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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatcttttgtctgtaacactcttgaaatattctctcattcatgaagctgaaatatttataaatatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCGGCCGTAGTGACTGGAAAGCCAATA

Basic information

species Vitis vinifera
transcript Vv16s0039g02750.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0039g02750.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g45970.1 (Oryza sativa), 3'ss of exon 3
--gttatcttttgtctgtaacactcttgaaatattctctcattcatgaagctgaaatatttataaatatgg-gcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCGGCCGTAGTGACTGGAAAGCCAATA----
   |  |||  | ||| ||  | | ||  | || |  |   ||||| | |    |     | ||| | ||   ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||| || || ||||| |||||||||    
gtatattctgctttctctagtatttttctactacttccc--ttcatcatgtaacatcccctgtaattttgacacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATAGTAA

upper sequence: Vv16s0039g02750.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os04g45970.2 (Oryza sativa), 3'ss of exon 3
--gttatcttttgtctgtaacactcttgaaatattctctcattcatgaagctgaaatatttataaatatgg-gcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCGGCCGTAGTGACTGGAAAGCCAATA
   |  |||  | ||| ||  | | ||  | || |  |   ||||| | |    |     | ||| | ||   ||||| ||||| ||||||||||| |||||||| |||||||||||||| |||||||| || || ||||| |||||||||
gtatattctgctttctctagtatttttctactacttccc--ttcatcatgtaacatcccctgtaattttgacacagACCATGGCTTGGATTTTGGATGAGTACTCGAAATTCCATGGTCATTCACCGGCAGTTGTCACTGGGAAGCCAATA

upper sequence: Vv16s0039g02750.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G427097_T01 (Zea mays), 3'ss of exon 3
--------------------gttatcttttgtctgtaacactcttgaaatattctctcattcatgaagctgaaatatttata-aatatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCGGCCGTAGTGACTGGAAAGCCAATA
                    ||||| |||| | ||||    |  | |  |||  | |  |||||     || |   |||||  |||   | ||||| |||||||||||  |||| |||||||| ||||| ||||||||||| || || || || ||||| |||||||||
gtaggcctaacattgcttttgttatttttt-tttgta----tgctcagctatcttgtttttcat----ttgtaccttttatgcaattgtgacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATA

upper sequence: Vv16s0039g02750.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G427097_T02 (Zea mays), 3'ss of exon 3
--------------------gttatcttttgtctgtaacactcttgaaatattctctcattcatgaagctgaaatatttata-aatatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCGGCCGTAGTGACTGGAAAGCCAATA-------------------------
                    ||||| |||| | ||||    |  | |  |||  | |  |||||     || |   |||||  |||   | ||||| |||||||||||  |||| |||||||| ||||| ||||||||||| || || || || ||||| |||||||||                         
gtaggcctaacattgcttttgttatttttt-tttgta----tgctcagctatcttgtttttcat----ttgtaccttttatgcaattgtgacagACCATGGCATGGATGCTGGATGAGTACTCGAAATTTCATGGTCACTCCCCAGCAGTCGTCACTGGGAAGCCAATAGTAAGTGAAAAAATGTGGCAGCAAG

upper sequence: Vv16s0039g02750.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S62_236V6.1 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------gttatcttt-tgtct-gtaacactcttgaaatattctctcattcatgaagctgaaatatttataaatatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCGGCCGTAGTGACTGGAAAGCCAATA
                                                ||     |  ||||  | |  |||     | |    | | |   |||     |    ||| |   | ||  ||||||||||| |||||||||||||||||||| ||||| |||||  |  | |||||||| || ||||| || ||  | 
gtatgttccgtatattgaagctctctcgtgttccactaacatgccgtattgctgatgcgtctcatcatgctcagtgcagagaaacccctctctgatctcaacgactttgtt--tttgtacagACTATGGCTTGGATTTTGGACGAGTACTCGAAATTTCATGGGTATACTCCGGCCGTCGTAACTGGTAAACCGGTG

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|30251187|gb|CB968920.1|CB968920
EST:     TTGGAACTCATACTGATGTACCTGCACCGGACATGGGAACTAATGCTCAG                         ACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCG
genomic: TTGGAACTCATACTGATGTACCTGCACCGGACATGGGAACTAATGCTCAGgttatctttt ... atatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCG
EST: gi|161720824|gb|FC069589.1|FC069589
EST:     TTGGAACTCATACTGATGTACCTGCACCGGACATGGGAACTAATGCTCAG                         ACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCG
genomic: TTGGAACTCATACTGATGTACCTGCACCGGACATGGGAACTAATGCTCAGgttatctttt ... atatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCG
EST: gi|161712921|gb|FC062394.1|FC062394
EST:     TTGGAACTCATACTGATGTACCTGCACCGGACATGGGAACTAATGCTCAC                         ACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGGCACTCACCG
genomic: TTGGAACTCATACTGATGTACCTGCACCGGACATGGGAACTAATGCTCAGgttatctttt ... atatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCG
EST: gi|156737272|gb|EV241386.1|EV241386
EST:     AACTAATGCTCAG                         ACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATTGTCACTCACCG
genomic: AACTAATGCTCAGgttatctttt ... atatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactcttgaaatattctctcattcatgaagctgaaatatttataaatatgggcagACTATGGCATGGATTTTGGACGAGTACTCAAAATTCCATGGTCACTCACCGGCCGTAGTGACTGGAAAGCCAATA
                           aagctgaaatatttat  TA-rich tract