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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCTGGAGATAGGAGGAGAACAGTTATGAGGCCCCCACAAGTCCTTCGTGAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcatgttattttgcttcatctattttatatatatatttaattagcaagatttctgttgctctagcaagactgtatttgcactggataatttcat...

Basic information

species Vitis vinifera
transcript Vv06s0004g08180.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g08180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA14G38600.1 (Glycine max), 5'ss of exon 7
TTGCTGGAGATAGGAGGAGAACAGTTATGAGGCCCCCACAAGTCCTTCGTGAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcatgttattttgcttcatctattttatatatatatttaattagcaagatttctgttgctcta-gcaagac--tgtatttgcactggata-atttcat
||||||||||| || | || |||||||||||||| || ||||| |||||||| ||||||||||||||||| ||||| || || |||||||| ||||| ||||||| | || || || ||||  ||      ||  |  | | | |  |    | | || | |  |   |  |  | |  ||| | ||   |   |  ||||   
TTGCTGGAGATCGGCGAAGGACAGTTATGAGGCCTCCTCAAGTTCTTCGTGAGGGCACAAAGAAAACTGTGTTTGTCAATTTTATGGATCTATGCAAAACgtatgttaatatt-ttatgctaaatgctgaata-gttcagagtaatgtgatgaaagttgtttcacaaaacacttggccttgtttctgtgttttctgtatttt--

upper sequence: Vv06s0004g08180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA02G40310.1 (Glycine max), 5'ss of exon 7
TTGCTGGAGATAGGAGGAGAACAGTTATGAGGCCCCCACAAGTCCTTCGTGAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcatgttattttgcttcatctattttata-tatatatttaattagcaagatttctgttgctctagcaagactgtatttgcactggataatttcat----
| ||||||||| || | || |||||||||||||| || ||||| |||||||| ||||||||||||||||| ||||| || || |||||||| ||||| ||||||| | |   ||||||     |  |  || ||| || | | | |  |    | | || | |  |   |  |    ||   |||     |    ||   |    
TAGCTGGAGATCGGCGAAGGACAGTTATGAGGCCTCCTCAAGTTCTTCGTGAGGGCACAAAGAAAACTGTGTTTGTCAATTTTATGGATCTATGCAAAACgtatgtttaa--tattttatgcaaaatgcttaatagtacaaagtaatgtgatgaaagttgtttcac---aaaacacttgggcttgtttctgtcttttctctattt

upper sequence: Vv06s0004g08180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: PP1S93_178V6.2 (Physcomitrella patens), 5'ss of exon 5
TTGCTGGAGATAGGAGGAGAACAGTTATGAGGCCCCCACAAGTCCTTCGTGAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcatgttattttgcttcatctattt-tatatatatatttaattagcaagatttctgttgctctagcaa-gactg-tatttgc-actggataatttcat
|  ||| ||| || ||| | ||  | ||||| || || || || || || ||||| || |||||||| |||||||| ||||| ||||| || |||||||||||||    |      | ||    ||   || |  |  |   | | ||| |    | |||| || |  |    | || |  ||   || | || |||| ||   
TATCTGCAGAGAGAAGGCGTACCATCATGAGACCTCCTCAGGTTCTCCGAGAAGGAACCAAGAAAACCGTTTTTGTCAACTTTATGGACCTTTGCAAGACgtatgt--gtcccgactcgcgctttcggcttgtgcacttgcttgttattcgtggaagttctctttcattgattacgattactagcagccaatgtataacttt--

upper sequence: Vv06s0004g08180.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: PP1S280_23V6.1 (Physcomitrella patens), 5'ss of exon 5
TTGCTGGAGATAGGAGGAGAACAGTTATGAGGCCCCCACAAGTCCTTCGTGAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcatgttattttgcttcatctattttatatatatatttaattagcaagatttctgttgctctagcaagactgtatttgcact-ggataatttcat-----------------------------------------------------------------------------------------------------
|  |||  || |||||| | ||| ||||||| || || || ||  |  | ||||| || ||||| ||||||||||  || ||||||||||| |||||||||||||    | | |  |  ||     | | |||  | | ||    | |||  |    ||| ||    |    |||  |     || ||  || ||| | ||                                                                                                     
TATCTGCGGAGAGGAGGCGTACAATTATGAGACCTCCTCAGGTTTTGAGGGAAGGAACCAAGAAGACTGTTTTTGCCAATTTCATGGATCTTTGCAAGACgtatgtatct-tcacctccctaggcttctcttaggt-tttaagcgactagtgactcgtcttttttcgtgttcagaagggcggggctctcagaaaatcttattcattcgtctagttatctggtattttgaagtttgtaaatctgagactaagcgcaatatgaatggtttgatttttacccgcgtaaaacttgttgttgtgcag

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|22008615|gb|BQ793649.1|BQ793649
EST:     AAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGAC                         GATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
genomic: AAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcat ... tatttttcagGATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
EST: gi|26258607|gb|CA809670.1|CA809670
EST:     GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTATGCAAGAC                         GATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
genomic: GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcat ... tatttttcagGATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
EST: gi|34548729|gb|CF516961.1|CF516961
EST:     GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGAC                         GATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
genomic: GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcat ... tatttttcagGATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
EST: gi|26257846|gb|CA808909.1|CA808909
EST:     GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTATGCAAGAC                         GATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
genomic: GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcat ... tatttttcagGATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
EST: gi|110412214|gb|EC977955.1|EC977955
EST:     GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGAC                         GATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
genomic: GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcat ... tatttttcagGATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
EST: gi|34548647|gb|CF516879.1|CF516879
EST:     GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGAC                         GATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
genomic: GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcat ... tatttttcagGATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
EST: gi|352785931|gb|FQ475934.1|FQ475934
EST:     GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGAC                         GATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
genomic: GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcat ... tatttttcagGATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
EST: gi|110363156|gb|EC926727.1|EC926727
EST:     GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGAC                         GATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG
genomic: GAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcat ... tatttttcagGATGCATAGGCAGCCAGATCATGTCATGGCCTTCTTGCTGGCTGAACTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCTGGAGATAGGAGGAGAACAGTTATGAGGCCCCCACAAGTCCTTCGTGAAGGCACAAAGAAAACTGTTTTTGTGAACTTCATGGATCTGTGCAAGACgtatgctcatgttattttgcttcatctattttatatatatatttaattagcaagatttctgttgctctagcaagactgtatttgcactggataatttcat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA