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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattctatattccaactgtcttctcttttcaattgtcaaacacatccgatgcaaattcagtaaattttttttgttaattggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG

Basic information

species Vitis vinifera
transcript Vv18s0001g00480.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g48290.1 (Oryza sativa), 3'ss of exon 8
cattctatattccaactgtcttctcttttcaattgtca--aacacatccgatgcaaattcagtaaattttttttgttaatt--ggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG
 |   ||| |   ||   || | | ||   |   | ||  | || |||  |   || | | |     ||    ||  ||||     || || |||  |   |||||| ||||| |||||||| || ||  |||| ||||| ||  | || || || || ||||||||||| ||||||||||| ||||||||||| ||||| |||
gaaattatgta--aatcatcatatgttggaagcagccatgagcagatcaaactgaagtcctgct--cttgaggtggcaatttcatgattttttttcttttgtagGTTCATTCTAGACAAGAAAATCGGTCTTGGCCAACCGAAGAGGATTGAAAACGCCAAGATTTTGGTTGCAAATACTGCTATGGACACCGACAAAGTTAAG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: EF517601.1_FGT012 (Zea mays), 3'ss of exon 16
-----cattctatattccaactgtcttctcttttcaattgtcaaacacatccgatgcaaattca-gtaaattttttttgttaattggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG
       | |  | |    | |||  |  |       |    ||      || |   ||| | |     || | |||| ||| |||        | || |  ||||||| |||||||||||||| || |||||||| || || || ||||| |||||||| || |||||||| ||||| ||||| |||||||| |||||||| |||
ctgtgagtaccttttattgagtgttcttgcaggcatctatgtaattgttcccaacagaaaatgacactgatatctttttttatttg------cttcttatatatagGTTCATTCTTGACAAGAAAATTGGCATTGGGCAGCCCAAGCGCATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G058276_T01 (Zea mays), 3'ss of exon 7
-cattctatattccaactgtcttctcttttcaattgtcaaacacatccgatgcaaattcagta--aattttttttgttaattggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG
   | | || |    | ||| |  |   | ||  | |  ||    ||| |    ||    ||   ||| | |||| || ||| |  | ||  | | ||||  | || |||||||||||||| || ||||| || || ||||| || || |||||||| || |||||||| ||||| ||||| |||||||| |||||||| |||
gagtacaatttattgagtgt-tcatgcatgcatctatgtaatgtttcccaacagaaaatggtcctaatatcttttttttatttgcttgtttctatttgca--gATTCATTCTTGACAAGAAAATTGGCATCGGGCAGCCAAAGCGGATTGAGAATGCCAAAATTTTGGTTGCAAACACTGCTATGGACACAGATAAAGTTAAG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G09250.1 (Glycine max), 3'ss of exon 9
--cattctatattccaactgtcttctcttttcaattgtcaaacacatccgatgcaaattcagtaaa---ttttttttgttaattggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG
  ||||   || ||    | | |  |  || |||   |     |     |    |   |  |||||   |    | |||   ||  ||  |||||||  |   || || |||||||||||||| || || ||||| ||||| ||||| |||||||||||||||||  |||||||||| ||||| |||||||| || ||||| |||
tgcatta-gtaatcttgttatttatt--ttccaagcattgcttatccttgcattactctgggtaaaaagtaagctctgtctgttttaaatttgtttt--ggtcagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAACGTATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G19220.1 (Glycine max), 3'ss of exon 9
cattcta-tattccaactgtcttctcttt-----tcaattgtcaaacacatccgatgcaaattcagtaaattttttttgttaattggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG
  || || || ||    | | |  | ||      |   || |||      | |  ||   |   |||||  ||| ||| |      |  | |  |||| ||   || || |||||||||||||| || || ||||| ||||| || || |||||||||||||||||  |||||||||| ||||| |||||||| || ||||| |||
tgttttaataatcttgttatttatttttcaagcattgcttatcattttattactctgggtaaaaagtaagctttctttct------gtttttaattttttgatcagATTCATTCTTGACAAGAAAATTGGTATTGGACAACCCAAGCGGATAGAGAATGCAAAGATACTGGTGGCAAACACTGCCATGGACACAGACAAAGTGAAG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT5G20890.1 (Arabidopsis thaliana), 3'ss of exon 8
cattctatattc-caactgtcttctcttttcaattgtcaaacacatccgatgcaaattcagtaaatt--ttttttgttaattggaatcttgttttctgc--atagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG
      || ||   |    || | || | |   ||||        ||   | | | |  |||||  |  | |  ||| |  |  | |     | | |||   ||||||||||||||||||||| ||||| ||||| || || || ||||||||||||||||| || || || || |||||||| ||||| ||||||||||| |||
---ggaatgttgatagtcatcatgtcatcttg-ttgtgttgtgtttcttcttcta-tcgagtaatatggtctcatgtcacctcaacttaaaatctatgcctgtagGTTTATTCTTGACAAGAAAATAGGAATTGGGCAGCCTAAGCGCATAGAGAATGCAAATATCTTAGTAGCTAATACTGCTATGGATACCGATAAAGTGAAG

upper sequence: Vv18s0001g00480.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S116_55V6.1 (Physcomitrella patens), 3'ss of exon 8
--cattctatattccaactgtcttctcttttcaattgtcaaac--acatccgat-gcaaattcagtaaattttttttgttaattg--gaatcttgttttctgca----tagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG
     |  ||    ||| |   |  |   | |   |   || |    |||     |||  |  | |  ||||| | | ||| |     ||| | |  | |||       ||||||||||| ||||||||||| ||  | |||||||| ||||| || || ||||| || ||| | ||||| |||||||| ||||| || || || ||||| 
gtaggttaatgaatcaaattcttcttggctacctctaagaagcttgtatctaccagcatttatactcgattttctctcttagtgactaaatttggaatcctggggttccagGTTTATTCTGGACAAGAAGATCGGAGTCGGTCAACCCAAACGGATTGAAAATGCCAAAATTCTTGTGGCTAATACTGCCATGGATACTGACAAGGTCAAA

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|352777695|gb|FQ466748.1|FQ466748
EST:     ATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG                         GTTTATTCTTGACAAGAAGATAGGCATTGGTCCACCAAAACGCA
genomic: ATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGGgtagagcata ... ttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCA
EST: gi|352781730|gb|FQ469028.1|FQ469028
EST:     ATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGG                         GTTTATTCTTGACAAGAAGATAGGCATTG
genomic: ATTATTAAGAAGCCTGGAGGATCACTCAAAGACTCATTTTTGGATGAAGGgtagagcata ... ttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgatgcaaattcagtaaattttttttgttaattggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG
                          tgttaat  putative branch site (score: 3)
                                      tcttgttttct  putative PPT
       aaattcagtaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattctatattccaactgtcttctcttttcaattgtcaaacacatccgatgcaaattcagtaaattttttttgttaattggaatcttgttttctgcatagGTTTATTCTTGACAAGAAGATAGGCATTGGTCAACCAAAACGCATAGAGAATGCAAAGATTTTGGTGGCAAATACTGCAATGGACACCGATAAAGTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - tccaact
- - - - - - - - - - - - - - - - - - - - cacatcc
- - - - - - - - - - - - - - - - - - - - - - - -gatgcaa