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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttaaatgcctatggccttttacaattttcatattaaactttgacatgtcttttttcggtttatcctaatatgtctgcttaaatctttaccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCAAAGACGAACATACTTGTTGTCGAAGGATATTTGTTTGAACTTCCTGACA

Basic information

species Vitis vinifera
transcript Vv16s0039g01580.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G11620.1 (Glycine max), 3'ss of exon 3
----------------------------ccttaaatgcctatggccttttacaattttcatattaaactttgacatgtcttttttcggtttatcc-taatatgtctgcttaaatcttta----ccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCAAAGACGAACATACTTGTTGTCGAAGGATATTTGTTTGAACTTCCTGACA
                                  ||   |  ||| ||||  | |||   |        ||| | |   | | |  | | |||   || | |   |||| | || | |     ||  ||||||||||||||||| || ||| | |||||||||| |||||||||  || |||| ||||| |||||||||||||||||||||||| | |||||||||||||| |
gttcagtacactacaaatgtcatctttcagcaggatattttaggcattttgaagtttcttttacctttattggc-taattctatgagctctataaatagtgtagatgctaacatttctgtactccggtttcagGGCACATCTTCAACTGTTAACTATGATGCATCCTTGGCTAGTGCAGTTTCCAAGACCAACATACTTGTTGTCGAAGGATATCTATTTGAACTTCCTGATA

upper sequence: Vv16s0039g01580.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA12G01920.1 (Glycine max), 3'ss of exon 3
----------------------------------ccttaaatgcctatggccttttaca----atttt---catattaaactttgacatgtcttttttcggtt-tatcctaa----tatgtctgcttaaatctttaccattt-------------tcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCAAAGACGAACATACTTGTTGTCGAAGGATATTTGTTTGAACTTCCTGACA
                                    || | |   |||   || || ||    |||||   ||| || || |||    |  |||| || | |  || | | |    ||||  |  | ||     ||  ||||             ||||||||||||||| || ||| | |||||||||| ||| ||||   || |||| ||||| ||||||||||| |||||||| ||| | |||||||||||||| |
gtttaatatgctataaatggcatctttcagtatctattcagtctttatatgctatttcaggatattttaggcattttgaagtttcttttacctttattggctaataccatgagctctatgaatagtgaagatgctaatatttctgtactctggtgtcagGGCACATCTTCAACTGTTAACTATGATGCATCCTTAGCTAATGCAGTTTCCAAGACAAACATACTTGTCGTCGAAGGGTATCTATTTGAACTTCCTGATA
















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|32267928|gb|CD717087.1|CD717087
EST:     TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAG                         GGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
genomic: TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAGgtttaatctg ... ccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
EST: gi|110390815|gb|EC955744.1|EC955744
EST:     CACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAG                         GGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
genomic: CACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAGgtttaatctg ... ccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
EST: gi|32267415|gb|CD716378.1|CD716378
EST:     TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAG                         GGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
genomic: TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAGgtttaatctg ... ccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
EST: gi|30326863|gb|CD010125.1|CD010125
EST:     TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAG                         GGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
genomic: TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAGgtttaatctg ... ccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
EST: gi|110707202|gb|EE083397.1|EE083397
EST:     TGATAGTTCTCACAACTCCAGATGCTCAGCGCACGATGCTTGCATATCAG                         GGCACATCTTCTACTGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
genomic: TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAGgtttaatctg ... ccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
EST: gi|37188180|gb|CF607529.1|CF607529
EST:     TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAG                         GGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
genomic: TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAGgtttaatctg ... ccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
EST: gi|30324410|gb|CD007672.1|CD007672
EST:     TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAG                         GGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
genomic: TGATAGTTCTCACGACTCCAGATGCTCAGCGCACGATGCTTGCATATCAGgtttaatctg ... ccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCA
EST: gi|30303065|gb|CB979859.1|CB979859
EST:     AGATGCTCAGCGCACGATGCTTGCATATCAG                         GGCACATCTTCTACCG--GATCTNATGATGCATGCTTGGCTAGCACAATTT
genomic: AGATGCTCAGCGCACGATGCTTGCATATCAGgtttaatctg ... ccattttcagGGCACATCTTCTACCGTTGAT-T-ATGATGCATGCTTGGCTAGCACAATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtcttttttcggtttatcctaatatgtctgcttaaatctttaccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCAAAGACGAACATACTTGTTGTCGAAGGATATTTGTTTGAACTTCCTGACA
                   tcctaat  putative branch site (score: 2)
                                       tctttaccattttc  putative PPT
                                  ttaaatcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttaaatgcctatggccttttacaattttcatattaaactttgacatgtcttttttcggtttatcctaatatgtctgcttaaatctttaccattttcagGGCACATCTTCTACCGTTGATTATGATGCATGCTTGGCTAGCACAATTTCAAAGACGAACATACTTGTTGTCGAAGGATATTTGTTTGAACTTCCTGACA

- - aaatgcc
- - - - - -tatggcc
- - - - - - - - - - - - - - - - - - - - - tgacatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtctgc