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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttatttacccctgccttttttagtgacctttccttcaatcttttagccttgtgaactagtaatgagtgcaaagattttcaattgcagTTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG

Basic information

species Vitis vinifera
transcript Vv05s0062g01220.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G39250.2 (Glycine max), 3'ss of exon 9
gtaagttatttacccctgccttttttagtgacctttccttcaa-----tcttt----tagccttg-tgaa---ctagtaatga------gtgcaaagattttcaattgcagTTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG
||||||| | |    ||   ||||  | | |          ||     || ||    | || |   ||||   | |   || |      ||||     ||||      ||||| ||||||||||||||||| || ||| |||| |||||||| || ||||||||||| ||| |||| || |||||||||||||||||  ||
gtaagttgtatttttcttaattttcaaattatagccaacataagaatttccttagagtggcttcaatgaaatcccatctataaccttttgtgcctttcttttttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTAAGTGACAATATTGAAGGAGGAGAAACATATTTCCCATTG

upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G44480.3 (Glycine max), 3'ss of exon 9
gtaagtt--atttacccctgcc--ttttttagtgacc-------------tttccttcaatc--ttttagcct--tgtgaactagtaatgagtgcaaagattttcaattgcagTTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG
|||||||  ||||  |  ||    ||||  ||| |               ||||||| ||     || | |    |   | |||  |     ||      ||||      ||||| ||||||||||||||||| || ||| |||| |||||||| || ||||||||||| ||| |||| || |||||||||||||| ||  ||
gtaagttgtatttgtctttgttaattttcaagttatagccaagataataatttccttgaagtggcttcaacgaaatcccatctacaaccttttgtgtttcttttttgagacagTTCAACTTGAAGCGTGGTGGGCAGCGAATAGCCACAATGCTTATGTATTTAAGTGACAATATTGAAGGAGGAGAAACATATTTTCCATTG

upper sequence: Vv05s0062g01220.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G43080.1 (Arabidopsis thaliana), 3'ss of exon 9
---------gtaagttatttacccctgccttttttagtgac-ctttccttcaatcttttagccttgtgaactagtaatgagtgcaaagattttcaattgcagTTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG
          |   | || |         |  ||| |     | ||  ||     | ||   | | |   || ||      |   | | ||   |    ||||| ||  | |||||||||||||| || |||||||| ||||| || ||| ||| |||| | || || || |||||||| ||||||||| ||
cttctccttcttcatcatcttagaacatttagtttggaagtacgtttattgtgggtgttcatcatatttcctcgtttcttttcttatggttgcta--cacagTTCAATCTAAAGCGTGGTGGTCAGCGCGTAGCAACTATGCTTATGTATCTAACTGATGACGTCGAAGGAGGAGAAACTTATTTCCCTTTG

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|110427318|gb|EC993753.1|EC993753
EST:     ATAAAAAGAGTCAGTTCTACAAGCCTCACCATGACTACTTCTCTGATTCT                         TTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTA
genomic: ATAAAAAGAGTCAGTTCTACAAGCCTCACCATGACTACTTCTCTGATTCTgtaagttatt ... tcaattgcagTTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTA
EST: gi|349820405|gb|FQ406961.1|FQ406961
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|349815347|gb|FQ400502.1|FQ400502
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351036556|gb|FQ457269.1|FQ457269
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351046420|gb|FQ453036.1|FQ453036
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|349811155|gb|FQ406107.1|FQ406107
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|34319741|gb|CF372495.1|CF372495
EST:     ATAAAAAGAGTCAGTTCTACAAGCCTCCCCATGACTACTTCTCTGATTCT                         TTTACCTTGAAGCGTGGTGGTCACCGAGTAGCAACAATGCTCATTTATTTA
genomic: ATAAAAAGAGTCAGTTCTACAAGCCTCACCATGACTACTTCTCTGATTCTgtaagttatt ... tcaattgcagTTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTA
EST: gi|351056456|gb|FQ454317.1|FQ454317
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|349821182|gb|FQ408769.1|FQ408769
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|349807356|gb|FQ401348.1|FQ401348
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351044260|gb|FQ447614.1|FQ447614
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|349817923|gb|FQ407912.1|FQ407912
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351033401|gb|FQ462052.1|FQ462052
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|349808011|gb|FQ402402.1|FQ402402
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351042433|gb|FQ442900.1|FQ442900
EST:     CACTCGGCCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351037271|gb|FQ457104.1|FQ457104
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|349824801|gb|FQ414659.1|FQ414659
EST:     CACTCGGTCTCCGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351032228|gb|FQ460485.1|FQ460485
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351049572|gb|FQ429194.1|FQ429194
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351052197|gb|FQ450767.1|FQ450767
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
EST: gi|351055664|gb|FQ452129.1|FQ452129
EST:     CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA
genomic: CACTCGGTCTCTGATTCTGTCAGTCTCTTCGTTTTCTCCATGGCGGCTCCAATGAAATTCGTAATTGGTCTCCTTGCTTTAGTCTCTTTCGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcaatcttttagccttgtgaactagtaatgagtgcaaagattttcaattgcagTTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG
                                          ttttc  CT-rich tract
                                     aaagattttcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttatttacccctgccttttttagtgacctttccttcaatcttttagccttgtgaactagtaatgagtgcaaagattttcaattgcagTTTAACTTGAAGCGTGGTGGTCAACGAGTAGCAACAATGCTCATTTATTTAAGTGATAATGTTGAGGGGGGAGAAACATATTTCCCTATG

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