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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaatgtaaggatactatataccgagctggtatgttttctatccattttgattataataaatagttatttcttacag

Basic information

species Vitis vinifera
transcript Vv06s0080g00560.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os02g33080.2 (Oryza sativa), 5'ss of exon 3
GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtat-gtgaatgta-aggatactatataccgagc-tggtatgttttctatccattttgattataataaatagttatttcttacag------
|| ||||| |||||||| |||||||||||| | |||||  |||||||||||||||||||||||||  | ||| | || || ||||| ||||||||||||||||| |   ||||| ||  ||  | | |   |   | |  |  |      | || |   ||| |  |  ||| |||||| |          
GAGGAGGCGAACAATGCACATTACAATTCAGTAGCCATTATTGATGCTGATGGCACTGATCTTGGCCTGTACCGCAAATCACATATTCCAGATGGACCAGgtattgcccatgtatagtttatgacagattcactatagactagtcatggactatctgatttaaacaagttagctatttcctttttggctag

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G073950_T01 (Zea mays), 5'ss of exon 4
GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaatgtaaggatactatataccgagctggtatgttttctatccattttgattataataaatagttatttcttacag
||||| ||||||||||| ||||| |||||  | || ||  | |||||||||||| ||||||||||| ||||  | || || || || |||||||||||||||| |     || |  |  || | | | |  |||  ||   ||   |  || |    ||||| |     || | | |  |||
GAAGAAGCAAACAATGCACATTATAATTCGGTGGCTATTATCGATGCTGATGGCGCTGATCTTGGACTCTATCGCAAATCACACATTCCAGATGGACCAGgtaag-----gtcaataggcttt-tcctgttctgccatacattgggtt-atctcatctataa-agccgcttctgtttgtcag

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA12G31100.2 (Glycine max), 5'ss of exon 5
GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaatgtaaggatact-atataccgagctggtatgttttctatccattttgattataataaatagttatttcttacag
|| |||||||||||||| ||||| |||||||| |||||| ||||| ||||||| ||||||||||| || || |||||||||||||| ||||||||||||||||||  |   | |||| | | ||||  | |  | |||||| | |     ||  | | |  |  ||| | |  |  | |||||
GAGGAGGCAAACAATGCACATTATAATTCAATAGCCATAATTGATTCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaatattcaggacatttatatgtc-atttagtatgtctac-----atcctaact-catcaaacaatc-tcccctacag

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G07960.1 (Glycine max), 5'ss of exon 4
GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaatgtaaggatact-atataccgagctggtatgttttctatccattttgattataataaatagttatttcttacag
|| |||||||||||||| ||||| || ||||| |||||| ||||||||||||| ||||||||||| || || |||||||||||||| ||||||||||||||||||  |   | |||  | | || |  | |  | |||||  | |   | |  | |  |  || ||||     |  | |||||
GAGGAGGCAAACAATGCACATTATAACTCAATAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCCCATATTCCAGATGGACCAGgtatgcaatattcaggtcatttatgtgtc-atttagtatgcgtacatcctaactcg--tccaacaaat-----tcccctacag

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA13G39210.1 (Glycine max), 5'ss of exon 4
GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaatgtaaggatact-atataccgagctggtatgttttctatccattttgattataataaatagttatttcttacag
|| |||||||||||||| ||||| |||||||  |||||| ||||||||||||| ||||||||||| || || |||||||| ||||| || ||||||||||||||   |   | |||  | | ||||  | |  | |||| | | |   |||  |       |  ||| | |  |  | |||||
GAGGAGGCAAACAATGCACATTATAATTCAACAGCCATAATTGATGCTGATGGAACTGATCTTGGGATTTATAGAAAGTCTCATATTCCGGATGGACCAGgtatacaatattcaggccatttatatgtc-atttagtatatctacatcccaactc------atcaaacaatc-tcccctacag

upper sequence: Vv06s0080g00560.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT2G27450.2 (Arabidopsis thaliana), 5'ss of exon 4
GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaatgtaaggatactatataccgagctggtatgttttctatccattttgattataataaatagttatttcttacag
|| |||||||| | ||| ||||||||||| ||||| ||| ||||||||||||| |||||  | ||||| || || ||||| ||||| || |||||||| |||  || ||  |  |  |   | |||   |||| |  | | || |  || ||||| | | |     |  || | |||||   
GAGGAGGCAAATACTGCACATTACAATTCGATTGCTATAATTGATGCTGATGGAACTGACTTGGGAATTTATAGGAAGTCTCATATTCCTGATGGACCTGgtgagtcaagtttggagttggaaatat--agcttgagtttcttgttacctttttgctgagacc---tctttttatcttaag-

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|294965150|gb|GW836981.1|GW836981
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|30320849|gb|CD004111.1|CD004111
EST:     CAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: CAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|22014795|gb|BQ799829.1|BQ799829
EST:     T-GCACTGATC-TGGAATCTACAGAAAGTCCCATATCCCAGACGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|71863030|gb|DT012085.1|DT012085
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|71859592|gb|DT008647.1|DT008647
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|71864994|gb|DT014049.1|DT014049
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|294963940|gb|GW836815.1|GW836815
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|26257496|gb|CA808559.1|CA808559
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|71863516|gb|DT012571.1|DT012571
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|110385570|gb|EC950109.1|EC950109
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|352782096|gb|FQ469394.1|FQ469394
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|71865063|gb|DT014118.1|DT014118
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|71858886|gb|DT007941.1|DT007941
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
EST: gi|18459688|gb|BM437966.1|BM437966
EST:     TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAG                         GCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG
genomic: TGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaat ... tttcttacagGCTACCAGGAAAAGTTTTACTTCAATCCAGGCGACACTGGCTTTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAGAGGCAAACAATGCTCATTACAATTCAATTGCCATAGTTGATGCTGATGGCACTGATCTTGGAATCTACAGAAAGTCCCATATCCCAGATGGACCAGgtatgtgaatgtaaggatactatataccgagctggtatgttttctatccattttgattataataaatagttatttcttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA