtaagcttaatagt-aacaagggtgttgaagt---tttcttatttttgtgtgtgtctcttcccttgcag----------
  |||||||||| || ||| |||||||||||||||| |||||||| |||| | | || |||||||||||||||||||||||||| ||| | || |||||||||| ||| |||     |||    | ||  | ||||       |||      | | ||||||| ||       |  |   ||  |           
GATGAAGCTGGACCTGTCTGTGATGGAGCACTATGAGAGACATTGTCCTCCTGCAGAAAGGCGGTACAATTGCTTGATTCCTCCTCCATCTGGATACAAGgtgaaaatttgctaagagtatatgtgatcttcaacacaccctctgatacatatgtattattttagtccaacatttgttgtttctataatgttgcag

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA10G00880.2 (Glycine max), 5'ss of exon 3
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtga-gaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcag---------------------------------
| ||||| ||||||||||||||||||| |||||||| |||||||| |||| | | || ||| | | |||||| |||||||||||||| ||||| |||||||| | |||| |||  |  ||  ||   | |       |  |  | | ||  ||  |   | ||| || |      |||                                 
ACTGAAGTTGGATCTTTCTTTGATGGAACACTATGAGAGACATTGTCCTCCTGCAGAAAGGAGATTCAATTGTTTGATTCCTCCACCGGCAGGATACAAGgtaaagaatatgccgagactagatgcgatcttaaacatcaacatatcctcgttaatacatttgtatcatgttcatcagtgtctaataatttctgtttctatggtgttgcag

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G00550.1 (Glycine max), 5'ss of exon 2
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtga-gaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcag---------------------------------
| ||||||||||||||||||||||||| |||||||| |||||||| |||| | | || ||| | |  ||||| ||||||||||| || ||||| |||||||| | |||| |||  |  ||  ||   | |       |  |  | | || |||  |   | ||| |  |    |  |                                  
ACTGAAGCTGGATCTTTCTTTGATGGAACACTATGAGAGACATTGTCCTCCTTCAGAAAGGAGATTTAATTGTTTGATTCCTCCTCCGGCAGGATACAAGgtaaagaatatgccgagactcgatgtgatcttcaacttcaacatatcctcattaatacatttgtataattttgtcaatgctaaaacaattgttgtttctatggtgtttcag

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT4G14360.2 (Arabidopsis thaliana), 5'ss of exon 3
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcag----------
||||||||||||| | |||||||||||||| |||||| | ||||| |||| ||||||||| || | ||||||||||||||| || ||    || || ||||||    | |   || | |  | |||   |  | | |    | ||  |||   |    |   | | ||| ||| ||           
ATTGAAGCTGGATTTGTCTTTGATGGAGCATTATGAACGTCATTGTCCTCCTCCTGAGAGACGATTCAATTGCTTGATTCCGCCTCCTAATGGATATAAGgtgtc--tatcgatatgttatacagttttatcgatat----gattagttacgatgacataactgttttctcttccaatatgttttag

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 5'ss of exon 3
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgtgcgtaagcttaatag---taacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcag
||||||||| ||| | |||||||||||||| |||||| | || || |||| |||||| ||| |||  ||||||||||||||||| ||  ||||||| |||||| |    | |   |||||  | |   | |  || || ||||  | || | |  ||| | | | | |       |  ||
ATTGAAGCTTGATTTGTCTTTGATGGAGCATTATGAACGTCACTGTCCTCCTCCTGAAAGGAGGTTTAATTGCTTGATTCCTCCTCCTCCAGGGTATAAGgtgtgttatttctctagctttgttgatatgatcagtgtcttgacatattttgaagtttttttctatgtgaatgtgtctag

upper sequence: Vv05s0049g01180.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: AT1G04430.1 (Arabidopsis thaliana), 5'ss of exon 3
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgaga-atgtgcgta---agcttaat---agtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcag--------------
 |||||||| ||||| ||||| ||||| || |||||| | ||||| |||| ||| || || ||||  ||||| ||||||||||||||| | || |||||||||  | || ||| |       ||  |   | |    |  |  |    |||   || | ||  | | ||| |  | | ||| |               
GTTGAAGCTTGATCTCTCTTTAATGGAACATTATGAACGGCATTGTCCTCCTCCCGAAAGACGGTTTAATTGTTTGATTCCTCCACCATCTGGATACAAGgtgctatatttgctttcttgttttgctttgatttgtgattggttcctggttacattgtcttgatat-tgttttgttctttgtattgatttgcgtttag

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|110384343|gb|EC948773.1|EC948773
EST:     TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAG                         ATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
genomic: TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
EST: gi|161710886|gb|FC058577.1|FC058577
EST:     ACCAGCAGGGTACAAG                         ATCCCAATCAAGTGGCCAAAAAGTAGAGATGAAGTATGGAAAGCAAACATA
genomic: ACCAGCAGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
EST: gi|110724467|gb|EE100319.1|EE100319
EST:     TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAG                         ATCCCAATCAAGTGGCCAAAAAGTAGAGATGAAGTATGGAAAGCAAACATA
genomic: TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
EST: gi|110357412|gb|EC920933.1|EC920933
EST:     TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAG                         ATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
genomic: TTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA
EST: gi|110722017|gb|EE097877.1|EE097877
EST:     TCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCNAGG-TACAAG                         ATCCCAATCAAGTGGCCAAAAAGTAGAGATGAAGTATGGAAAGCAAACATA
genomic: TCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGC-AGGGTACAAGgtgagaatgt ... tcccttgcagATCCCAATCAAGTGGCCAAAAAGCAGAGATGAAGTATGGAAAGCAAACATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGAAGCTGGATCTTTCTTTGATGGAGCACTATGAAAGACATTGCCCTCTTCCTGAGAGGCGGTACAATTGCTTGATTCCTCCACCAGCAGGGTACAAGgtgagaatgtgcgtaagcttaatagtaacaagggtgttgaagttttcttatttttgtgtgtgtctcttcccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG