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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttatgattaagttgcatccttcttatagattgctttccttcttttctttaaataatatgtaatcttcttataaatattttaacctggctggagaagtgccttttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTT

Basic information

species Vitis vinifera
transcript Vv13s0073g00170.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G34000.1 (Glycine max), 3'ss of exon 10
gttatgattaagttgcatccttcttatagattgctttccttcttttctttaaataatatgtaatcttcttataaatattttaacctggctggagaagtgccttttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTT
              | | ||||    | | ||  ||      |||| | |  |      |||   ||  |  |  | |||| ||    |     | |||  || |||| ||||||| ||| |||| |||||   ||||||||| || ||||||||||||||||| ||||||||||||||||||||| ||||||||||||| ||||||||||||
--------------gtagcctttcagttgcttttttatggagttttttgtttagggagagta--ttttctgcacttcttttcacgcatc----aatgtgtattgtgttgtcagGTTTAAGTCATTCAATATTATGTTTGAGGAACTCCATCAGAAACAATCTCAATGGACAGTTCCTGACACTGAGTTGCGAGAGTCTCTTAGGCTTGCAGTT

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G23810.1 (Glycine max), 3'ss of exon 10
gttatgattaagttgcatccttcttatagattgctttccttcttttctttaaataatatgtaatcttcttataaatattttaacctggctggagaagtgccttttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTT
              | | | ||  | | | || |||     ||||  || ||||||    |   |   || |      ||||||  | |     | |||   ||| |  | |||||||||||||| ||||    ||||||||| || |||||||||||||||||||||||||| || ||  | ||| ||||||||||||| |  |||||||||
--------------gtagcttttctgttgcttccttatggactttatttcaaataaagcatttgccctttct------tttaacacgtc----aaggtg---tttatgtttagGTTCAAGACATTCAATACTATGTTTGAGGAACTTCATCAGAAACAATCTCAGTGGACAGTACCAGATGCAGAGTTGCGAGAGTCTCTTATTCTTGCAGTT

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G33590.1 (Glycine max), 3'ss of exon 10
gttatgattaagttgcatccttcttatagattgctttccttcttttctttaaataatatgtaatcttcttataaatattttaacctggctggagaagtgccttttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTT
              | | ||||    | | ||  ||     ||||| | |     |   ||||  || || ||  | |||| || || ||    | |||  || |||| ||||||| ||| |||| |||||   ||||||||| || |||||||||||||| || ||||||||||| ||| | ||| ||||||| ||||| ||||| ||||||
--------------gtagcctttcagttgcttttttatgggcttttgtctgggaga---gtaacttttttttacttcttttgacatgtct----atgtgtattgtgttgtcagGTTTAAGGCATTCAATATTATGTTTGAGGAACTCCATCAGAAACAATCGCAATGGACAGTTCCAGACTCCGAGTTGCGAGAATCTCTTAGGCTAGCAGTT

upper sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G03540.1 (Arabidopsis thaliana), 3'ss of exon 10
gttatgattaagttgcatccttcttatagat-tgctttccttcttttctttaaataatatgtaatcttcttataaatattttaacctggctggagaagtgccttttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTT
                 |   || || | || |    |        |  ||    ||| | ||    | |  |||  ||  |||    |    | ||              |||||||||||  || |||||||||||||| ||| ||||||||| |||||| || ||||||||||| ||||| ||| |  ||||||| || || ||||| |||
----------------gtaagtcctaaacatgtaaaataaacacagtaattggcaaatgtttatatatttggtaatgatgataaatctgtaaaaaaaaaatggaa------cagGTTCAAGATGTTCAATATGCAGTTTGATGAGTTGCATCAGAGACAATCGCAATGGACAGTTCCAGACACAGAGTTAAGAGAGTCACTAAGACTTGCTGTT

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|46918058|gb|CN547387.1|CN547387
EST:     ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAG                         GTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
genomic: ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAGgttatgatta ... ttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
EST: gi|352778157|gb|FQ468819.1|FQ468819
EST:     ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAG                         GTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
genomic: ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAGgttatgatta ... ttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
EST: gi|110363112|gb|EC926682.1|EC926682
EST:     ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAG                         GTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
genomic: ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAGgttatgatta ... ttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
EST: gi|110730993|gb|EE108709.1|EE108709
EST:     ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAG                         GTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
genomic: ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAGgttatgatta ... ttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
EST: gi|352769772|gb|FQ468700.1|FQ468700
EST:     ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAG                         GTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
genomic: ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAGgttatgatta ... ttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
EST: gi|30136995|gb|CB922333.1|CB922333
EST:     ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAG                         GTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
genomic: ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAGgttatgatta ... ttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
EST: gi|30297777|gb|CB974571.1|CB974571
EST:     ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAG                         GTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
genomic: ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAGgttatgatta ... ttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
EST: gi|110361233|gb|EC924691.1|EC924691
EST:     ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAG                         GTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
genomic: ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAGgttatgatta ... ttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA
EST: gi|352773081|gb|FQ470696.1|FQ470696
EST:     ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAG                         GTTCAAGACATTTAATATGCAGTTNGAGGAGCTGCATCAGAAACAATCTCA
genomic: ACTGATGGTGGAAATAGTAGTGGAGTTTCAAGGGCAATGGTTAAAGACAGgttatgatta ... ttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatcttcttataaatattttaacctggctggagaagtgccttttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTT
                   ttttaac  putative branch site (score: 2)
                                       tgccttttgttctc  putative PPT
     tcttcttataaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttatgattaagttgcatccttcttatagattgctttccttcttttctttaaataatatgtaatcttcttataaatattttaacctggctggagaagtgccttttgttctcagGTTCAAGACATTTAATATGCAGTTTGAGGAGCTGCATCAGAAACAATCTCAGTGGACAGTTCCTGACACTGAGCTGCGAGAGTCTCTGAGGCTTGCAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC