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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaaagtcccatttatcttagcatgaaaaagttactctactccattttttaatcatgcgttgcttttgaatttgatcccaatggatgcttagagaatttgttatctagttttatttgttggctattttctttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAG

Basic information

species Vitis vinifera
transcript Vv03s0097g00590.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G174696_T02 (Zea mays), 3'ss of exon 8
gtaagaaagtcccatttatcttagcatgaaaaagttactctactccattttttaatcatgcgttgcttttgaatttgatcccaatggatgcttagagaatttgttatctagtt------ttatttgttggctattttctttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAG
                                                             ||||  ||  |   |||   ||||      | | |   | ||||  ||  ||      ||| |   ||| ||   |  ||  || |||||||  | || || || |||||||| ||  |||||||||||||||| ||||| || ||||||||||||||| | ||| | |||
-------------------------------------------------------------gttgacttccaccatgacagcaatatgctttcacatgctgtgttggctgcttattgccttactctatggttacccttatt--tgcagGTTTCCCTTGCGTCTGACTTCATGTATAACCATATGTCAAGAGATGTAACTGCCAGCTTTGGTTATGATTACTTGCTTAGGCAG

upper sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G120876_T01 (Zea mays), 3'ss of exon 8
gtaagaaagtcccatttatcttagcatgaaaaagttactctactccattttttaatcatgcgttgcttttgaatttgatcccaatggatgcttagagaatttgttatctagtttta--tttgttggctattttctttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAG
                                                           |||    ||||  || | ||    |   || |||| |   ||| |  | || |   |  ||  ||   ||     ||   || |||||||  | ||||| ||||||||||||||| | ||| |||  ||||| || ||||| |||||||||||||| || ||  |||||
-----------------------------------------------------------gcgagtttttttcatatcattttta---atacttacatttttt-tgctttaatagcagcttcattacataagaaattgtgtgcagGTTTCCCTTGCATCTGATTTCATGTACAATCAAATGACAAAGGATGTAACAGCAAGCTTTGGTTATGATTATATGCTGAGACAG

upper sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G34360.2 (Glycine max), 3'ss of exon 8
gtaagaaagtcccatttatcttagcatgaaaaagttactctactccattttttaatcatgcgttgcttttgaatttgatcccaatggatgcttagagaatttgttatctag--ttttatttgttggctattttctttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAG---
                                                          || |||| |  |||  ||       || |||   ||     |||   ||  |   |||||||| ||    |   | || | |  |||||||| ||||||| || || |||| ||| ||  |||||||||||||||| || || ||||||||||| ||||||||| |||||   
---------------------------------------------------------gtgagttgataatgacatt-------atagatatatatgttgttttcaattgaactttttatttcttatacaaaatgttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACAGCTAGCTTTGGTTATGACTACATCCTTAGACAGGTA

upper sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA05G34360.3 (Glycine max), 3'ss of exon 8
gtaagaaagtcccatttatcttagcatgaaaaagttactctactccattttttaatcatgcgttgcttttgaatttgatcccaatggatgcttagagaatttgttatctag--ttttatttgttggctattttctttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAG
                                                          || |||| |  |||  ||       || |||   ||     |||   ||  |   |||||||| ||    |   | || | |  |||||||| ||||||| || || |||| ||| ||  |||||||||||||||| || || ||||||||||| ||||||||| |||||
---------------------------------------------------------gtgagttgataatgacatt-------atagatatatatgttgttttcaattgaactttttatttcttatacaaaatgttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACAGCTAGCTTTGGTTATGACTACATCCTTAGACAG

upper sequence: Vv03s0097g00590.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA08G05280.1 (Glycine max), 3'ss of exon 8
gtaagaaagtcccatttatcttagcatgaaaaagttactctactccattttttaatcatgcgttgcttttgaatttgatcccaatggatgcttagagaatttgttatctag--ttttatttgttggctattttctttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAG
                                                          || |||| |  |||       |  | | |||  |||     |||   ||  |   |||||||| ||    |   | || | |  |||||||| ||||||| || || |||| ||| ||  |||||||||||||||| || || |||||||| || ||||||||| |||||
---------------------------------------------------------gtgagttgataatga-------catagtagat-tttatgttgttttcaattgaactttttatttcttatacaaaatgttcctttcagGTTTCTCTAGCATCTGAGTTTATGTGCAACTACTTGTCAAGAGATGTCACAGCTAGCTTTGGTTACGACTACATCCTTAGACAG

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|110370748|gb|EC932839.1|EC932839
EST:     CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAG                         GTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACT
genomic: CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAGgtaagaaagt ... tttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACT
EST: gi|110428685|gb|EC995164.1|EC995164
EST:     CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAG                         GTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACT
genomic: CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAGgtaagaaagt ... tttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACT
EST: gi|110376048|gb|EC941087.1|EC941087
EST:     CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAG                         GTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACT
genomic: CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAGgtaagaaagt ... tttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACT
EST: gi|110698670|gb|EE076432.1|EE076432
EST:     CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAG                         GTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACT
genomic: CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAGgtaagaaagt ... tttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACT
EST: gi|352765105|gb|FQ465802.1|FQ465802
EST:     CTAGCACTGGCATGGTTGCTTTGAGCTATGTTCAGAAAGTATCAGAGAAG                         GTTTCTTTAGCATCGGATTTCATGTACATTTATATGTCAAGAGATGTCACT
genomic: CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAGgtaagaaagt ... tttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACT
EST: gi|351046106|gb|FQ442484.1|FQ442484
EST:     CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAA                         GTTTCTTTAGCATCAGATTTCATGTACA
genomic: CTAGCACTGGCATGGTTGCTCTGAGCTATGTTCAGAAAGTATCAGAGAAGgtaagaaagt ... tttcctgtagGTTTCTTTAGCATCAGATTTCATGTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcttagagaatttgttatctagttttatttgttggctattttctttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAG
                                     ctattttctttcctgt  CT-rich tract
          aatttgttatctagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaaagtcccatttatcttagcatgaaaaagttactctactccattttttaatcatgcgttgcttttgaatttgatcccaatggatgcttagagaatttgttatctagttttatttgttggctattttctttcctgtagGTTTCTTTAGCATCAGATTTCATGTACAATTATATGTCAAGAGATGTCACTGCAAGTTTTGGTTATGATTACATCCTTCGACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG