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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatcatgatgaatggtttatctaaagttgatccaggtgattcctgagtggcaactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC

Basic information

species Vitis vinifera
transcript Vv04s0008g06040.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 3'ss of exon 9
---atatc-atgatgaatggtttatctaaagttgatccaggtgattcctgagtggcaactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC
   || |     |    || ||| | | ||      | |  |  | |       |  ||  ||    | | |  |  ||| |   ||   |||   | || |||||| ||||| ||| ||||| |  | || || || ||||| || ||||| ||||||||||| |||||||| |||||||| |||||||| |||||| |  | 
ctaatgtttgcaacagttgctttgtatgaatcaatacaaaatagtactcttactgtgacactgcaaagcttattt-ttaactgaaattccttt---ccttgcagGGTGAAGAGCCAGCTGAAACGATTGGCACGGCCCATGTATTCGAATCCCCCTATTCATGGTGCTAGGATAGTTGCCAACGTTGTTGGGGATCCAACCATG

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM5G836910_T01 (Zea mays), 3'ss of exon 9
atatcatgatgaatggtttatctaaagttgatccaggtgat----tcctgagtggcaactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC
   |    ||   || || || || ||      ||||  ||    | |    |||     | |  | |    | | |    || ||  |   |  || ||||||||||||||| ||| ||||| |  | || || || |||||||| || || |||||||| || || | ||| |||||||| ||||||||||||||| |  | 
--tttccaatagttgcttcatatacagaatcggcaggcaatagtcttccttttggtgcaatagacttgtctccttacggcattccacgtcact--tcctttcagGGTAAAGAGCCAGCTGAAACGATTGGCACGTCCCATGTACTCGAACCCCCCTATTCACGGTGCCAAGATAGTTGCCAACGTTGTTGGTGATCCAACCATG

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA14G13480.1 (Glycine max), 3'ss of exon 9
atatcatgatgaatggtttatct--aaagttgatccaggtgattc--ctgagtggcaactttgggtggatgacctg--ctaatttgcatatttttattct-tttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC
        ||   || |||| ||  |||| |||       |||||  ||   | |  ||  ||  ||  | |   |   |  |||    ||    | | | |||||||||||| || ||||||||||||||||| |||||||||||||| ||||||||  | || || |||||||| |||||| ||||||||||  | |||| ||||
-------tatttctgttttaactagaaagatgacatcttagattcaacttgattgtgacaatgtatgcctcagtagaagttctttcttgatcgacaatgtgtttcagGGTAAAAAGCCAGTTGAAAAGGATTGCCCGACCAATGTACTCTAATCCTCCAGTACACGGGGCTAGGATAGTTGCCGATGTTGTTGGAAACCCAGTTCTC

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G33050.4 (Glycine max), 3'ss of exon 9
---atatcatgatgaatggtttatctaaagttgatccaggtgatt----cctgagtggcaactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC
    ||  | |||||    ||    | || |||||   ||  ||     ||| ||| | |  | || || ||| | |    ||| ||    |    || | ||||||||||||||| ||  ||||||||||||| |||||||||||||| ||||| ||  | || || |||||||| |||||| ||||||||||  | |||| ||||
taactagaaagatgacatcttagattcaacttgattgtggcaatgtatgcctcagtagaagttctgtgttgatcaac----aatgtg---gtaacgatgcgtttcagGGTAAAGAGCCAACTGAAAAGGATTGCCCGACCAATGTACTCTAATCCACCGGTACACGGGGCTAGGATAGTTGCCGATGTTGTTGGAAACCCAGTTCTC

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 3'ss of exon 10
----------------------------------------atatcatgatgaatggtttatctaaag-ttgatccaggtgattcctgagtggcaactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC
                                        |  | ||  || |   |   | |  |  || | |     ||  | |   | || ||   || |  |||      | |   | | |   |  ||  ||||||||| ||||| |||||||||||||||||||| || |||||||| ||||| ||  ||||||| || || || || |||||||| || ||||||  | || | 
gtaaaacttactctaaattttcttatcatgagcctgttgcaagtgatcctggagtctcagtttctatctttaccgtcacgaaccatatctagctaca--ggttttatggaacctttaccagta-acactacttgctttcagGGTCAAGAGCCAGTTGAAAAGGATTGCTCGGCCTATGTACTCGAATCCACCAGTTCATGGGGCGAGAATCGTGGCCAATGTAGTGGGTGATGTAACTATG

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S540_7V6.3 (Physcomitrella patens), 3'ss of exon 9
-----------------------atatcatgatgaatggtttatctaaagttgatccaggtgattcctgagtggc-----aactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC
                       |  |||| |||   | ||| || |||||  |  ||  ||     || |  |        || |   || |  | ||| |  |      ||| || |   | ||||||| ||||| ||| |||| ||||||||  |||||||||||||||| || ||| |||| || ||  | ||||||||||| |||||||| || ||| || | 
gtatgccttatcaacatctctagagttcat-atgtgagctttgtc-aaagtcaacacaattgggcattgcgctgttcatagtctctaattgcagaatctgatgct----ggattgttgtgtgtatcagGGTTAAGAGCCAGCTGAAGAGGATTGCAAGACCAATGTACTCAAACCCACCTGTTCACGGTGCCCGTATTGTTGCCAACGTTGTTGGCGAGCCAACTATG

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|110396712|gb|EC962407.1|EC962407
EST:     AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAG                         GGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
genomic: AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAGgtacaacaaa ... ttcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
EST: gi|32270026|gb|CD719185.1|CD719185
EST:     AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAG                         GGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
genomic: AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAGgtacaacaaa ... ttcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
EST: gi|32272538|gb|CD721697.1|CD721697
EST:     AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAG                         GGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
genomic: AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAGgtacaacaaa ... ttcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
EST: gi|30326281|gb|CD009543.1|CD009543
EST:     AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAG                         GGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
genomic: AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAGgtacaacaaa ... ttcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
EST: gi|30326632|gb|CD009894.1|CD009894
EST:     AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAG                         GGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
genomic: AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAGgtacaacaaa ... ttcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
EST: gi|161714230|gb|FC063508.1|FC063508
EST:     AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCACCAAG                         GGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
genomic: AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAGgtacaacaaa ... ttcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
EST: gi|29785081|gb|CB341792.2|CB341792
EST:     AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAG                         GGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
genomic: AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAGgtacaacaaa ... ttcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
EST: gi|32271796|gb|CD720955.1|CD720955
EST:     AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAG                         GGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC
genomic: AGGATTGGGGCAATCAATGTGGTCTGCTCATCAGCAGATGCAGCAGCAAGgtacaacaaa ... ttcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtggcaactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC
                         tgctaat  putative branch site (score: 2)
                                     tatttttattcttttc  putative PPT
                            taatttgcatattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatcatgatgaatggtttatctaaagttgatccaggtgattcctgagtggcaactttgggtggatgacctgctaatttgcatatttttattcttttcagGGTAAAGAGTCAGTTGAAAAGGATTGCTCGACCAATGTACTCAAATCCTCCTATTCATGGAGCTAGGATTGTTGCCAATGTTGTTGGTGATCCAGCTCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - -tgaatgg
- - - - - - - - - - - - - - - - - - - - ttcctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgcta