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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattgttactcaacagtccgccccatttgcactttatatctcagaaaccttttctttagtattgatggcagtgttctttcattgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACCAGATAGTTT

Basic information

species Vitis vinifera
transcript Vv02s0025g03700.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os04g58700.2 (Oryza sativa), 3'ss of exon 8
gtaaaattgttactcaacagtccgccccatttgcactttatatctcagaaaccttttctttagtattgatggcagtgttctttcattgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACC--AGATAGTTT
                   ||  |  |  ||  |  || ||   |    |    |   || | || || ||  | | |  |     |     |||| ||||| ||| ||||     |    |  || ||  | ||||||||||||||||| ||||| ||||| |||||||| || || || || ||  ||| |||  
-------------------gttagtgctgttatcggttaattaattgata----tgatttgaatagtgctgttaatatcttaatgctctcaccagATTCTGATATGCTGAAAAGCCTGCCAAAGTTAAGTCGCCAAGAGCTTGAAGTAGCTTGTGAGGATTTTAGCAACATTATTGGTTCATCTCCTGAGACAGT--

upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G37960.1 (Glycine max), 3'ss of exon 8
gtaaaattgttactcaacagtccgccccatttgcactttatatctcagaaaccttttctttagtattgatggcagtgttctttcattgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACCAGATAGTTT
       ||||  |   |  |   |    | |  | | | ||   | || |  || | |    | ||||    |   | || ||| ||  | ||||||| |||||||||||||||||  | || |  |||||||| || |||||||| || |||||||| |||||||||||||| || ||||||||||||||| |
--gtttgtgtttgtttgctttttactgtgtatttagtatttactactgatattttgtatagtattttgaacatatcatactatcaatg--tgcagACTCCGAGATGTTGAAGGATGTGATGAGGTATAGCAGGCAGGACCTTGAAGTGGCCTGTGAAGACTTCAGCAACATAATTGGGTCCTCACCAGATAGTGT

upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G02690.1 (Glycine max), 3'ss of exon 8
----gtaaaat-tgttactcaa-cagtccgccccatttgcactttatatctcagaaaccttttctttagtattgatggcagtgttctttcattgat-tacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACCAGATAGTTT
    ||| | | |||| ||    |  | |   | |||| ||  |  ||| ||   | |  |||  | |  ||   ||||        || ||| || | ||||| ||||| ||||||| |||||    || |  ||||| |||||||||||||| || |||||||| |||||||||||||| || ||||||||||||||| |
gtatgtagattctgtttctttttccctactttctatttacatctagtatttctagagctgttt--tcaacataattggc--------tttattaatgtgcagACCCTGAGTTGTTGAAAGATGTGAGAAGGTATAGCAGACAAGAGCTTGAAGTTGCCTGTGAAGACTTCAGCAACATAATTGGGTCCTCACCAGATAGTGT

upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G01640.1 (Glycine max), 3'ss of exon 7
gtaaaattgttactcaacagtccgccccatttgcactttatatctcagaaaccttttctttagtattgatggcagtgttctttcattgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACCAGATAGTTT
      | ||| ||   |   |       | |  | | | ||   | || |  || | ||     ||||    | |   || ||| ||  | |||||||||||||||||||||||||  | || |  ||||| || || |||||||| || |||||||| |||||||||||||| || |||||||| |||||| |
---gtttagtttctttgcttcctaatgtgtatttagtatttactactgatattttgtattgtactttgaacatattacactatcaatg--tgcagACTCTGAGATGTTGAAGGATGTGATGAGTTATAGCAGACAGGACCTTGAAGTGGCCTGTGAAGACTTCAGCAACATAATTGGGTCCTCACCGGATAGTGT

upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA01G42770.1 (Glycine max), 3'ss of exon 9
----gtaaaat-tgttactcaacagtccgcc--ccatttgcactttatatctcagaaaccttttctttagtattgatggcagtgttctttcattgat-tacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACCAGATAGTTT
    ||| | | ||||  |   |   |  |   | |||| || || |||| ||   | |  |||  | |  ||   ||||        || ||| || | ||||| ||||| | |||||||||||    || |  ||||| || ||||||||||| || |||||||| |||||||||||||| || ||||||||||||||| |
gtatgtagattctgtttttttgccccctactttctatttaca-ttaatatttctagagctgttt--tcaacataattggc--------tttattaatgtgcagACCCTGAGTTTTTGAAGGATGTGAGAAGGTATAGCAGACAGGAGCTTGAAGTTGCCTGTGAAGACTTCAGCAACATAATTGGGTCCTCACCAGATAGTGT

upper sequence: Vv02s0025g03700.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G41180.1 (Arabidopsis thaliana), 3'ss of exon 8
gtaaaattgttactcaacagtccgccccatttgcactttatatctcagaaaccttttctttagtattgatggcagtgttctttcattgatt----acagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACCAGATAGTTT
      | |  ||||   |     |     || || |  | ||  | ||||    |||   ||   |||    | |  |  |  | || ||    ||||| ||||| ||| |||||||||| |  ||||  |  || |||||||| ||||||||||||||||| ||||||||||| || |  ||     |||| |||  
----gttagaaactcttaaaaattctaagatttcaatacaaataactgaaagagcttcc--agagatgaaaaaattactgataaactgtttttctacagATTCTGAAATGCTGAAGGATGTTTCAAGATATACAAGACAAGAGCTAGAAGTAGCATGTGAAGACTTCAGCAACATCATTGATTCTAGTGCAGAGAGTCA

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|351013321|gb|FQ425026.1|FQ425026
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|161709105|gb|FC058383.1|FC058383
EST:     GGAAC-TATGCAAGTATACACAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: GGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|351028312|gb|FQ427208.1|FQ427208
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|351024123|gb|FQ423546.1|FQ423546
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|349810552|gb|FQ402795.1|FQ402795
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|33401750|gb|CF207377.1|CF207377
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACACAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|349808127|gb|FQ403314.1|FQ403314
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|351021708|gb|FQ437093.1|FQ437093
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|351028536|gb|FQ444817.1|FQ444817
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|161713607|gb|FC063417.1|FC063417
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACACAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|351031421|gb|FQ445446.1|FQ445446
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|71862677|gb|DT011732.1|DT011732
EST:     CCCTTGGAAAAAATCAGCAAGTGAGGAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|349811570|gb|FQ409566.1|FQ409566
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|349814064|gb|FQ414322.1|FQ414322
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
EST: gi|349812384|gb|FQ406405.1|FQ406405
EST:     CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAG                         ACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG
genomic: CCCTTGGAAAAAATCAGCAAGTGAGAAGGAACATATGCAAGTATACATAGgtaaaattgt ... ttgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatctcagaaaccttttctttagtattgatggcagtgttctttcattgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACCAGATAGTTT
                                     ttctttcatt  CT-rich tract
             ttttctttagtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattgttactcaacagtccgccccatttgcactttatatctcagaaaccttttctttagtattgatggcagtgttctttcattgattacagACTCTGAGATGTTGAAGGATGTATTTAGATTCAGCAGGCAAGAGCTTGAAGTAGCATGTGAAGATTTCAGCAACATAATAGGCTCCTCACCAGATAGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC