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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attgaacactgtctggttcagttatatggccatatctctcatgtctcagatatgtggactttaactttccttttctaaaaacttccaatttttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTTGTTAGGCAATCCAACTTCAAACTTCCTGCTGATACTTCAGTGCCGATTA

Basic information

species Vitis vinifera
transcript Vv11s0052g00880.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 12
---------------------------------------------------------------------------------------------attgaacactgtctg----gttcagttatatggccatatctctc---atgtctcagatatgtggactttaactttccttttctaaaaacttccaatttttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTTGTTAGGCAATCCAACTTCAAACTTCCTGCTGATACTTCAGTGCCGATTA
                                                                                             |  |||| ||  |||    ||| | ||  |   ||  |  |  |   |  || |  | |     |   |  |||    | | |    |   | | |   |||||||| ||||| | || |  || || |   | || ||||||||||| ||| ||||||| || ||||| ||||||||||| ||||||||| ||||||| ||| |||
gtaactaatcaacgtcatatcaacccctattgagtattctaggtcggattatttacctatatatcatctgaagttctaagtatcctgcaaagtacagaacccttgctgcaacgttgaattgaaacacctgagttgacagtaaatccctcagaccataaacatgtcttctgatatttctctatcactattcaatttcgcagAATGCTATTCCATCAGAAGAGACAAAGGACTGCAGCTGGGCTCCAGTTTTTGTGAGACAATCAAACTTCAAACTGCCTGCTGATCCTTCAGTACCGGTTA

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AC217947.4_FGT002 (Zea mays), 3'ss of exon 12
-attgaacactgtctggttcagttatatggccatat-ctctcatgtctcagatatgtggactttaactttccttttctaaaaacttccaatttttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTTGTTAGGCAATCCAACTTCAAACTTCCTGCTGATACTTCAGTGCCGATTA
   ||    |    | || |  || || | |  |   ||   | |  |   ||   ||  ||||| ||    ||   |    | | ||||||   || |||| ||||||| || | |||||| ||| | || ||||||||||| || || ||||| |||||||| ||||||||||| || |||||| ||||||| |||||||
ccctgcttcccaatttgtactttt-taagtcagtccactagaacgattttcatggttgagctttacctgaagttgcttggcca-tcccaattggatttgcagAATGCTGTTCCTTCGGAGGAGAGCAAGGAATGCAGCTGGGCTCCGATATTTGTGAGGCAATCAAACTTCAAACTACCCGCTGATCCTTCAGTACCGATTA

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GRMZM2G144407_T01 (Zea mays), 3'ss of exon 13
--attgaacactgtctggttcagttatatggccatatctctcatgtctcagatatgtggactttaactttccttttctaaaaacttccaatttttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCA---GCTGGGCGCCAATTTTTGTTAGGCAATCCAACTTCAAACTTCCTGCTGATACTTCAGTGCCGATTA
  ||  ||| ||  ||     |   |||   ||    ||  |   | |    | |||   |   |  |  ||    | |    ||       | |   |||| | ||||| || | ||| |  ||| | |||||||   ||||||| || || ||||| |||||||| ||||||||||| || |||||| ||||||||||||   
gaatgcaactcttgctttacaaaaaatacaacccctgcttcccaatttgcactttgtaagcc--agttcaccaggacaatttcctgattggatctgctgcagAACGCTGTTCCATCGGAAGGGAGCGAGGATTGCAGCAGCTGGGCTCCGATATTTGTGAGGCAATCAAACTTCAAACTGCCCGCTGATCCTTCAGTGCCGA---

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA13G00990.1 (Glycine max), 3'ss of exon 13
---attga--acactgtctggttcagttatatggccatatctctcatgtctcagatatgtggactttaactttccttttctaaaaacttccaatttttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTTGTTAGGCAATCCAACTTCAAACTTCCTGCTGATACTTCAGTGCCGATTA
    ||||  ||| |  |||||||  ||| ||  |||||    ||     | |  | | |  | || ||        ||     | | |    |||  |   ||| || ||||||| |||||| ||||||| || ||||| ||||| || ||||||||||||   |||||||| | ||| |||||||||| |  |||||| || |
acttttgatgacaatacctggttcttttagatatccataatcttctgagtttatttttctccatttcaaaacaaaactt-----accatttggtttgatgtccagAATTCTGTGCCATTGGAGAAAAGCCAGGACTGCAGTTGGGCTCCTATTTTTGTTAGGACGTCCAACTTTAGACTCCCTGCTGATAATAAAGTGCCTATAA

upper sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------------attgaacactgtctggttcag--ttatatggccatatctctcatgtctcagatatgtggactttaactttccttttctaaaaacttcc--aatttttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTTGTTAGGCAATCCAACTTCAAACTTCCTGCTGATACTTCAGTGCCGATTA
                                ||| | ||    || ||  |  |  | |  |  | | | |||| ||| |   || ||   |     |||   |   ||   | ||     ||  |  || ||| |||||||||| |  ||| | ||  || | ||   || |||||| || ||||||||||||||||||||||| |||||| ||||| ||   || ||||| |
gtaaatataaaaaacttaaatctgatagcttcttgcaaacatattgctttggaatctttttactgtttgtgtcatttcttatccat-tgtcttggtgtttttgctgggtactgattttttgcatcgtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTTGTTAGGCAATCCAACTTCAAGCTTCCTTCTGATTCTAAGGTACCGATCA

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|32267884|gb|CD717043.1|CD717043
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|110695029|gb|EE072582.1|EE072582
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|27582064|gb|CB004759.1|CB004759
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|32270252|gb|CD719411.1|CD719411
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|30324587|gb|CD007849.1|CD007849
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|30326071|gb|CD009333.1|CD009333
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|352774216|gb|FQ474739.1|FQ474739
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|30300181|gb|CB976975.1|CB976975
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|110699884|gb|EE077290.1|EE077290
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|71864604|gb|DT013659.1|DT013659
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGTGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|32270293|gb|CD719452.1|CD719452
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTNT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
EST: gi|32271899|gb|CD721058.1|CD721058
EST:     AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAG                         TATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT
genomic: AGATGCCCACAGGACGGATTCACAAGGGTATTTGTTCAACTTGGATGAAGgtactgcatt ... tttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagatatgtggactttaactttccttttctaaaaacttccaatttttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTTGTTAGGCAATCCAACTTCAAACTTCCTGCTGATACTTCAGTGCCGATTA
                           ttctaaa  putative branch site (score: 2)
                                    cttccaatttttttc  putative PPT
                         ttttctaaaaactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attgaacactgtctggttcagttatatggccatatctctcatgtctcagatatgtggactttaactttccttttctaaaaacttccaatttttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTTGTTAGGCAATCCAACTTCAAACTTCCTGCTGATACTTCAGTGCCGATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - -tgtctgg
- - - - - - - - - - - - tatggcc
- - - - - - - - - - - - - - - - - - - tcatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaact