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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggattgtttatctttttcttgtcttttcaaatatgtaatttaaatccctaggctgtaaatataacttagggtatcaagccccaacatattccttcgataatgtcttattgagtgaattgaggagtttcttgttcttattggttataacccgttttcagGAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCCAATGTTCTTTTGGTAGAGAAGTCAGTATCTCGATTTGCACAAGAGTATC

Basic information

species Vitis vinifera
transcript Vv11s0016g00360.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA13G17510.1 (Glycine max), 3'ss of exon 3
gtttggattgtttatctttttcttgtcttttcaaatatgtaatttaaatccctaggctgtaaatataacttagggtatcaagccccaacatattccttcgataatgtcttattgagtgaattgagga-gtttcttgttcttattgg-ttataacccgttttcagGAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCCAATGTTCTTTTGGTAGAGAAGTCAGTATCTCGATTTGCACAAGAGTATC
                                                               ||| || |  |   |||      |  |||   ||| | |    |  | |||  |    | |  |  || ||   | | ||    || | || | ||  ||||| |||||||||||||| |||||||| |||| |||  ||| |||||||||||||||||||||||| ||||||||||||||||| | ||| ||||| || |
--------------------------------------------------------------ctattacct--gacctcatcttgtaggataaaacttggttgtcatagtcttgtttctgataataatattcctgaatttcatcatctttttactcattcccagGAGATGGACCATTTGAAAATGGCAGTAGCAAGGATTGATGCTCATCACCCCAATGTTCTTTTGGTGGAGAAGTCAGTATCTCGTTATGCTCAAGAATACC

upper sequence: Vv11s0016g00360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G05000.1 (Glycine max), 3'ss of exon 6
gtttggattgtttatctttttcttgtcttttcaaatatgtaatttaaatccctaggctgtaaatataacttagggt-atcaagccccaacatattccttcgataatgtcttattgagtgaattgaggagtttcttgttcttattgg-ttataacccgttttcagGAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCCAATGTTCTTTTGGTAGAGAAGTCAGTATCTCGATTTGCACAAGAGTATC
                                                               ||| || |   || | |  |    |  | | |   | |  |  ||||| ||   |  | | |    || ||   | |||||   || | ||   ||  ||||| |||||||||||||| |||||||| |||| |||  ||| |||||||||||||||||||||||| || |||||||||||||| | ||| ||||| || |
--------------------------------------------------------------ctattacctgacgtcaccttgtaggataaaacttgattgtcatagtcttgtttgttataataata--ttcctgaattttattatctttttacttattcccagGAGATGGACCATTTGAAAATGGCAGTAGCAAGGATTGATGCTCATCACCCCAATGTTCTTTTGGTGGAAAAGTCAGTATCTCGTTATGCTCAAGAATACC

upper sequence: Vv11s0016g00360.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT4G33240.1 (Arabidopsis thaliana), 3'ss of exon 4
gtttggattgtttatctttttctt-gtcttttcaaatatgta---atttaaatccctaggctgtaaatataacttagggtatcaagccccaacatattccttcgataatgtcttattgagtgaattgaggagtttcttgttcttattggttataacccgt-tttcagGAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCCAATGTTCTTTTGGTAGAGAAGTCAGTATCTCGATTTGCACAAGAGTATC
|| || || |||| || | |||||  | ||| | ||||   |   |  | ||||| | | ||| ||  | ||   |  | ||  |   |   || ||          | || |    |  | ||||      ||     || ||   || |||  |  || ||||||||||||||||||||||||||||| ||||| || ||  ||  |||  | ||  |  |||| ||||| ||||| || || || || ||||| || || ||||
gtctgaatcgtttctcatcttctttatttttcccaataaccatggacatgaatccttcgactgaaagga-aaggaaaagcat--aattctgtcacatca-------gaggtttaggcggttaaatt------ttctgcattattgaaggctatctctggtgtttcagGAAATGGACCATTTGAAGATGGCTGTTGCCAAAATTGATTCTCACAATCCTGACATTCTCTTGGTGGAGAAATCTGTCTCGCGGTTTGCGCAGGAATATC

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|71888054|gb|DT037109.1|DT037109
EST:     ATCAGCGGGTTTCTAATCACTTGTCAAGTTTTGATACTTTGTTGCAGCAG                         GAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCC
genomic: ATCAGCGGGTTTCTAATCACTTGTCAAGTTTTGATACTTTGTTGCAGCAGgtttggattg ... ccgttttcagGAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCC
EST: gi|71888025|gb|DT037080.1|DT037080
EST:     ATCAGCGGGTTTCTAATCACTTGTCAAGTTTTGATACTTTGTTGCAGCAG                         GAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCC
genomic: ATCAGCGGGTTTCTAATCACTTGTCAAGTTTTGATACTTTGTTGCAGCAGgtttggattg ... ccgttttcagGAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCC
EST: gi|71882383|gb|DT031438.1|DT031438
EST:     ATCAGCGGGTTTCTAATCACTTGTCAAGTTTTGATACTTTGTTGCAGCAG                         GAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATG
genomic: ATCAGCGGGTTTCTAATCACTTGTCAAGTTTTGATACTTTGTTGCAGCAGgtttggattg ... ccgttttcagGAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttattgagtgaattgaggagtttcttgttcttattggttataacccgttttcagGAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCCAATGTTCTTTTGGTAGAGAAGTCAGTATCTCGATTTGCACAAGAGTATC
                                      ttataac  putative branch site (score: 2)
                                            cccgttttc  CT-rich tract
                            ttcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggattgtttatctttttcttgtcttttcaaatatgtaatttaaatccctaggctgtaaatataacttagggtatcaagccccaacatattccttcgataatgtcttattgagtgaattgaggagtttcttgttcttattggttataacccgttttcagGAAATGGACCATTTGAAGATGGCAGTTGCAAAGATCAATGTTCATCACCCCAATGTTCTTTTGGTAGAGAAGTCAGTATCTCGATTTGCACAAGAGTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT