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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgatgctaataatatgtagacaaattcccctttacactcctatattttatacatattgttatcctcaaaagtttgaattaggatgtaattagaa...

Basic information

species Vitis vinifera
transcript Vv02s0012g01170.t01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 7
GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgt-------aacttgatgctaataata----tgtagacaaattcccctttacactcctat-attttatacatat-tgttatc--ctcaaaagtttgaattaggatgtaattagaa-----------------------------------------------
|| ||||| ||| | ||||||||||| ||||||||||||||||||||||| |||||  |||||||       || |||  | ||||  ||    || |   |||      |||   | ||  | | | | |||||   | ||||    | |  ||   |   ||  ||| ||  |                                                  
GCGATGGTGGCAAGAGGGGATCTTGGTGCTGAACTTCCAATTGAGGAAGTTCCTTTGCTGCAGgttagtttaaatttgtagataattttactagtgcaagaaaacatgtgtttgttcccccctcactctctacatcccttttatttgtttattagcacgc-ctaaaatgcaacaaatgaataaagcactaacaacatttaaatcacatgtgttttacttctccag

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GRMZM2G144730_T01 (Zea mays), 5'ss of exon 7
GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgatgctaataatatgtagacaaattcccctttacactcctatattttat---acatattgttatcctcaaaagtttgaattaggatgtaattagaa---------------------------------
|||||||| |||||||| || ||||| ||||||||||| |||||||| || |||||  | ||||| |  | |   ||    ||       |  | | ||    || | || || | |||     | |   | ||    ||||     |   || ||     ||| |                                 
GCAATGGTGGCACGTGGAGACCTTGGTGCTGAACTTCCGATTGAGGATGTTCCTTTGCTACAGgtgagatcacattacatgtacagttttaggtgcaccaagtcatttct-tactgtatctagtaaaggatgatgtgtaaaaacgcaaccaagcatcagcatagtataaattgtgactgttttacttctcttttttcag

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA01G40860.1 (Glycine max), 5'ss of exon 6
GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgatgctaataatatgtagacaaattcccctttacactc-ctatattttatacatat-tgttatcctcaaaagtttgaattaggatgtaattagaa
|| ||||| || ||||||||||||||||||||||||||||| |||||||| ||||||||||||||||  ||||||| | | ||    || |  |   || ||    || | ||   | | |  |||      || |  |     |||  ||  |  ||  | |  
GCCATGGTCGCTCGTGGGGATCTTGGAGCTGAACTTCCAATAGAGGAAGTTCCTTTATTGCAGgtaatgtgatgctcagagtaacacgatatgtatgccattttgttcacaatgggtgagatgtatgcaagctctttcatgagatgatctacaaaatatgttg--

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: GLYMA11G04490.1 (Glycine max), 5'ss of exon 3
GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgatgctaataatatgtagacaaattcccctttacactcctatattttatacatattgttatcctcaaaagtttgaattaggatgtaattagaa---
|| |||||| |  |||||||||||||||||||||||||||| |||||||| |||||||||||||| |  | ||||| | | ||  |||    ||     | | |  |  | |     ||   |   | | |   |||    ||  || ||    |    | ||   
GCCATGGTTACTTGTGGGGATCTTGGAGCTGAACTTCCAATAGAGGAAGTTCCTTTATTGCAGgtgatgttatgctcagagtagctagcatgatatg--tatgccattttgttcacaatgggtga-gatgtatgcaagttctttcatgagatgatctacaaaatat

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: AT1G32440.1 (Arabidopsis thaliana), 5'ss of exon 7
GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgatgctaataatatgtagacaaattcccctttacactcctatattttatacatattgttatcctcaaaagtttgaattaggatgtaattagaa
||||||||||| ||||| |||||||||||||||||||| ||||| || ||||| || || ||||||| |  | |  | |    |   || | ||| |  |  || ||  |    ||||| ||| ||| |||  |     || | ||||               
GCAATGGTTGCTCGTGGAGATCTTGGAGCTGAACTTCCCATTGAAGAGGTCCCGTTGTTACAGgtaaatccaag--acttggtttctgaaacattactttagactctgttggtatttatgcat-ttgctattgt-----gtcttaattttag-----------

