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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccaccctaccatctaccattctttcagaatcatgccttttctcatattggtaacacaagaaattatccgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATGGTATGCGGGGTTTATGTGGCATGGAAAGGATGCATTTTCGTAGTTTTGA

Basic information

species Vitis vinifera
transcript Vv10s0003g01700.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA05G29410.1 (Glycine max), 3'ss of exon 5
gta-tgccaccctaccatctaccattctttcagaatcatgccttttctcatattggtaacacaagaaattatccgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATGGTATG----CGGGGTTTATGTGGCATGGAAAGGATGCATTTT-CGTAGTTTTGA
|||  |  |   | || | | ||||  | |    |  || |   |  | | || ||||| | ||| |  | |  |||||||||||||||||||||||| || ||| |||||||||| ||||  |     || || | ||       |   | |||| |  |  |  | |  ||||| |  ||      
gtaacgatattgt-ccgttttccatcttgtttttactatactcataataa-ataggtaatataaggagcttt--gttttgcagCTGGAAGAACAATTCGAAACTGAAGTTGCCTGCCTGAATTATCTCAAGTTGTTTTGGAATTTAGACCTGTGTGACCAGTCACCGCTAAATTTTACAGAGC-----

upper sequence: Vv10s0003g01700.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA08G12570.1 (Glycine max), 3'ss of exon 5
---gtatgccaccctaccatctaccattctttcagaatcatgc-cttttctcatattggtaacacaagaaattatccgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATGGTATGCG----GGGTTTATGTGGCATGGAAAGGATGCATTTTCGTAGTTTTGA
    | |      ||   |    | ||  | |     | |||| | | |  || || ||||| | ||| | || |  |||||||||||||||||||||||| || ||| |||||||||| ||||  |    ||| || |  |      ||     |||| |  |  |  | |  |||| |  ||      
gtaatgttattgtctgttaaggtcgatcttgtttttgttatgctcatataacaaatgggtaatataaggagtttt--gttttgcagCTGGAAGAACAATTCAAAACTGAAGTTGCCTGCCTGAATTATCACGAGGTGTTTAGGAATTTGGACCCGTGTGACCAGTCACTGCTAAATTTACAGAGCG----
















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|352787179|gb|FQ477799.1|FQ477799
EST:     CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAG                         CTGGAAGAACAATTCCAAG
genomic: CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAG
EST: gi|30298685|gb|CB975479.1|CB975479
EST:     CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAG                         CTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
genomic: CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
EST: gi|110720994|gb|EE097488.1|EE097488
EST:     CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAG                         CTGGAAGAACAATTCCCAGCTGCAGTTGCCTGCTTGA-CCAAAAAGAGATG
genomic: CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
EST: gi|71890673|gb|DT039728.1|DT039728
EST:     CTTCTACTACTACTTTATTAG                         CTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
genomic: CTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
EST: gi|110686747|gb|EE064739.1|EE064739
EST:     CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAG                         CTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGA-AGATG
genomic: CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
EST: gi|110703644|gb|EE080669.1|EE080669
EST:     CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAG                         CTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
genomic: CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
EST: gi|30298746|gb|CB975540.1|CB975540
EST:     TTGGTCCAAACAGCACTTTATGCAGANNNNNNNNACTACTACTTTATTAG                         CTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
genomic: CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
EST: gi|110688848|gb|EE067872.1|EE067872
EST:     CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAG                         CTGGAAGAACAATTCCA-GCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
genomic: CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
EST: gi|110687293|gb|EE064579.1|EE064579
EST:     CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAG                         CTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
genomic: CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATG
EST: gi|351040756|gb|FQ438300.1|FQ438300
EST:     CTGGGCCAAACAGCACTTTATGCAAATTTCTTCCACTACTACTTTATTAG                         CTGGAAGAACAATTCCAAGCTGCAGTTGC
genomic: CTGGTCCAAACAGCACTTTATGCAGATTTCTTCTACTACTACTTTATTAGgtatgccacc ... cgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagaatcatgccttttctcatattggtaacacaagaaattatccgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATGGTATGCGGGGTTTATGTGGCATGGAAAGGATGCATTTTCGTAGTTTTGA
                         tggtaac  putative branch site (score: 2)
                                           tccgtttt  putative PPT
                                  aagaaattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccaccctaccatctaccattctttcagaatcatgccttttctcatattggtaacacaagaaattatccgttttgcagCTGGAAGAACAATTCCAAGCTGCAGTTGCCTGCTTGAACCAAAGAGAGATGGTATGCGGGGTTTATGTGGCATGGAAAGGATGCATTTTCGTAGTTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG