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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaatattctcggcaatcaaacaatggtttactatggtttcaacctttttaatttcgttctggagcgtatagttttgttaagaattgattttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAATCAAGCACAGGTCGATAACATTGCTGAATTGGAAAGAAG

Basic information

species Vitis vinifera
transcript Vv11s0037g00110.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g51220.1 (Oryza sativa), 3'ss of exon 1
-ttaatattctcggcaatcaaacaatggtttactatggtttcaacctttttaatttcgttctggagcgtata-gttttgttaagaattgattttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAATCAAGCACAGGTCGATAACATTGCTGAATTGGAAAGAAG
 |    | | |  |   |  |    |  |     ||  ||| |     ||  |  |  ||  |    ||||  | ||  | ||   ||  | |   |   |||| ||||||||||||||||| ||| |||| || ||| | || || ||||| ||  ||||||| ||||||||||||||  ||||||||||
gtatgcagtttgtgtgttttacaggttctggcaaataattttagttcctt--acctgtttaggtgttgtatttgcttaatgaatgttttgtgtatttgatagGTCAGTTTGAGTGCATTTGCGTTCCTGTTCTCAGAGTTGGTTCAATACAACCAGACACAGGTTGATAACATTGCTGAGCTGGAAAGAAG

upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G03480.1 (Glycine max), 3'ss of exon 2
-------------ttaatattctcggcaatcaaacaatggtttactatggtttcaacctttttaatttc--gttctggagcgtatagttt---tgttaagaattgattttg--gtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAATCAAGCACAGGTCGATAACATTGCTGAATTGGAAAGAAG-
              |     ||||     ||  |   |  ||  |     ||    || ||   || ||  ||  |  | |   | | ||   ||||  |||||   | ||  | | ||||| |||||||||||||| || |||||||| ||||||||||| |||||||| ||| | |||||||| |||||||  ||  | ||| |||| 
gtcctctctctctctctctctctctctcttcttatttttcttctcctcttttatttccattcagatctcgcgtaattcatcacttcgattccgtgtttcgaatttgatgtgttggtgcagGTTAGTTTGAGTGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAACATTGGCGAGCTCGAACGAAGG

upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G34840.1 (Glycine max), 3'ss of exon 2
-ttaatattctcggcaatcaaacaatggtttactatggtttcaacctttttaatttcg--ttctggagcgtatagttttgttaa--gaattgat-tttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAATCAAGCACAGGTCGATAACATTGCTGAATTGGAAAGAAG
 |   |  ||||  |  ||   |  |  ||| ||    |     |||||   || |||  || |    |   | | ||   |     | ||||| | | | | ||||| |||||||| ||||| || |||||||| ||||||||||| |||||||| ||| | |||||||| || ||||  ||  | ||| ||||
gtcctttctctct-ctctctctctctctttttcttctctgatttcctttcagatctcgcgttattcgtcacttcgcttccgtggttaatttgatgtgttggtgcagGTTAGTTTGAGCGCATTCGCGTTCTTGTTCTCGGAGCTTGTTCAGTACAACCAAACGCAGGTCGACAATATTGGCGAGCTTGAACGAAG

upper sequence: Vv11s0037g00110.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G58030.1 (Arabidopsis thaliana), 3'ss of exon 1
-----ttaatattctcggcaatcaaacaatggtttactatggtttcaacctttttaatttcgttctggagcgtatagttttgttaagaattgattttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAATCAAGCACAGGTCGATAACATTGCTGAATTGGAAAGAAG
     || || ||||      |  | |  |   ||| | || |       |||  |   ||  |   ||  |  ||||  | ||   | |  | ||  |||  ||||||| ||||  |||||||||||||| || |||||||| || |||||||||||| | ||||| || || || |||||| | ||||||||
gggttttgatcttcttcttctttgatctct---ttattgtgatcattcgatttcgagcatc--tgctgattggttagtcgttttggaactgtacttgtgttgtagGTGAGCTTGACCGCATTTGCTTTCTTATTCTCGGAGCTCGTTCAGTACAATCAAACCCAGGTTGACAATATAGCTGAACTTGAAAGAAG

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|34543277|gb|CF511509.1|CF511509
EST:     AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAG                         GTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
genomic: AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAGgtacttaaaa ... ttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
EST: gi|349827547|gb|FQ422415.1|FQ422415
EST:     AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAG                         GTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
genomic: AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAGgtacttaaaa ... ttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
EST: gi|351018852|gb|FQ425754.1|FQ425754
EST:     AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAG                         GTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
genomic: AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAGgtacttaaaa ... ttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
EST: gi|33408903|gb|CF214530.1|CF214530
EST:     AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAG                         GTGAGTCTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
genomic: AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAGgtacttaaaa ... ttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
EST: gi|110406906|gb|EC972493.1|EC972493
EST:     AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAG                         GTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
genomic: AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAGgtacttaaaa ... ttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
EST: gi|351041121|gb|FQ444098.1|FQ444098
EST:     AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAG                         GTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
genomic: AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAGgtacttaaaa ... ttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
EST: gi|33408990|gb|CF214617.1|CF214617
EST:     GATAAACCCCTCAGCAAGGGCAAACAAGAG                         GTGAGTCTGAGTGCATTTGCATCGATCG-ATCCGGAGCTTGTCCAGTACAA
genomic: GATAAACCCCTCAGCAAGGGCAAACAAGAGgtacttaaaa ... ttggtttcagGTGAGTTTGAGTGCATTTGC-TTTCTTGTTTTCGGAGCTTGTCCAGTACAA
EST: gi|349827476|gb|FQ422344.1|FQ422344
EST:     AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAG                         GTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
genomic: AGCAGTATTCTAACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAGgtacttaaaa ... ttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
EST: gi|110362846|gb|EC926403.1|EC926403
EST:     AACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAG                         GTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT
genomic: AACGTACTCGATAAACCCCTCAGCAAGGGCAAACAAGAGgtacttaaaa ... ttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttaatttcgttctggagcgtatagttttgttaagaattgattttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAATCAAGCACAGGTCGATAACATTGCTGAATTGGAAAGAAG
                                ttaagaattgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaatattctcggcaatcaaacaatggtttactatggtttcaacctttttaatttcgttctggagcgtatagttttgttaagaattgattttggtttcagGTGAGTTTGAGTGCATTTGCTTTCTTGTTTTCGGAGCTTGTCCAGTACAATCAAGCACAGGTCGATAACATTGCTGAATTGGAAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - aaacaat
- - - - - - - - - - - - - - - - - - - ttcaacc