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 7
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 5'ss of exon 6
GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgta--acttgatgctaataatatgtagacaaattcccctttacactcctatatttta-tacatattgttatcctcaaa-agtttg--aattaggatgtaattagaa-------------------------------------------------------------------------------
|| |||||||| || || |||||||||||||| || |||||||||||||| ||  |  ||||||||  |   ||   ||      | ||   |  || | ||| | | ||  || |   | |    | | || |  ||||  ||  ||  |  ||   |||||    |                                                                                
GCTATGGTTGCTCGAGGAGATCTTGGAGCTGAGCTGCCAATTGAGGAAGTGCCCCTTCTGCAGgtacaatgcgaaattagctgagtctacttacttttctctt-atagtcgcatttgagaatgggaactcttttagtcaatcagcatggtatgtatcgtgtaacagtacggtccttgttgatttgtagtgcacatgggcttctcagtgttcaccatagagggttgacgacatgcataactttctgcag

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|110711036|gb|EE087773.1|EE087773
EST:     GTGGGGATCTCGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG                         GAGGACATCATTAGAAGGTGTCACAGCATGCAGAAACCTGTTATTGTAGCA
genomic: GTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgat ... ttttaaatagGAGGACATCATTAGAAGGTGTCACAGCATGCAGAAGCCTGTTATTGTAGCA
EST: gi|27586266|gb|CB008961.1|CB008961
EST:     GTGGGGATCTCGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG                         GAGGACATCATTAGAAGGTGTCACAGCATGCAGAAACCTGTTATTGTAGCA
genomic: GTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgat ... ttttaaatagGAGGACATCATTAGAAGGTGTCACAGCATGCAGAAGCCTGTTATTGTAGCA
EST: gi|351025070|gb|FQ433487.1|FQ433487
EST:     GTGGGGATCTCGGAGCTAAACTTCCAATTGAGGAAGTCCCTTTATTGCAG                         GAGGACATCATTAGAAGGTGTCACAGCATGCAGAAACCTGTTATTGTAGCA
genomic: GTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgat ... ttttaaatagGAGGACATCATTAGAAGGTGTCACAGCATGCAGAAGCCTGTTATTGTAGCA
EST: gi|351014767|gb|FQ437967.1|FQ437967
EST:     TGGGGATCTCGGAGCTAAACTTTCCAATTGAGGAAGTCCCTTTATTGCAG                         GAGGACATCATTAGAAGGTGTC
genomic: TGGGGATCTTGGAGCTGAACTT-CCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgat ... ttttaaatagGAGGACATCATTAGAAGGTGTC
EST: gi|110388166|gb|EC952886.1|EC952886
EST:     GTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAG                         GAGGACATCATTAGAAGGTGTCACAGCATGCAGAAACCTGTTATTGTAGCA
genomic: GTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgat ... ttttaaatagGAGGACATCATTAGAAGGTGTCACAGCATGCAGAAGCCTGTTATTGTAGCA
EST: gi|351030123|gb|FQ430865.1|FQ430865
EST:     GTGGGGATCTCGGAGCTAAACTTCCAATTGAGGAAGTCCCTTTATTGCAG                         GAGGACATCATTAGAAGGTGTCACAGCATGCAGAAACCTGTTATTGTAGCA
genomic: GTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgat ... ttttaaatagGAGGACATCATTAGAAGGTGTCACAGCATGCAGAAGCCTGTTATTGTAGCA
EST: gi|351027131|gb|FQ439993.1|FQ439993
EST:     GTGGGGATCTCGGAGCTAAACTTCCAATTGAGGAAGTCCCTTTATTGCAG                         GAGGACATCATTAGAAGGTGTCACAGCATGCAGAAACCTGTTATTGTAGCA
genomic: GTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgat ... ttttaaatagGAGGACATCATTAGAAGGTGTCACAGCATGCAGAAGCCTGTTATTGTAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAATGGTTGCACGTGGGGATCTTGGAGCTGAACTTCCAATTGAGGAAGTCCCTTTATTGCAGgtaacttgatgctaataatatgtagacaaattcccctttacactcctatattttatacatattgttatcctcaaaagtttgaattaggatgtaattagaa

- - - - - - - - - - - TTGGAG
- - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcccct