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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaaattggaaccagatctgtgtccactttgttaaatggtgtagtatcaggcactaagctatacatggtcttgctaattattgtttttctagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG

Basic information

species Vitis vinifera
transcript Vv02s0025g03550.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os04g58750.1 (Oryza sativa), 3'ss of exon 8
gttaaattggaaccagatctgtgtccactttgttaaatggtgtagtatcaggcactaagctata--catggtcttgc-taatt-attgtttttctagctt---gcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG
  || |  | |     | || ||||     || | |||| | ||| | |   |       |||    ||| | |||| | ||  |||||||| || | ||   |||||| ||||| |||||||||||||| || |||||||| ||||||||||||||||| ||||||||   |||||| || || || || ||     |||||||||
--tatac-gtagttgaaactttgtca----tgctgaatgatttagcaaccatcctcgttatattgttatgctgttgcatgatccattgttttccttgtttgctgcagCTCTCATTTCAGATGTGGACCAATCAAATGCAAGATACATTGAACTCAAAGAAGAAGGGTGACAATGCTTTTCGACAAAAGGACTTCTCTTCTGCAATTG

upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G382104_T02 (Zea mays), 3'ss of exon 9
-gttaaattggaaccagatctgtgtccactttgttaaatggtgtagtatcaggcactaagcta-tacatggtcttgctaattattgtttttctagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG
   |  |||| ||   ||  | | || ||    ||   |        |    ||    |  |  | |   ||| | ||  ||||  ||||| |  || |||||| || || ||||||||||| || ||||||||||| || ||||||||||| || ||||||||   |||||| || || || |||||||  ||||| ||||
acgtggattgaaatttgacgttt-tctaccacattttttttccagaaaaactgcttagatttgctgctatgtcatcctctttatactttttttttct-gcagCTCTCTTTTCAGATGTGGACGAATCAGATGCAAGATACGTTGAACTCAAAAAAGAAGGGTGACAATGCTTTTCGACAGAAGGATTTTACTGCTGCCATTG

upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G01730.1 (Glycine max), 3'ss of exon 10
---gttaaattggaaccagatctgtgtccactttgttaaatggtgtagtatcaggcactaagctatacatggtcttgctaattattgtttttctagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG
   ||    |   |     |||  | |  || | |||      |||||  |     | |    | | |   |  ||  | ||| | ||||| ||| |  ||||||||||||||| |||||||| ||||||||||| |||||||||||||||||||| || || || | |||||| |||||||| ||||||| | |||||||||
tatgtcttttcacatttgtatc-atattgacct-gtttttccatgtagactggctgaatggattgttccctgatttctttatt-tcgttttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACATTGAACTCAAAGAAGAAAGGGGACGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG

upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA05G37870.1 (Glycine max), 3'ss of exon 10
---gttaaattggaaccagatctgtgtccactttgttaaatggtgtagtatcaggcactaagctatacatggtcttgctaattattgtttttctagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG
   ||    |   |     || | |    || | |||      |||||  |     |  | | | | ||  |  ||  | ||| || |||| ||| |  ||||||||||||||| |||||||| ||||||||||| ||||| |||||||||||||| || || |||| |||||| |||||||| ||||||| | |||||||||
tatgtcttttcacatttctat-tataatgacct-gtttttccatgtagattggctgaacaggttgtccactgatttctttatt-ttattttcctatcaagcagCTTTCATTCCAAATGTGGACGAACCAGATGCAGGAAACGTTGAACTCAAAGAAGAAAGGGGATGCTGCTTTTCGGCACAAGGATTTTAAAACTGCAATTG

upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT1G63500.1 (Arabidopsis thaliana), 3'ss of exon 8
-------gttaaattggaaccagatctgtgtccactttg--ttaaatggtgtagtatcaggcactaagcta--tacatggtcttgctaattattgtttttctagc-ttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG
         | |||   ||     ||  |||  | || |  ||        | || ||      ||| ||   ||| |  ||   ||  || ||  | | | |   || |||||||| ||||||||||||||||| |||||||| ||  |  ||||||  ||||| |||||||||||||||||||| || ||||| |||  |  ||| || |
gtttctttcttaatcacaattgtctcattgtgtatttgggattgggctaccttgtttcttattgtaatctgattactttttccgcctgcttttttctgtgcaaaaatttcagCTTTCGTTCCAGATGTGGACCAATCAGATGCAGGACTCGCTGAACTTCAAGAAGAAGGGTGATGTTGCTTTCCGACATAAAGAATTTGCAAATGCCATCG

upper sequence: Vv02s0025g03550.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G41260.1 (Arabidopsis thaliana), 3'ss of exon 8
-------------------------------------------------gttaaattggaa---ccagatctgtgtccactttgtta-aatg---gtgtagtatcaggcacta-agctatacatggtcttgcta--------------attattgtttttctagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG
                                                 |||  |||  ||   | | || |||     ||| |  | ||||    ||| |||||    |||   ||||| |||| || |  ||              ||| |   || | |      |||||||| ||||||||||||||| |||||||||| || ||||||  ||  ||||||||||| |||  ||| ||||| || ||||| |||  |   || || |
gttcgttgcgtattttcaaccttgcgttatactatttcggtcttctaatgtttgattctaatgtcgatatttgtaattccttggaaataatgcatctgtggtatctttgactgtggctat-catgttccttatattcaaatctaaaacattttcacttgtttctgcaacagCTTTCTTTCCAGATGTGGACCGACCAGATGCAGGACACATTGGTCTTCAAGAAAAAGGGGGATTCTGCATTCCGACATAAAGACTTTGCAAAGGCCATCG

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|110372521|gb|EC936697.1|EC936697
EST:     GGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACTAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: GGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|110724183|gb|EE099790.1|EE099790
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|349816388|gb|FQ399498.1|FQ399498
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|110361227|gb|EC924685.1|EC924685
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|33403470|gb|CF209097.1|CF209097
EST:     AGATTTTAGAAAAGCTTGGCTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACTAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|349815797|gb|FQ400953.1|FQ400953
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|349822082|gb|FQ408411.1|FQ408411
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|110718884|gb|EE096229.1|EE096229
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACCAACCAGAT-CAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|351015072|gb|FQ444361.1|FQ444361
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|349812229|gb|FQ411824.1|FQ411824
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGGGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACTAACCAGATGCAAGAAACATTGAAACTCAA-
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAA-CTCAAA
EST: gi|349818651|gb|FQ403286.1|FQ403286
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACTAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|349822573|gb|FQ412797.1|FQ412797
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|351042322|gb|FQ442789.1|FQ442789
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACTAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|349813169|gb|FQ411409.1|FQ411409
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG
EST: gi|33401490|gb|CF207117.1|CF207117
EST:     AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAG                         CTTTCATTCCAGATGTGGACTAACCAGATGCAAGAAACATTGAACTCAAAG
genomic: AGATTTTAGAAAAGCTTGGGTATAAAGATGATGAGGGAGCAACAACTGAGgtttgtttct ... tagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcaggcactaagctatacatggtcttgctaattattgtttttctagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG
                           tgctaat  putative branch site (score: 2)
                                    ttgtttttct  putative PPT
                              taattattgtttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaattggaaccagatctgtgtccactttgttaaatggtgtagtatcaggcactaagctatacatggtcttgctaattattgtttttctagcttgcagCTTTCATTCCAGATGTGGACCAACCAGATGCAAGAAACATTGAACTCAAAGAAAAAGGGTGATGTTGCTTTCCGGCACAAAGATTTTAGAGCTGCAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - aaccaga
- - - - - - - - - - - gtccact
- - - - - - - - - - - - - - - - - - -tggtgta
- - - - - - - - - - - - - - - - - - - - - - - -tcaggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - catggtc