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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG

Basic information

species Vitis vinifera
transcript Vv12s0028g01810.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 8
gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaa--tcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
||   |||| || |  ||        ||      |  | ||| | ||  |  || |||  |||  ||      || || |   |||||||||||||||||||  | || ||||| ||||| |||||||| || |||||||| ||||  ||||||||||| || ||||||||||||||||||
gtattgcatgatgttgtgcaagctacattttt--ttttttgccacgggtatttcttgtgttaacttg------atattatggcagGTTCTTGGTACTCCAACCCGTGAGGAAATACGATGCATGAACCCCAACTATACTGAGTTCAAATTTCCTCAGATTAAGGCTCATCCTTGGCACAAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 8
gtgcagcat--catttcttgttgatattatcgagg----atcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
|| | |||   |||  | ||  | | | ||   |     |  ||    |||||  ||| | |   |   ||| ||| || ||||   ||||||||||||| |||||  | || ||||| || || ||||||||||| ||||| || || |||||||| ||||| |||||||| ||||||||||||
gtactgcaagacatgccatgcagttctaattttgctcctactattgagtatgggcatcttctctaaccttgt-atg-atattcttgcagGTTCTTGGTACACCAACCCGTGAGGAAATACGTTGCATGAACCCGAACTATACAGAGTTTAGGTTTCCACAGATAAAAGCTCACCCTTGGCACAAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G472625_T01 (Zea mays), 3'ss of exon 8
gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
|| | |||  || |      |     ||      || ||| |   ||   |  | ||    | |||||||    |     ||||||||||||||||||||  | || || || ||||| ||||| || || |||||||| ||||||||||||||||| || |||||||| |||||||||
gtactgcaaaatgttccaaagtagacattctat-tcttctaccggggtgtttct-tatggttatgtgatgtgcct----gtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G472625_T02 (Zea mays), 3'ss of exon 8
gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG----
|| | |||  || |      |     ||      || ||| |   ||   |  | ||    | |||||||    |     ||||||||||||||||||||  | || || || ||||| ||||| || || |||||||| ||||||||||||||||| || |||||||| |||||||||    
gtactgcaaaatgttccaaagtagacattctat-tcttctaccggggtgtttct-tatggttatgtgatgtgcct----gtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGATGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCGTGGCACAAGGTAT

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 8
gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
||   |||  || |       |||  |       || |||||   | |  | |  || |  | ||||||     |     ||||||||||||||||||||  | || || || || || ||||| || || |||||||| ||||||||||||||||| || |||||||| |||||||||
gtattgcaaaatgttcca--aatagaaattctattcctctgccgcgacg-ttacttattggtatgtgatatgcct----gtagGTTCTTGGTACTCCAACCCGTGAGGAGATACGGTGCATGAATCCCAACTATACTGAGTTCAGGTTTCCTCAGATAAAGGCTCATCCATGGCACAAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 8
gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
|||  |  || |||  | ||  | ||  | | |||       |||  |  |||   |  | | | |   |  | ||||  ||||||||||||||||| ||| |||| ||||| || || |||||||| |||||||| ||||| || || |||||||| |||||||||||||||||||||
gtgatgtctc-tttgatattagtgttgcc-atgattgcagaatatatct-tcagagatcattatttag-gtgtcttcttgtagGTTCTTGGTACTCCGACTCGAGAGGAAATCCGTTGCATGAACCCAAATTATACAGATTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 8
gtgcagcatcatttcttgttgatattatcgaggatcatctgc-tatggcaatcatgtagtaatgtgtgatgcat---tttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
|||   | |  | | | | |||| ||| |  ||||  | ||  | ||||      |   ||||   | |||  |   |||||  ||| ||||||| ||||| ||| |||||||||||||||| ||||| || |||||||| |||||||| || || || |||||||||||||||||||| |||
gtgattccttgtctat-gctgatgttaccctggattgtatgaatctggctgctgagagataattactaatgtgttgttttcttgtagATTCTTGGCACTCCTACTCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 8
gtgcagcatcatttct-tgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
  |     ||  |||| | |   | |   |  ||||       |||  |      |   ||||   | |    | ||||  ||||||||||||||||||||  | || ||||| || ||||||||||| |||||||| || || || || |||||||| |||||||||||||||||||||
--gtgatgtcccttctatatgagtgtctccatggattgcagaatatatctgcagag--ataattatttagatgtcttcttgtagGTTCTTGGTACTCCAACACGCGAGGAAATCCGTTGTATGAACCCAAATTATACAGAGTTTAGATTCCCTCAGATTAAAGCTCATCCTTGGCACAAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 7
gtgcagcatcatttcttgttgatattatcgaggatcatctgc-tatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
|||   | |  | | ||||| || ||| |  ||||    ||  | | ||      |   ||||   | |||  ||||||  ||| ||||||| ||||| ||  |||||||||||||||| ||||| || |||||||| |||||||| || || || |||||||||||||||||||| |||
gtgattccttgtct-ttgttaatgttaccctggattggatgaatctagctgctgagagataattactaatgtgttttcttgtagATTCTTGGCACTCCCACCCGAGAAGAAATTCGATGCATGAATCCTAATTATACAGATTTCAGATTCCCCCATATCAAAGCTCATCCTTGGCATAAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 8
---------------------------gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaatcat-gtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
                            ||     |  ||| |  ||| |||||  ||  |  ||||  ||      | |   ||   |    || | | || | |  ||||||||||||||||||||| | |||||||||||||||||||||||||| || || ||||| ||||| || || ||||||||||| ||||||||||||
gtgaagtctcctttattagactaatggatgtgctcttttttgtctttggtatta--gactagaatctagtaaatatgttaccataagtacacttgctaccttgttt--tagGTTCTTGGTACTCCAACTCGTGAAGAAATTCGATGTATGAACCCGAACTACACAGATTTTAGGTTCCCACAAATCAAAGCTCACCCTTGGCACAAG

upper sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT2G30980.1 (Arabidopsis thaliana), 3'ss of exon 8
gtgcagcatcatttcttgttgatattatcgaggatcatctgctatg-gcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
||| |   |  |||  |  |  | |  |   |  |||| | || |  |   |||||        |||| ||  ||   |  ||||||||||||||||||||| | |||||||| || || |||||||| || || || || ||||| || || || |||||||| || |||||||| |||
gtgaactcttcttttattatattttgttttggcgtcatttcctgtctgtgctcatg-------atgtgctgtgttggtt--tagGTTCTTGGTACTCCAACTCGCGAAGAAATCCGGTGCATGAACCCAAACTACACAGACTTCAGATTCCCACAAATCAAAGCCCACCCTTGGCATAAG

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|110711443|gb|EE087924.1|EE087924
EST:     CCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAG                         GTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTAT
genomic: CCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAGgtgcagcatc ... tttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTAT
EST: gi|27582878|gb|CB005573.1|CB005573
EST:     CCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAG                         GTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTAT
genomic: CCTTGTTTCCTGGAGAGAGTGCAGTAGACCAACTTGTTGAAATTATAAAGgtgcagcatc ... tttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTAT
EST: gi|33402557|gb|CF208184.1|CF208184
EST:     CTTGTTTCCTGGAGAGAGTGCAGT-GATANAACTTGTTGAAATTATAAAG                         GTTCTTGGTACTCCAACT
genomic: CTTGTTTCCTGGAGAGAGTGCAGTAGACC-AACTTGTTGAAATTATAAAGgtgcagcatc ... tttctaatagGTTCTTGGTACTCCAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG
                                          cattttct  CT-rich tract
                                           attttctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcagcatcatttcttgttgatattatcgaggatcatctgctatggcaatcatgtagtaatgtgtgatgcattttctaatagGTTCTTGGTACTCCAACTAGAGAAGAAATTCGATGTATGAACCCGAATTATACTGATTTCAGGTTTCCTCAGATCAAAGCTCATCCTTGGCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA