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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgaacttttaacccaactctagcctctgaaagcaatactctttttattgaaatgtatgacaagttcccatgatttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGTAAAGAATTGCAGGAATTGAGGGTTTTTCCTTCTGATCCGTTTGGGGTTG

Basic information

species Vitis vinifera
transcript Vv14s0068g01330.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01330.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G27280.1 (Glycine max), 3'ss of exon 2
gtatgaacttttaacccaactctagcctctgaaa---gcaatactctttttattgaaatgtatgacaagttcccatgatttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGTAAAGAATTGCAGGAATTGAGGGTTTTTCCTTCTGATCCGTTTGGGGTTG
|||      |  ||  ||| |||    ||||  |       |  |  || |||||     ||| |  |  |   | || || |||||||| ||||||||||||||||||| |||||||| ||||| |||   || |||||||| ||||| ||||||||||||||||| |||| ||| ||||||| | 
gtaaatctatcaaattcaaatcttttttctgttatatttgttgattcttatattggtgaatatcaataaatttta-gacttgtgcagATAATGGATTGCATTGGAGACAAAGGACTAGGTGTTGTAGCTACGACATGTAAAGATTTGCAAGAATTGAGGGTTTTTCCATCTGTTCCCTTTGGGGATC

upper sequence: Vv14s0068g01330.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G26200.1 (Glycine max), 3'ss of exon 2
gtatgaacttttaacccaactctagcctctgaaagcaatactctttttattgaaatgtatgacaagttcccatgatttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGTAAAGAATTGCAGGAATTGAGGGTTTTTCCTTCTGATCCGTTTGGGGTTG
|||   | |   |||| || |||  | | | |      | ||  | || |||||   |||    | || | || | |  |||||||| ||||||||||||||||||| |||||||| ||||| |||   || |||||||| ||||| ||| | |||||||||||   || ||   |||| |   
gtaaata-taccaacctaagtct--cttttcatctatgttcttatgttgttgaa---tatctataattgctat-actggtgcagATAATGGATTGCATTGGAGACAATGGACTAGGTGTTGTGGCTGCCACATGTAAAGATTTGCAAGAACTAAGGGTTTTTCCGGTTGTTCGTGTTGGTGGAA

upper sequence: Vv14s0068g01330.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G05500.1 (Glycine max), 3'ss of exon 2
gtatgaacttttaaccca--actctagcctctgaaagcaatactctttttattgaaatgtatgacaagttcccatgatttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGTAAAGAATTGCAGGAATTGAGGGTTTTTCCTTCTGATCCGTTTGGGGTTG
|||      |  ||  ||  ||| |  ||| | |      || |  || |||||     ||| |  | ||   | || || |||||||| ||||||||||||||||||| ||||| |  ||||| |||  | | |||||||| ||||| ||||||||||| ||||| |||| ||| |||||   | 
gtaaatctatcaaattcaaaactttttccttttatt-tgttaattcttatattggtgaatatcaataattttta-gacttgtgcagATAATGGATTGCATTGGAGACAAAGGACTTGATGTTGTAGCTACTTCATGTAAAGACTTGCAAGAATTGAGGGTGTTTCCATCTGTTCCCTTTGGAAATC

upper sequence: Vv14s0068g01330.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G07240.1 (Glycine max), 3'ss of exon 2
gtatgaacttttaacccaactctagcctctgaaagca-atactctttt-tattgaaatgtatgacaagttcccatgatttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGTAAAGAATTGCAGGAATTGAGGGTTTTTCCTTCTGATCCGTTTGGGGTTG
|||   | | | | || || |||   || |  |   |  ||  || || | |||     ||| |  | || | || | |  |||||||| |||||||||||||||||   ||||||   ||||| ||||  || |||||||| ||||| ||| | ||||||||||| |||| ||   ||||     
gtaaata-tatcagcctaagtcttttcttttcatctatgtatgctcttatgttgttgaatatcaataatttctat-actggtgcagATAATGGATTGCATTGGAGACTTTGGACTACATGTTGTGGCTTCCACATGTAAAGATTTGCAAGAACTAAGGGTTTTTCCGTCTGTTCGTGTTGGTAGAA

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|110359254|gb|EC920449.1|EC920449
EST:     ATGAGCTGATAAAGCTAATCCACCACTGCAGGAAACTTCAGCGACTGTGG                         ATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
genomic: ATGAGCTGATAAAGCTAATCCGCTACTGCAGGAAACTTCAGCGACTGTGGgtatgaactt ... atttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
EST: gi|22010853|gb|BQ795887.1|BQ795887
EST:     ATGAGCTGATAAAGCTAATCCACCACTGCAGGAAACTTCAGCGACTGTGG                         ATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
genomic: ATGAGCTGATAAAGCTAATCCGCTACTGCAGGAAACTTCAGCGACTGTGGgtatgaactt ... atttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
EST: gi|71861101|gb|DT010156.1|DT010156
EST:     ATGAGCTGATAAAGCTAATCCACCACTGCAGGAAACTTCAGCGACTGTGG                         ATATTGGATTGCATTGGAG
genomic: ATGAGCTGATAAAGCTAATCCGCTACTGCAGGAAACTTCAGCGACTGTGGgtatgaactt ... atttatgcagATATTGGATTGCATTGGAG
EST: gi|110705852|gb|EE083178.1|EE083178
EST:     ATGAGCTGATAAAGCTAATCCACCACTGCAGGAAACTTCAGCGACTGTGG                         ATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
genomic: ATGAGCTGATAAAGCTAATCCGCTACTGCAGGAAACTTCAGCGACTGTGGgtatgaactt ... atttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
EST: gi|110686606|gb|EE064438.1|EE064438
EST:     ATGAGCTGATAAAGCTAATCCGCTACTGCAGGAAACTTCAGCGACTGTGG                         ATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
genomic: ATGAGCTGATAAAGCTAATCCGCTACTGCAGGAAACTTCAGCGACTGTGGgtatgaactt ... atttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
EST: gi|110707279|gb|EE083551.1|EE083551
EST:     ATGAGCTGATAAAGCTAATCCACCACTGCAGGAAACTTCAGCGACTGTGG                         ATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
genomic: ATGAGCTGATAAAGCTAATCCGCTACTGCAGGAAACTTCAGCGACTGTGGgtatgaactt ... atttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
EST: gi|110359076|gb|EC919958.1|EC919958
EST:     ATGAGCTGATAAAGCTAATCCACCACTGCAGGAAACTTCAGCGACTGTGG                         ATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT
genomic: ATGAGCTGATAAAGCTAATCCGCTACTGCAGGAAACTTCAGCGACTGTGGgtatgaactt ... atttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaagcaatactctttttattgaaatgtatgacaagttcccatgatttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGTAAAGAATTGCAGGAATTGAGGGTTTTTCCTTCTGATCCGTTTGGGGTTG
              tttttattgaaatgta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgaacttttaacccaactctagcctctgaaagcaatactctttttattgaaatgtatgacaagttcccatgatttatgcagATATTGGATTGCATTGGAGACAAGGGACTAGGAGTTGTCGCTTGTACTTGTAAAGAATTGCAGGAATTGAGGGTTTTTCCTTCTGATCCGTTTGGGGTTG

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