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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaagtgcttgttgatattgtttttatttttattattaatttctgtcattatgtgagtctgggtggctatgttaagggaattttagctataagttgttccattgtgatatttggtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATAGCAAGGCGGAATGCTGGGCTCAATACTACATTTAGATTAAGGAGGCTGG

Basic information

species Vitis vinifera
transcript Vv17s0000g09390.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G34520.1 (Glycine max), 3'ss of exon 3
gtatgtaagtgcttgttgatattgtttttatttttattattaatttctgtcattatgtgagtctgggtggctatgttaagggaattttagctataagttgttccattgtgatatttggtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATAGCAAGGCGGAATGCTGGGCTCAATACTACATTTAGATTAAGGAGGCTGG
                   ||| |  |||||||||  |||| || | |||  || | ||  | | | | |  ||  |||    || ||         |||||    |   | || || ||| | |||||||| || ||||| |||||||||   ||  || | ||||| |||||||| |||||||| |||||||| |||||||||||||| ||| | ||||||| ||
------------------gtatggaatttattttt--tattcatatttgt--ttgtttggtttttgtttgtgatagtaatttgatctt---------ttgtt----tactaaatctgatataa-cagGAAGTACCTGAGAATAAGAGGCGTGTCTCTATTATAAAAGGCATTGTTATTGCAAGGCGTAATGCTGGACTCAATACTACATTCAGAATTAGGAGGCAGG

upper sequence: Vv17s0000g09390.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA18G08770.1 (Glycine max), 3'ss of exon 3
gtatgtaagtgcttgttgatattgtttttatttttattattaatttctgtcattatgtgagtctgggtggctatgttaagggaattttagctataagttgttccattgtgatatttggtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATAGCAAGGCGGAATGCTGGGCTCAATACTACATTTAGATTAAGGAGGCTGG
                 | ||| |  ||||||||   |||| || | |||  ||   ||  | | | | |  ||  |||    || ||   | |   |||||   |  | | || || ||| | |||||||| || || || |||||||||   ||  || | ||||| |||||||| ||||| || |||||||| |||||||||||||| ||| | ||||||| | 
-----------------ggtatggaatttattttc--tattcatatttgt--ttgcttggtttttgtttgtgatagtaatatgatctt--ttgttttttgtt---tactaacatctgatataa-caGGAAGTACCTGAAAATAAGAGGCGTGTCTCTATTATAAAAGGCATTGTTATTGCAAGACGTAATGCTGGACTCAATACTACATTCAGAATTAGGAGGCAG-
















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|349827639|gb|FQ422507.1|FQ422507
EST:     AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTG                         GAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
genomic: AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTGgtatgtaagt ... gtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
EST: gi|30251442|gb|CB969175.1|CB969175
EST:     AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTG                         GAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
genomic: AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTGgtatgtaagt ... gtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
EST: gi|349825024|gb|FQ415571.1|FQ415571
EST:     AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTG                         GAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
genomic: AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTGgtatgtaagt ... gtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
EST: gi|110382393|gb|EC939358.1|EC939358
EST:     AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTG                         GTATGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGT
genomic: AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTGgtatgtaagt ... gtatgagcagG-A--A-GTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGT
EST: gi|110381353|gb|EC946681.1|EC946681
EST:     AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTG                         GAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
genomic: AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTGgtatgtaagt ... gtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
EST: gi|349829899|gb|FQ422212.1|FQ422212
EST:     AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTG                         GAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
genomic: AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTGgtatgtaagt ... gtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
EST: gi|110703698|gb|EE080772.1|EE080772
EST:     AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTG                         GAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
genomic: AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTGgtatgtaagt ... gtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATA
EST: gi|110385492|gb|EC950024.1|EC950024
EST:     AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTG                         GTATGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGT
genomic: AGAGAGAGATACCTGAGATAAAGCCTGGTTATATTGTTCAGCTCAAAGTGgtatgtaagt ... gtatgagcagG-A--A-GTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgttaagggaattttagctataagttgttccattgtgatatttggtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATAGCAAGGCGGAATGCTGGGCTCAATACTACATTTAGATTAAGGAGGCTGG
          aattttagctataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaagtgcttgttgatattgtttttatttttattattaatttctgtcattatgtgagtctgggtggctatgttaagggaattttagctataagttgttccattgtgatatttggtatgagcagGAAGTGCCAGAGAACAAGAGGCGTACTTCAGTTCTGAAAGGTATTGTTATAGCAAGGCGGAATGCTGGGCTCAATACTACATTTAGATTAAGGAGGCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG