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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taggtgatatctgaactgaacttctgatgcaactattatctgatctaatgattttgagtcttaatcaggagtaaccattcacttttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA

Basic information

species Vitis vinifera
transcript Vv06s0009g02790.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os01g59340.2 (Oryza sativa), 3'ss of exon 9
taggtgatatctgaactgaacttctgatgcaactattatctgatctaatgattttgagtcttaatcaggagtaaccattcacttttcttt-tgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
| | |      ||  |   |  ||| |      ||| |  |   | |   || |  | |    |     || |   ||| |      ||  |    |||||| ||||| || ||||| || || || ||||||||| |||| |||||||||||| |||| |||||||| |||||||| |  ||  ||||
tggattgatcatgccccagatatct-acattgatataaatttggcaagatatctcaatttgacaaacaaagcatatattgatacaaattcatactttgcagGGCAGAGAGTCATTGGTGAACCTGTGGTTTCTGGGCTAGTACTTGATGATTCTTGGCTTTGGGATCCGGACTTCATGATAGCTTCAAA

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G020002_T03 (Zea mays), 3'ss of exon 6
taggtgatatctgaactgaacttctgatgca-actattatctgatctaatgattttgagtcttaatcaggagtaacc--attcacttttcttttgaa-----ctgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
    ||| | ||| |   |  || |||   | |  |||  ||||     |   ||   | || |||    ||||||   | |   || |  ||| ||      |||||| ||||| || || || || || || ||||||||  |||| |||||||||||| |||| ||||||||||||||||  |  ||  ||||
---ctgagaactggat--actttttgagatagatcatttactgaatgcctcgctt---gactcaatttttagtaactggactaggttatactttaaaaaactttgcagGGCAGAGAGTCATCGGTGAACCTGTGGTTTCTGGACTAGTGCTTGATGATTCTTGGCTTTGGGATCCTGACTTCACGATTGCTTCAAA

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G18920.1 (Glycine max), 3'ss of exon 7
---------------------------------------------------------------------------------------taggtgatatctgaactgaacttct-gatgcaactattatctgatctaatgattttgagt--cttaatcaggagt--aaccattcact--tttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
                                                                                       |||    |  |   ||  || |    ||| |  ||   |    | | ||  ||||||      |  ||||   ||   || | | |||  || ||||    |||||||||| ||||| |||||||||||||| |  |||||||||| ||||||||| ||| |||| ||| ||||||||||    |  || |||||
gttctcaattttaatccttttagagtttttattgattttcattaatgtgttccacagtaacagtgcatgcattcattcaagagagagtagacagttacaacacaaaattaaaagattcttctgc-agaaaaaccaaaaattttgcacaaatatatcaaatgttccactaataactaattgctttcatgctgcagGACAAAGGGTAATTGGAGAGCCAGTTGCCTCTGGGTTAGCCCTTGATGAATCTTGGCTTTGGCATCCTGACTTTGAGACTGCTGCAAA

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA15G06100.1 (Glycine max), 3'ss of exon 6
taggtgatatctgaactgaacttctgatgcaact-attatctgatctaatgattttgagtcttaatcaggagtaaccattc-act--tttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
   ||||| ||     ||    | |||  | ||  |  ||   ||    | || ||   | ||     |         ||| |||  ||  |||    |||||||||| ||||| ||||||||||| || |  |||||||||| ||||||||| ||| |||| ||| ||||||||||    |  || |||||
--agtgatctccc--ttgcttgtttgaaactacagaacatgcaattagtttatatttttttttcccatgacacttttgttccactaattggtttcatgctgcagGACAAAGGGTAATTGGAGAGCCCGTTGCCTCTGGGTTAGCCCTTGATGAATCTTGGCTTTGGCATCCTGACTTTGAGACTGCTGCAAA

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA14G04030.1 (Glycine max), 3'ss of exon 6
taggtgatatctgaactgaacttctgatgcaactattatctgatctaatgattttgagt--cttaatca--ggagtaaccattcacttttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
 |   ||| | |  |    | |||   ||  | |||| |  |   || || |  |   |  || | |    | | ||| ||   |   |  | |||  |||||||||| ||||| |||||||||||  | |  |||||||||| ||||||||| ||| |||| ||| ||||||||||    |  ||||||||
aaaaggatctttacat---atttccactgtga-tattttaagtattattgttccttgataactcagtttttgcaataatcaggtaacctgttattgtgctgcagGACAAAGGGTAATTGGAGAGCCTATTGCCTCTGGGTTAGCCCTTGATGAATCTTGGCTTTGGCATCCTGACTTTGAGATTGCAGCAAA

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G44690.1 (Glycine max), 3'ss of exon 6
---taggtgatatctgaactgaacttctgatgc--aactattatc-tgatctaatgattttgagtcttaatcaggagtaaccattcacttttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
   |     || ||     |||  || | ||    || | ||||  |    | || | ||||  | |      | | ||   |   |   |  | |||  |||||||||| ||||| |||||||||||  | |  |||||||||| ||||||||| ||  |||| ||| ||||||||||   ||  ||||||||
tctttatacatttccactgtgatattttaatttttaagtgttattgttccttgatcactttgttttt------gtaatagtaaggtaacctgttcttgtgctgcagGACAAAGGGTAATTGGAGAGCCGATTGCCTCTGGGTTAGCCCTTGATGAATCCTGGCTTTGGCATCCTGACTTTGACATTGCAGCAAA

upper sequence: Vv06s0009g02790.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G12200.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------------------------------taggtgatatctgaactgaacttc---tgatgcaactat---tatctgatctaatgattttgag--tcttaatcagga---------gtaaccattca-----cttttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
                                                                     |    || ||  | | |||| ||   |  |||||  |    | | |     | |   ||| |   | ||| | || |          |||  ||  |      |||| || || | | ||||||||| ||||||||||||||| || || ||||| ||| |||||||||||  | |||| ||||||||||||||||  |  ||  | ||
gttttctgttacaactcatgtaggactaaccttttgcttttctcattgtatggacattatcctgttagaaatcaatctcctatccgaacatccactagtgcaataacatatgtgtagaaaagtacctttcaaatttttacttagtatttggcttaataaatatgaaaagtttttttgttatgtatttcagGACAGAAGGTTATTGGAGAGCCTGTTGTGTCTGGATTAATCCTTGATGATCATTGGCTTTGGGATCCTGACTTCACAATTGCGTCCAA

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|30137635|gb|CB922973.1|CB922973
EST:     TGTGATGAGCATTGATGCGATGGAAGAAATAGCTAAAGCTCGAAAATCAG                         GACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATT
genomic: TGTGATGAGCATTGATGCGATGGAAGAAATAGCTAAAGCTCGAAAATCAGgtttttttaa ... tgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATT
EST: gi|30131395|gb|CB916734.1|CB916734
EST:     TGTGATGAGCATTGATGCGATGGAAGAAATAGCTAAAGCTCGAAAATCAG                         GACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATT
genomic: TGTGATGAGCATTGATGCGATGGAAGAAATAGCTAAAGCTCGAAAATCAGgtttttttaa ... tgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATT
EST: gi|30295952|gb|CB972746.1|CB972746
EST:     TGTGATGAGCATTGATGCGATGGAAGAAATAGCTAAAGCTCGAAAATCAG                         GACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATT
genomic: TGTGATGAGCATTGATGCGATGGAAGAAATAGCTAAAGCTCGAAAATCAGgtttttttaa ... tgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatgattttgagtcttaatcaggagtaaccattcacttttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA
                       gagtaac  putative branch site (score: 2)
                             ccattcacttttcttt  CT-rich tract
                                     ttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taggtgatatctgaactgaacttctgatgcaactattatctgatctaatgattttgagtcttaatcaggagtaaccattcacttttcttttgaactgcagGACAGAGGGTTATTGGAGAGCCAGTAGTTTCTGGGTTAGTCCTTGATGATTCTGGGCTCTGGGATCCTGACTTCATCAACGCAGCAAA

- - - - - - - - - - cttctga
- - - - - - - - - - - - - - gcaacta