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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atttaggttcagtttcttggtaccctctgacctaagtttgacttagataatttaattttctgcaaatatgttctaacttttgtttgattggattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG

Basic information

species Vitis vinifera
transcript Vv07s0005g03790.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g40830.2 (Oryza sativa), 3'ss of exon 10
atttaggttcagtttcttggtaccctctgacctaagtttgacttagataatttaattttctgcaaatatgttctaacttttgtttgattggattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG
  ||  |         || | |   |||  |    | || |  || |  ||  || ||||    | | | ||  | | ||   ||||  |        |||||   || || || || || ||||||||| | ||||||||||||||||||||||| || || ||||| |||
--ttttgcgggacaatttag-attatcttgct---ggttaatgtacaatataaaactttcctgcactgtattgaatcattctcttgaccgcc------aggttgacctgaagGTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 10
atttaggttcagtttct-tggtaccctctgacctaagtt--tgact--tagataatttaa---ttttctgcaaatatgttctaacttttgtttgattggattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG
 | ||  ||   ||| |  || ||  | |    ||  ||  ||  |  |  | ||| |||   ||| |||||  | | ||  | | ||   ||||  |        |||||   || || || || || ||||||||| | ||||||||||||||||||||||| || || ||||| |||
-tatatttttgttttttgcgggacaatttagattatcttgctggttaatgtacaatataaaactttcctgcac-tgtattgaatcattctcttgaccgcc------agGTTGACCTGAAGGTGCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTTGACCAAGGGAAGAGGATTCTAAAG

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G064695_T02 (Zea mays), 3'ss of exon 10
--------atttaggttcagtttcttggtaccctctgacctaagtttgacttagataatttaattttctgcaaatatgttctaacttttgtttgattggattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG
        ||   | |   |||| ||     ||| ||  ||| || |  || || |  |||  | | ||| | ||   |  |||  ||||    |  |   ||   |||||   || ||||| || || ||||||||| | |||||||||||||| ||||||||||| || ||||| |||
aacaccccataaggatcatgtttttttaggacctgtg--ctatgtatatctcaggtt-tttcttgtactgaatattattgttaa--tttgcccaaccg---ttgtcagGTTGACCTGAAAGTTCCTGTTGTTGTTCGGTTGGAAGGCACCAATGTAGACCAAGGAAAGAGGATTCTTAAG

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G04480.1 (Glycine max), 3'ss of exon 10
atttaggttcagtttcttggtaccctctgacctaagtttgacttagataatttaatt-ttctgcaaatatgttctaactt---ttgtttgattggattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG
   ||  ||    || ||  |        |  |  | ||||    ||||  |   || | |||  | |||  |   | ||   ||  |||     || || |||||| |||| |||||||| || || ||||| || ||||||||||||||||| ||||||||||||||  |||||
---tattttttcctttttaat-tttaaaaaattgtgattgaacatgatacctatcttatcctggtattataatagcatttacttttcttgccattatattcaagGTTGCACTGAAAGTACCAGTTGTAGTTCGTCTGGAAGGCACCAATGTTGATCAAGGAAAAAGAATATTGAAG

upper sequence: Vv07s0005g03790.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G18730.1 (Glycine max), 3'ss of exon 10
atttaggttcagtttcttggtaccctctgacctaagt-ttgacttagataatttaatt-ttctgcaaatatgtt----ctaacttttgtttgattggattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG
       | |  ||| ||  ||       |  || |  ||||    ||||  |  ||| | | |  | |||| |     |||||||| ||  | |  || || |||||| |||| |||||||| || || ||||| || ||||||||||||||||| || |||||||||||| |||||
-----cctccttttttttattaattgaaaaaatagggattgaacatgatacctatattatcccgatattatgatagcattaacttttcttgcaatt-atattcaagGTTGCACTGAAAGTACCCGTAGTAGTTCGTCTGGAAGGCACCAATGTTGATCATGGAAAAAGAATTTTGAAG

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|32458077|gb|CD799251.1|CD799251
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAGGGCACCAACGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|34545859|gb|CF514091.1|CF514091
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|71881691|gb|DT030746.1|DT030746
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|110379096|gb|EC944270.1|EC944270
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|46910485|gb|CN545860.1|CN545860
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|30255821|gb|CB971953.1|CB971953
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|110390462|gb|EC955371.1|EC955371
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|110428351|gb|EC994820.1|EC994820
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|110702283|gb|EE080823.1|EE080823
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|22007633|gb|BQ792667.1|BQ792667
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCCCTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCCCCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|30256178|gb|CB972021.1|CB972021
EST:     TAATGAAATGTGCCATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTCCCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|71883833|gb|DT032888.1|DT032888
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|30256398|gb|CB972241.1|CB972241
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|110714835|gb|EE092196.1|EE092196
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|30305949|gb|CB982743.1|CB982743
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|110362830|gb|EC926386.1|EC926386
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
EST: gi|30256478|gb|CB972321.1|CB972321
EST:     TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAG                         GTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC
genomic: TAATGAAATGTGACATAATAGCAAGTGGAATTGTTAATGCTGCTAAAGAGgtaagatctg ... gattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataatttaattttctgcaaatatgttctaacttttgtttgattggattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG
     tttaattttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttaggttcagtttcttggtaccctctgacctaagtttgacttagataatttaattttctgcaaatatgttctaacttttgtttgattggattttgaagGTTTCACTAAAAGTACCGGTGGTTGTTCGGCTTGAAGGCACCAATGTTGACCAAGGAAAAAGAATTCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - -ttcttgg
- - - - - - - - - - taccctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgcaaa