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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatttcagaatttttgttatgttttttgctggtgggtttagatgtgtatgatgattttggtgaagccctgtttgatgcatgatttttgtttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAAGTCGGAGACGAAGACCCCTAGTGGGTTAGTGGCACGTCCGGTGCTGACC

Basic information

species Vitis vinifera
transcript Vv07s0129g00660.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0129g00660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os01g55940.1 (Oryza sativa), 3'ss of exon 2
gtgagtatttcagaatttttgttat---gttttttgctggtgggtttagatgtgtatgatgattttggtgaagccctgtttgatgcatgatttttgtttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAAGTCGGAGACGAAGACCCCTAGTGGGTTAGTGGCACGTCCGGTGCTGACC
   ||||    || ||| | | ||    ||  | | || |||  || | |||| |||      ||   | ||     | |   |  || |            | || || ||||| || |||||||| |||||||| || |||||| ||||  | ||||||||||||||||| ||  | ||| |   |||  | ||||||||||||
agtagtaaactagtattatagctagatagtactgtactagtga-ttaatatgtttatctcagattaaattaactaaaggtaattaaataa-----aaaaatgacagGTACGTGCCAGGGCTGGACAAGGGCAAGGGGCTCTACTTCCTGTTCATCAAGTCGGAGACGAAGACGCCCGGCGGGCTGCCGGCGAGGCCGGTGCTGACC

upper sequence: Vv07s0129g00660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os07g40290.1 (Oryza sativa), 3'ss of exon 1
gtgagtatttcagaatttttgttat-gttttttgctggtgggtttagatgtgtatgatgattttggtgaagccctgtttgatgcatgatttttgtttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAAGTCGGAGACGAAGACCCCTAGTGGGTTAGTGGCACGTCCGGTGCTGACC
|| ||| |   |  | |  | | || || |  | ||| | |    | |   |||  | ||    | |||     || || |||    ||   |  ||||| ||| |||||||| || || ||||| || ||||| || |||||| |||| || ||||||||||||||||| ||  | ||  |   |||  | || |||||||| 
gtaagt-tgatactactcctatcattgtctcattctgatag-cacacacacgtacaa-gaagcagatga-----tgattaatg-gccatgaatcattgca-tagGTATGTGCCTGGGCTTGACAAGGGGAAGGGGCTCTACTTCCTGTTCGTCAAGTCGGAGACGAAGACGCCGGGAGGCCTGACGGCGAGGCCCGTGCTGACG

upper sequence: Vv07s0129g00660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G033359_T01 (Zea mays), 3'ss of exon 2
gtgagtatttcag-aatttttgttatgttttttgctggtgggtttagatgtgtatgatgattttggtgaagccctgtttgatgcatg-atttttgtttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAAGTCGGAGACGAAGACCCCTAGTGGGTTAGTGGCACGTCCGGTGCTGACC
     ||||  |  || |  |   |  |  |            |    |  || | ||||  | |   ||        | || |||  || |   | | ||  || || ||||| || |||||||| |||||||| || |||||| ||||  | ||||||||||||||||| ||  | ||| |   ||| || || |||||||||
-----tattgaaacaaataatcaaacctcatccaaaaaaacagtattttaggtctaatgaggtagcacaaatggccgatcattcatatatatgcatgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAAGTCGGAGACGAAGACGCCCGGGGGGCTCCCGGCGCGCCCCGTGCTGACC

upper sequence: Vv07s0129g00660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G068701_T01 (Zea mays), 3'ss of exon 2
gtgagtatttcagaatttttgttatgttttttgctggtgggtttagatgtgtatgatgattttggtgaagccctgtttgatgcatgatttttgtttgca---atagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAAGTCGGAGACGAAGACCCCTAGTGGGTTAGTGGCACGTCCGGTGCTGACC
            | | |    | |   ||  | || ||  |   ||  | | || ||  |      || |    |  ||||| || |||     |  ||   | || ||  ||||||| |||||||| |||||||  || |||||| |||| || ||||||||||||| ||| ||  | ||| |   ||| || || |||||||| 
------------gtaataagctcaccattgctactcgtcagcc-agtagcgaattatactcgcacggagggatggcatgatg-ataattcgacgtgacacacacagGTACCTGCCGGGGCTGGACAAGGGCAAGGCGCTCTACTTCCTGTTCGTCAAGTCGGAGACGACGACGCCCGGCGGGCTGACGGCGCGGCCCGTGCTGACG

upper sequence: Vv07s0129g00660.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA17G18080.1 (Glycine max), 3'ss of exon 2
-------------------gtgagtatttcagaatttttgttatgttttttgctggtgggtttagatgtgtatgatgattttggtgaagccctgtttgatgcatgatttttgtttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAAGTCGGAGACGAAGACCCCTAGTGGGTTAGTGGCACGTCCGGTGCTGACC
                      | |     |  ||   | | ||  | |    |  |  |||| | ||| ||| ||    ||  | ||    |   || |||||| | ||   || ||  || || ||||| | | |||| || || |||| |||   |||||||||  | ||  | ||||| ||||| || |||||||||||||||||||| ||||| || 
gtatgtttcccctacttcgtcaattgccctaagataaatataattatgtaactttttttgtttgg-tgtttat-atataattaattaactaattcatg-tgcatgttgttacgttaca-cagATACGTGCCTGATTTGGATAAGGGTAAGGCTCTACTCTTCTTGTTCATCAAAGCCGAGACAAAGACTCCGAGTGGGTTAGTGGCACGTCCAGTGCTAACT

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|161714657|gb|FC063892.1|FC063892
EST:     TGGGATCGTCGCCAGAAACTTTACAGCCTTCTCATGCCAGTGATGAACCT                         TTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAA
genomic: TGGGATCGTCGCCAGAAACTTTACAGCCTTCTCATGCCAGTGATGAACCTgtgagtattt ... tttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAA
EST: gi|161713635|gb|FC062543.1|FC062543
EST:     TGGGATCGTCGCCAGAAACTTTACAGCCTTCTCATGCCAGTGATGAACCT                         TTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAA
genomic: TGGGATCGTCGCCAGAAACTTTACAGCCTTCTCATGCCAGTGATGAACCTgtgagtattt ... tttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAA
EST: gi|161705588|gb|FC055767.1|FC055767
EST:     TGGGATCGTCGCCAGAAACTTTACAGCCTTCTCATGCCAGTGATGAACCT                         TTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAA
genomic: TGGGATCGTCGCCAGAAACTTTACAGCCTTCTCATGCCAGTGATGAACCTgtgagtattt ... tttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAA
EST: gi|161715493|gb|FC069056.1|FC069056
EST:     TGGGATCGTCGCCAGAAACTTTACAGCCTTCTCATGCCAGTGATGAACCT                         TTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAA
genomic: TGGGATCGTCGCCAGAAACTTTACAGCCTTCTCATGCCAGTGATGAACCTgtgagtattt ... tttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtatgatgattttggtgaagccctgtttgatgcatgatttttgtttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAAGTCGGAGACGAAGACCCCTAGTGGGTTAGTGGCACGTCCGGTGCTGACC
                          gtttgat  putative branch site (score: 5)
                                       tttttgttt  putative PPT
                                      atttttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtatttcagaatttttgttatgttttttgctggtgggtttagatgtgtatgatgattttggtgaagccctgtttgatgcatgatttttgtttgcaatagTTATGTGCCGGGTCTGGACAAAGGCAAGGGTCTGTACTTCTTGTTTGTGAAGTCGGAGACGAAGACCCCTAGTGGGTTAGTGGCACGTCCGGTGCTGACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA