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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaccaagagtggtggctgaattgtatatttaattccgtgattgtcatgcagatcttttttcaaatacttttcttatacttgtttttctgtgtaacagGAAGAGATTCAGAAGAAAACTGGTTATGTTGTAATGAAAGGTGAGGGAATATTTGATGTGGATGCAAATACATCAATTGATCAGCTCTCTGAAGATCTCA

Basic information

species Vitis vinifera
transcript Vv19s0090g01820.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 11
gaaaaccaagagtggtggctgaattgt-atatttaattccgtgattgtcatgcagatcttttttcaaatacttttcttatacttgtttttctgtgta---acagGAAGAGATTCAGAAGAAAACTGGTTATGTTGTAATGAAAGGTGAGGGAATATTTGATGTGGATGCAAATACATCAATTGATCAGCTCTCTGAAGATCTCA
     || ||    |    ||| || | ||   |||  |     |   | |||  || |||| | ||| |   || ||| | |  ||  |   | |    |||||| ||||| ||||| |||||||||||  ||||||||  || ||||||  | ||||||||||||||||| ||||| ||||||||||||||||||||| | |
----gcctagttatgcatttgattttttatgactaaaactactttctgcttgctaattttttattaaagaacctttttacattctttcctggttattcctacagGAGGAGATACAGAAAAAAACTGGTTACATTGTAATGCGAGCTGAGGGTGTTTTTGATGTGGATGCAAACACATCCATTGATCAGCTCTCTGAAGATTTGA

upper sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 11
gaaaaccaagagtggtggctgaattgtatatttaattccgtgattgtcatgcagatcttttttcaaatacttttcttatact-tgtttttctg--tgtaacagGAAGAGATTCAGAAGAAAACTGGTTATGTTGTAATGAAAGGTGAGGGAATATTTGATGTGGATGCAAATACATCAATTGATCAGCTCTCTGAAGATCTCA
 |   || |     |    ||| |||| |  | | |      |||    |||  || |||  |  || |   || ||| | | |||  |  ||  |   |||||| ||||| ||||| |||||||| ||  | ||||||  || ||||||  | ||||||||||||||||| || || ||||||||||||||||||||| | |
-atcgcctaattatgcatttga-ttgt-tgatgactataactatttgtttgctaatttttcatttaagaacgtttttacattctgtcctggtgattcctacagGAGGAGATACAGAAAAAAACTGGCTACATAGTAATGCGAGCTGAGGGTGTTTTTGATGTGGATGCAAACACTTCCATTGATCAGCTCTCTGAAGATTTGA

upper sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT3G13070.1 (Arabidopsis thaliana), 3'ss of exon 11
----------------------------------------------gaaaaccaagagtggtggctgaattgtatatttaattccgtgattgtc-at--gcagatcttttttcaaatacttttcttatacttgtttttctgtgtaacagGAAGAGATTCAGAAGAAAACTGGTTATGTTGTAATGAAAGGTGAGGGAATATTTGATGTGGATGCAAATACATCAATTGATCAGCTCTCTGAAGATCTCA
                                                | |     || |     | |  | ||| ||  ||  | |  ||| | ||  | |   || | ||| | | ||| |    | | || ||||  |   || |||| ||||||||||||||||| || ||| |||| |||| || |||||| |||| |||||| ||||| |||||||||||||| ||||| |||||||| || |
gtaagtgccctagtttcaactctttaagaaaatcgtcattctagacctacatttctagagaatattaacctatatcttacataacttatttgcccattagtaaggctctattccattgcttatggcctccatgattttg-gctcaatagGAGGAGATTCAGAAGAAAACAGGATATATTGTCATGAGAGATGAGGGCATATATGATGTTGATGCTAATACATCAATTGACCAGCTATCTGAAGAACTGA

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|71871934|gb|DT020989.1|DT020989
EST:     ATGTGGTTGAGGAAATTGTCGGTGAAATCTTCGATGAGAATGATTCAAAA                         GAAGAGATTCAGAAGAAAACTGGTTATGTTGTAATGAAAGGTGAGGGAATA
genomic: ATGTGGTTGAGGAAATTGTCGGTGAAATCTTCGATGAGAATGATTCAAAAgtaaagctcc ... tgtgtaacagGAAGAGATTCAGAAGAAAACTGGTTATGTTGTAATGAAAGGTGAGGGAATA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcatgcagatcttttttcaaatacttttcttatacttgtttttctgtgtaacagGAAGAGATTCAGAAGAAAACTGGTTATGTTGTAATGAAAGGTGAGGGAATATTTGATGTGGATGCAAATACATCAATTGATCAGCTCTCTGAAGATCTCA
                        cttttcttatacttgt  CT-rich tract
            ttttttcaaatacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaccaagagtggtggctgaattgtatatttaattccgtgattgtcatgcagatcttttttcaaatacttttcttatacttgtttttctgtgtaacagGAAGAGATTCAGAAGAAAACTGGTTATGTTGTAATGAAAGGTGAGGGAATATTTGATGTGGATGCAAATACATCAATTGATCAGCTCTCTGAAGATCTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- aaaccaa
- - - - - -gtggtgg
- - - - - - - - - - - - - - - - - - - - - - - tcatgca