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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatctacacttcccaatgtttactcaaagtttcttctcaattctaacatcataattatccacattctgcccaaaatattggatcatctatttcctcctcagagtctgtagataattcttcttcacataatgttgattttgaacaacaaaattttgtggttggcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTCCTAGAGAAAATCAACAAGTTGCAAGAAGAAGAAATCGAAGTGGGCTCGG

Basic information

species Vitis vinifera
transcript Vv00s1312g00010.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s1312g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G33590.2 (Glycine max), 3'ss of exon 1
gtgatctacacttcccaatgtttactcaaagtttcttctcaattctaacatcataattatccacattctgcccaaaatattggatcatctatttcctcctcagagtc-tgtagataattc--ttcttcacataatgttgattttgaacaacaaaattttgtggttggcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTCCTAGAGAAAATCAACAAGTTGCAAGAAGAAGAAATCGAAGTGGGCTCGG
                                                                            ||  | ||| || | |||| | |  | | |    |   |  ||   ||  |   ||||  ||| ||    |||  || ||           | ||  ||||||||||| || || || |||||||| ||||| ||||| ||||||||||| ||||| |  ||   ||||||||||||||||||||| || | |||  |  
------------------------------------------------------------------------tttcatgattgattatttttttcttaccaacacttgcatttgttgtttgatttgttctataaccttgttt----acactaacatgagacaacaaactttgacagATGGACAGGACCTCCATTCTTGGAGACACCATTGATTACATGAAAGAGCTTCTAGAAAGGATAGGCAAGTTGCAAGAAGAAGAAATGGAGGAGGGAACAA

upper sequence: Vv00s1312g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G65640.2 (Arabidopsis thaliana), 3'ss of exon 1
gtgatctacacttcccaatgtttactcaaagtttcttctcaattctaacatcataattatccacattctgcccaaaatattggatcatctatttcctcctcagagtctg-tagataattcttcttcacataatgttgattttgaacaacaa--aattttgtggttggcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTCCTAGAGAAAATCAACAAGTTGCAAGAAGAAGAAATCGAAGTGGGCTCGG
                                                                    ||  |  | | ||     |         ||  ||||  | | |  | | |  |   |||  |||   || |||  || ||  |  | |  | || |       | ||||||||||| ||||| ||| | |||||| |||||||||| |||||||||||  |||| ||||||||||| || ||||| || |||   ||| | ||     
--------------------------------------------------------------------tgttcttacttttaagggaa--------tctacagaaccggctgaaaagtgataaatcatttaaaagtgttttaaaataatgattattggtatgttcaaaaaaatcagATGGACAGGACATCGATATTAGGAGATGCCATAGATTACATGAAAGAGCTTTTAGACAAAATCAACAAATTACAAGATGAGGAACAAGAACTTGGAAATA

upper sequence: Vv00s1312g00010.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G10570.1 (Arabidopsis thaliana), 3'ss of exon 1
gtgatctacacttcccaatgtttactcaaagtttcttctcaattctaacatcataattatccacattctgcccaaaatattggatcatctatttcctcctcagagtctgtagataattcttcttcacataatgttgattttgaacaacaaaattttgtggttggcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTCCTAGAGAAAATCAACAAGTTGCAAGAAGAAGAAATCGAAGTGGGCTCGG
                                                                     |  ||   |  |  |   | |||| | |  |  || |||| | | | ||  |  | |    |   ||  | | |      |   ||  |   |      | |||||||| || ||||| ||||| |||||| | |||||||| ||||| |||||  | || || || ||||||||||||||||| |||   ||| | ||     
---------------------------------------------------------------------gttcac--tgataaaaggt-tattgctttttgtgaatctgcatagagtttgttgt-atgagaaaatgtatataatttttgatgattattatataataaaatcagATGGATAGGACATCGATACTAGGAGATGCAATAGATTACATGAAGGAGCTTTTGGACAAGATTAACAAGTTGCAAGAAGACGAACAAGAACTTGGAAGCA

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|110394718|gb|EC959980.1|EC959980
EST:     TCAATGATCGCCTTTCCATGCTCAGATCAATTGTTCCTAAGATCAGCAAG                         ATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTC
genomic: TCAATGATCGCCTTTCCATGCTCAGATCAATTGTTCCTAAGATCAGCAAGgtgatctaca ... gcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTC
EST: gi|110727369|gb|EE104048.1|EE104048
EST:     TCAATGATCGCCTTTCCATGCTCAGATCAATTGTTCCTAAGATCAGCAAG                         ATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTC
genomic: TCAATGATCGCCTTTCCATGCTCAGATCAATTGTTCCTAAGATCAGCAAGgtgatctaca ... gcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTC
EST: gi|30296268|gb|CB973062.1|CB973062
EST:     TCAATGATCGCCTTTCCATGCTCAGATCAATTGTTCCTAAGATCAGCAAG                         ATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTC
genomic: TCAATGATCGCCTTTCCATGCTCAGATCAATTGTTCCTAAGATCAGCAAGgtgatctaca ... gcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTC
EST: gi|30296364|gb|CB973158.1|CB973158
EST:     TCAATGATCGCCTTTCCATGCTCAGATCAATTGTTCCTAAGATCAGCAAG                         ATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTC
genomic: TCAATGATCGCCTTTCCATGCTCAGATCAATTGTTCCTAAGATCAGCAAGgtgatctaca ... gcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTC
EST: gi|30296316|gb|CB973110.1|CB973110
EST:     TGCTCAGATCAATTGTTCCTAAGATCAGCAAG                         ATGGACAGAA-NTCCTATACTTGGAGATACCATAGATTATATGAAAGAGCT
genomic: TGCTCAGATCAATTGTTCCTAAGATCAGCAAGgtgatctaca ... gcgttagcagATGGACAGAACAT-CTATACTTGGAGATACCATAGATTATATGAAAGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcttcacataatgttgattttgaacaacaaaattttgtggttggcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTCCTAGAGAAAATCAACAAGTTGCAAGAAGAAGAAATCGAAGTGGGCTCGG
             tgttgat  putative branch site (score: 4)
         ataatgttgatttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatctacacttcccaatgtttactcaaagtttcttctcaattctaacatcataattatccacattctgcccaaaatattggatcatctatttcctcctcagagtctgtagataattcttcttcacataatgttgattttgaacaacaaaattttgtggttggcgttagcagATGGACAGAACATCTATACTTGGAGATACCATAGATTATATGAAAGAGCTCCTAGAGAAAATCAACAAGTTGCAAGAAGAAGAAATCGAAGTGGGCTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA