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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgtttagtcgactgctctcatgttcataagccattgctttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagattcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG

Basic information

species Vitis vinifera
transcript Vv10s0003g04630.t01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os05g51490.1 (Oryza sativa), 3'ss of exon 17
cattgtttagtcgactgctctcatgttcataagccattgctttgataccaaaacaagtat-----tgtgtcaaatgaaatagcttcttatgga---gattcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG
        | || | | ||   ||    |        ||   ||||  | |  |||||||     | | |   ||    |   ||  | ||     | ||| |  |||||||||||||||||||||||||| |||||||| || ||||||||  |||| ||||| ||||||||||| ||
-------gaatctagtactagtataacaagtgtgttgtgtcctgatgtccag-caagtataaatgtattttcgatagtctgaatttctgtgctcctgtttcctttcagGATGTCTACTTTGATGATGAATCAGCTGAAGTAGTAATATCTTCGTTGCGTTTGGGTGATGATCAGGACAG

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g40340.3 (Oryza sativa), 3'ss of exon 15
cattgtttagtcgactgctctcatgttcataagccattgctttg----ataccaaaacaag-tattgtgtcaaatgaaatagcttcttatggagattcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG-----------------------------
        |   || || |  ||||   ||||   | ||  | |    |||       ||| | |  | |  | |||      |||   ||     || |  ||||||||||| |||||||||||||| || || || || |||||||| |||||| ||||||||||||||||  |                             
----aaagaacagaatgttg-catgcggataatatagtgtctagaaccatatttgttgaagctgtacttttgagtgagtggatttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGGGTAATTTGTGATCTTAAAACATACTTTGG

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g40340.1 (Oryza sativa), 3'ss of exon 15
cattgtttagtcgactgctctcatgttcataagccattgctttga----taccaaaacaag-tattgtgtcaaatgaaatagcttcttatggagattcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG
        |   || || |  ||||   ||||   | ||  | ||    ||       ||| | |  | |  | |||      |||   ||     || |  ||||||||||| |||||||||||||| || || || || |||||||| |||||| ||||||||||||||||  |
----aaagaacagaatgttg-catgcggataatatagtgtctagaaccatatttgttgaagctgtacttttgagtgagtggatttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATCTTCACTGCGACTGGGAGATGATCAGGATGG

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g40370.1 (Oryza sativa), 3'ss of exon 4
cattgtttagtcgactgct-ctcatgttcataagccattgctttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagat-tcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG----
        |   || || | |    |   |  ||    |      |||       |||   |   ||  |   | | | ||   || |   | || |  ||||||||||| |||||||||||||| || || || || |||| |||||||||| |||||||||| || ||  |    
--aaaaagaacggaatgttgcatgcggaaaatagtgtctataaccatatttgttgaagctgtacttctgacagagtggatttccattgttttctcctttcagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCAAGATGGGTAA

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: LOC_Os01g40390.1 (Oryza sativa), 3'ss of exon 6
cattgtttagtcgactgctctcatgttcataa--gccattgctttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagat-tcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG-----------------------------
        | | || || |  ||||   ||||  |    |      |||       || |  |   ||  |   | | | ||   || |   | || |   |||||||||| |||||||||||||| || || || || |||| |||||||||| |||||||||| |   | |                              
--aaaaagaatggaatgttg-catgcggataatagtgtctagaaccatatttgttgaaattgtacttctcactgagtggatttccattgttttctccttttagGATGTCTATTTTGATGATGAATCAGCAGAGGTCGTAATATGTTCTCTGCGACTGGGAGATGACCTTAAAACTTACTTTGGTATCCTCTTTTTTTTTTTGC

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM2G149321_T01 (Zea mays), 3'ss of exon 8
cattgtttagt-cgactgctctcatgttcataagccattgctttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagattct-tggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG
   | |  ||| | |    | | |  |  ||  |   |||||    ||  ||||    |    |   | || |     ||  || |    ||||| |  |||||||| || |||||||||||||| ||||| ||||| ||||||||| ||||  |||||||||| ||||| ||
ggatatgaagtgcaataaatatgaactatatt-gtttttgctcaagtagaaaaa-ggttgaacttctatatcagtggactgtttttcttcattctctttcagGATGTGTATTTTGATGATGAATCAGCTGAGGTTGTAATATCTTCTTTGCGTCTGGGAGATGACCAGGACAG

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GRMZM5G812498_T01 (Zea mays), 3'ss of exon 7
-----------------------------------------------------------------------cattgtttagtcgactgctctcatgttcataagccattgctttgataccaaaacaagtattgtgtcaaatg-aaatagcttcttatggagattcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG
                                                                       ||| ||  |  |   || |   ||  |   || |   |  | | || | | ||||   || |  | |  ||  |   | ||  | || |  |  ||  |||||||||||||||||||| || || |||||||| || ||||||||  || | ||||| ||||||||||| ||
gtatgcttaccgtactatttatgtaaatgtttatattgttttacttcaatacggtcaatgtaagattggtgcatggtcaatacttttgattggataattgaaaacatattgtatcatgctataacagacatggatttatctgtgagctgatttctgtgcatgtattt--cagGATGTCTACTTTGATGACGAGTCAGCTGAAGTAGTAATATCTTCATTGTGTTTGGGGGATGATCAGGACAG

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: GLYMA15G13580.1 (Glycine max), 3'ss of exon 17
-cattgtttagtcgactgctc-tcatgt-tcataagccattgct-ttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagattcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG
   | |||| ||  |   ||  | |||| || |  |   ||  | ||||      |   |  ||  ||  |||  |  |  | |  |||| |   ||||| ||||||||||| |||||||||||||| || |||||||| ||||||||| |||| ||||||||||| || || ||
ttctagttttgtttaacacttatgatgtatcttgggatttttttgttgaggtttgatttacgatcatgataaaacatctgacataatatgta---tcttg-cagGATGTCTATTTTGATGATGAATCTGCAGAAGTTGTTATATCTTCTTTGCGGTTGGGAGATGACCATGAAAG

upper sequence: Vv10s0003g04630.t01 (Vitis vinifera), 3'ss of exon 17
lower sequence: AT1G30470.2 (Arabidopsis thaliana), 3'ss of exon 17
cattgtttagtcg--actgctctcatgttcataagccattgctttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagattct-tggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG
  | | | ||  |   |||  |   | || ||||||      | ||  | |      |||  | ||  | ||   | | | ||||||| ||  | | | ||||||||||||||||||||||||||| || ||||| |||||||| ||  ||||  | |||||||| ||||||||
actcgctcagcggctcctgtgcctgtttttataagcagccaatatggaagct---ttagtgatatggtagatatgaaaacctcttatgaagtctatgttgcagGATGTCTACTTTGATGATGAATCTGCAGAAGTCGTCATATCCTCCTTGCGCCTTGGAGATGACCAGGAGAG

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|30321554|gb|CD004816.1|CD004816
EST:     ACTCATGGCCAACTTGAACGGGATGATGAG                         GATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGA
genomic: ACTCATGGCCAACTTGAACGGGATGATGAGgtatgttcaa ... ttcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGA
EST: gi|110698945|gb|EE077019.1|EE077019
EST:     ACTCATGGCCAACTTGAACGGGATGATGAG                         GATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGA
genomic: ACTCATGGCCAACTTGAACGGGATGATGAGgtatgttcaa ... ttcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGA
EST: gi|30321558|gb|CD004820.1|CD004820
EST:     ACTCATGGCCAACTTGAACGGGATGATGAG                         GATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGA
genomic: ACTCATGGCCAACTTGAACGGGATGATGAGgtatgttcaa ... ttcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGA
EST: gi|30134857|gb|CB920195.1|CB920195
EST:     ACTCATGGCCAACTTGAACGGGATGATGAG                         GATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGA
genomic: ACTCATGGCCAACTTGAACGGGATGATGAGgtatgttcaa ... ttcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccaaaacaagtattgtgtcaaatgaaatagcttcttatggagattcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG
                                             ttctt  CT-rich tract
                     aaatgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattgtttagtcgactgctctcatgttcataagccattgctttgataccaaaacaagtattgtgtcaaatgaaatagcttcttatggagattcttggcagGATGTCTACTTTGATGATGAATCGGCTGAAGTTGTCATATCTTCTCTGCGATTGGGAGATGATCAGGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - -tgctctc
- - - - - - - - - - - - - - -taagcca
- - - - - - - - - - - - - - - - - - -tgctttg
- - - - - - - - - - - - - - - - - - - - - - - - -aaaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaatgaa