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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcaactcataaccctctccctctccctctccctctccctgttcacgttgctaaaatgctcttctactttaaatctatcgttactgcaagtggatgtataccttgcttagaccagtagcctgcaatgtgttgtttgcaagtctcggataatctaggtgttttattctcttaacttctggattgcagTGGCCTCGCATATTCCGTGTGGACTATGGACACCAGGAAGCTGCTGCCAAGTTCGGAAAAGACCCAAGGTCCTATGAAGTATTGACCAAGCGGTTTATTG

Basic information

species Vitis vinifera
transcript Vv16s0098g00290.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA14G32500.1 (Glycine max), 3'ss of exon 22
gttcaactcataaccctctccctctccctctcc-ctctccctgttcacgttgctaaaatgctcttct--acttt-aaatctatcgttactgcaagtggatgtataccttgcttagaccagtagcctgcaatgtgttgtttgcaagtctcggataatctaggtgttttattctcttaacttctggattgcagTGGCCTCGCATATTCCGTGTGGACTATGGACACCAGGAAGCTGCTGCCAAGTTCGGAAAAGACCCAAGGTCCTATGAAGTATTGACCAAGCGGTTTATTG
|||  | |   | |  |     |     ||||   | |   | |||       || |   | |      ||||  | |  | |  |||||   | ||| |  | |  ||  ||     ||||          |||| ||     | || |  |  |  ||    ||||  |   |   ||||||| ||||||||||||||||||||||||| || ||||| ||||| || ||||| ||||| || || ||||| ||||| || || || ||| | || ||| ||||||| |
gttagatttgaatcattagttttgaaagtctctgttatgtatcttcttagcaatagacaacccgagagaacttggagacttgtaattactagtaatggctcaacaatttatttca--tagtaat--------tgttctt-----gacttgagtggttgag----tttaaccaaatg-tttctggaatgcagTGGCCTCGCATATTCCGTGTAGATTATGGTCACCAAGAGGCTGCAGCCAAATTTGGCAAAGATCCAAGATCGTACGAGGTACTAACTAAGAGGTTTATCG

upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA04G41540.1 (Glycine max), 3'ss of exon 21
gttcaactcataaccctctccctctccctctccctctccctgttcacgttgctaaaatgctcttctactttaaatctatcgttactgcaagtggatgtataccttgcttagaccagtagcctgcaatgtgttgtttgcaagtctcggataatctaggtgttttatt-ctcttaacttctggattgcagTGGCCTCGCATATTCCGTGTGGACTATGGACACCAGGAAGCTGCTGCCAAGTTCGGAAAAGACCCAAGGTCCTATGAAGTATTGACCAAGCGGTTTATTG
                                                                                  |  | ||||   |  |  | |    |    | |||  |    ||| | ||  ||| || | | | || |  |   ||||| | | ||      ||||| |   |||||||||||||||| ||| || || ||||| ||||| |||| ||| || || || || ||||| ||||| || ||||| |||||||| ||||||||| | |
----------------------------------------------------------------------------------tggttcaagcaaaattgaaacgaaatggctcaagtgtc----aattttttcgttgtaattgt-gcatgactttt-tgtttaactactgagtgtttctgaaacacagTGGCCTCGCATATACCGAGTAGATTATGGGCACCAAGAAGGTGCGGCGAAATTTGGGAAAGATCCAAGATCTTATGAGGTATTGACTAAGCGGTTTGTGG

upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA19G16450.1 (Glycine max), 3'ss of exon 17
gttcaactcataaccctctccctctccctctccctctccctgttcacgttgctaaaatgctcttctactttaaatctatcgttactgcaagtggatgtataccttgcttagaccagtagcctgcaatgtgttgtttgcaagtctcggataatctaggtgttttattctcttaacttctggattgcagTGGCCTCGCATATTCCGTGTGGACTATGGACACCAGGAAGCTGCTGCCAAGTTCGGAAAAGACCCAAGGTCCTATGAAGTATTGACCAAGCGGTTTATTG
|||  | |   | |  |          ||||   | |   | |||       || |   |    |||    ||||    |  |  |  || |    |||     ||  || || | |    |   ||   |||||    |  || || |  |  |     ||||  |   |   ||| ||| ||||||||||||||||||||||||| || || || ||||| || ||||| ||||| || || ||||| || || || ||||| ||||| || ||| ||||||| |
gttagatttgaatcattagttaaaagtctctgt-tatgtatcttcttagcagtagacaac----ctaagagaaattgggcactttt--aattactagtaa----tggctaaacaattgttttcatattaattgttcttga--cttgggtggttgaa----tttaaccaaatg-tttccggaatgcagTGGCCTCGCATATTCCGTGTAGATTACGGTCACCAAGAGGCTGCAGCCAAATTTGGCAAAGATCCTAGATCGTATGAGGTATTAACTAAGAGGTTTATCG

upper sequence: Vv16s0098g00290.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA06G13280.1 (Glycine max), 3'ss of exon 22
gttcaactcataaccctctccctctccctctccctctccctgttcacgttgctaaaatgctcttctactttaaatctatcgttactgcaagtggatgtataccttgcttagaccagtagcctgcaatgtgttgtttgcaagtctcggataatctaggtgttttattctcttaacttctggattgcagTGGCCTCGCATATTCCGTGTGGACTATGGACACCAGGAAGCTGCTGCCAAGTTCGGAAAAGACCCAAGGTCCTATGAAGTATTGACCAAGCGGTTTATTG
                                                                                 ||  |   ||   |  |  |      | |  |||   | |   ||| | ||  ||| || | | | |  || |   ||||| |     |    ||||| | | |||||||||||||||| ||| || || ||||| ||||| |||| ||| || || || || ||||| ||||| || ||||| |||||||| ||||||||| | |
--------------------------------------------------------------------------------attggttttagcaaaattgaaatgaaatgactccaagtgtc---aattttttcgttgtaattgt-gcacgattttt-tgtttaacctagt--gtttctgaaatacagTGGCCTCGCATATACCGAGTAGATTATGGGCACCAAGAAGGTGCAGCAAAATTTGGGAAAGATCCAAGATCTTATGAGGTATTGACTAAGCGGTTTGTGG

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|110395579|gb|EC961246.1|EC961246
EST:     TCTCCCTCAGCCACCACAGACCCGGGCTCCCGGCAACCCATGGCCACAG                         TGGCCTCGCATATTCCGTGTGGACTATGGACACCAGGAAGCTGCTGCCAAG
genomic: TCTCCCTCAGCCACCACAGACCCGGGCTCCCGGCAACCCATGGCCACAGgttcaactca ... tggattgcagTGGCCTCGCATATTCCGTGTGGACTATGGACACCAGGAAGCTGCTGCCAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgcaagtctcggataatctaggtgttttattctcttaacttctggattgcagTGGCCTCGCATATTCCGTGTGGACTATGGACACCAGGAAGCTGCTGCCAAGTTCGGAAAAGACCCAAGGTCCTATGAAGTATTGACCAAGCGGTTTATTG
                                   tcttaac  putative branch site (score: 2)
                                ttctcttaacttct  CT-rich tract
                           ttttattctcttaa  TA-rich tract