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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agatatttgggtgtttgctctttgaatggaagattgcatcatctattatattgctattgattacttatttatttctgtttttggtgaatggctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTGCTTCATCTTGTCAGGCCATTTCTTTCTTTCCTGCCAGAAGTTCAGAGTG

Basic information

species Vitis vinifera
transcript Vv19s0014g01020.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g11440.1 (Oryza sativa), 3'ss of exon 1
agatatttgggtgtttgctctttgaatggaagattgcatcatctattatattgctattgattacttatttatttctgtttttggtgaatggctggtgcagGTTGGACCTGTTTAATT--TAGGCTA---AATAAGATGGGAGGAGGATTTAGGGTGCTTCATCTTGTCAGGCCATTTCTTTCTTTCCTGCCAGAAGTTCAGAGTG------------------------
                        | |   |  |   | ||  | | | |||  | |  |  ||  || | ||    ||||  ||| || |       |   | ||||| |||  ||  | ||  |    | |||||||  || || ||||||||  | |||||||||||||| |||||  |||||||||| ||||| |||||||                        
------------------------agtctgaact---accaagtttgaaatttttttacaagacacatgttttataattttgtgtgcattgt--acaaaatcttgacctatttttttgcttggtcacagGAAAAGATGGCTGGTGGCTTTAGGGTATTGCATCTTGTCAGGCCTTTTCTGGCTTTCCTGCCTGAAGTACAGAGTGCTGATAGGAAAATACCATTTAGAG

upper sequence: Vv19s0014g01020.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G307252_T03 (Zea mays), 3'ss of exon 1
agatatttgggtgtttgctctttgaatggaagattgcatcatctattatattgctattgattacttatttatttctgtttttggtgaatggctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTGCTTCATCTTGTCAGGCCATTTCTTTCTTTCCTGCCAGAAGTTCAGAGTG--------------------------
                    || |||| |  ||   || |||  | ||    | | |   |   ||| |   ||  ||      || |    |  ||| | |      | | |  ||||   || |  ||||||  || || ||| | || || |||||||| |||||||||||  ||||| |||||||||| |||||||                          
------------------cattagaattgt-gaccaca-catagagtaggaaggtttcattatgttactagatttggtgcacattgtaca--taatgctgatcaa---tatctcctttaatatagA-GAGATGGCTGGTGGTTTTCGAGTACTGCATCTTGTGAGGCCATTTCTGGCTTTCTTGCCAGAAGTACAGAGTGCTGATAGGAAAATACCATTCAGAGAG
















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|110688222|gb|EE066526.1|EE066526
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|161707141|gb|FC055564.1|FC055564
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|161718407|gb|FC066312.1|FC066312
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|161711947|gb|FC059564.1|FC059564
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTACATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|110698206|gb|EE075492.1|EE075492
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|110692118|gb|EE070996.1|EE070996
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|110687041|gb|EE064103.1|EE064103
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|110409186|gb|EC974845.1|EC974845
EST:     GGTTCTCTCCGACGGG                         GTTGAACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|110365093|gb|EC928838.1|EC928838
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|110698349|gb|EE075761.1|EE075761
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|37183757|gb|CF603111.1|CF603111
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
EST: gi|161721208|gb|FC070714.1|FC070714
EST:     GGTTCTCTCCGACGGG                         GTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG
genomic: GGTTCTCTCCGACGGGgtagggtccg ... gctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatattgctattgattacttatttatttctgtttttggtgaatggctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTGCTTCATCTTGTCAGGCCATTTCTTTCTTTCCTGCCAGAAGTTCAGAGTG
         tattgat  putative branch site (score: 3)
         tattgattacttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agatatttgggtgtttgctctttgaatggaagattgcatcatctattatattgctattgattacttatttatttctgtttttggtgaatggctggtgcagGTTGGACCTGTTTAATTTAGGCTAAATAAGATGGGAGGAGGATTTAGGGTGCTTCATCTTGTCAGGCCATTTCTTTCTTTCCTGCCAGAAGTTCAGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - ttgggtg
- - - - - - - - - - - tgaatgg
- - - - - - - - - - - - - - - - - - catcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgaatg