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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTTACTGCCCCTCATGGGCTCTTTCTTGGCCTTACCGCAAGCAGAATTTATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgaggttacactttaattgttattcaatttctcttgtgttgctagcaatgtattgagactttcaggttaagcttctgaccttttttgacatgtgt...

Basic information

species Vitis vinifera
transcript Vv08s0007g07020.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G26620.2 (Glycine max), 5'ss of exon 2
CAGTTACTGCCCCTCATGGGCTCTTTCTTGGCCTTACCGCAAGCAGAATTTATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgaggttacactt-----taattgttattcaatttctcttgtgttgctagcaatgtattgagactttcaggttaagcttctgaccttttttgacatgtgt
|| ||||||||| |||||||||||||||||||| || |||| ||| ||||| ||||||||||| ||||| || ||| | |||||| | ||||| || ||||||  |||   |   | |     | ||| |  || ||   || |  | |   ||      | || | | |||      |||  |      |   | |  |     
CAATTACTGCCCTTCATGGGCTCTTTCTTGGCCATATCGCAGGCAAAATTTGTTACGGGAAATTGTTGGTTACCGTCCAGACATTATTTGTCTTCAGGAGgtacatgaacatgttcctgcttgtgattttagtttaaaaact-tcatttcattacttggctcttcaaaattttttaacaagaatggtgtttaagtagctag----

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G15980.2 (Glycine max), 5'ss of exon 2
CAGTTACTGCCCCTCATGGGCTCTTTCTTGGCCTTACCGCAAGCAGAATTTATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgaggttacactttaattgttattcaatttct----cttgtgttgctagcaatgtattgagactttcaggttaagcttctgaccttttttgacatgtgt
|| ||||||||| |||||||||||||||||||| || |||| ||| ||||| |||||||||||  |||| |||||  | |||||| | ||||| || ||||||  |||   |   | |   |||| |||    ||      ||||  ||  |  |   |   |   |||||    | |      ||   |||    |  |    
CAATTACTGCCCTTCATGGGCTCTTTCTTGGCCATATCGCAGGCAAAATTTGTTACGGGAAATTATTGGTTATCGCCCAGACATTATTTGTCTTCAGGAGgtacatgaacatgttcct-gcttgtgattttgcttgaaaaacttgatttcattacttggctcttcaacttttttttaacaagattggtgtttaagtagcta---

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA19G39210.1 (Glycine max), 5'ss of exon 2
CAGTTACTGCCCCTCATGGGCTCTTTCTTGGCCTTACCGCAAGCAGAATTTATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgaggttacactttaattgttattcaatttctc-------ttgtgttgctagcaatgtattgagacttt-caggttaagcttctgaccttttttgacatgtgt
|| |||||||||  | ||||||||||| ||||| || || | ||| ||||| ||||| ||||||||||| || |||||||| ||| | ||||| || ||||||| | |   |    |||   ||| |||   ||  ||       || | ||  || ||  ||| |||   |   |   || |  |||     |||||| | |     
CAATTACTGCCCTACGTGGGCTCTTTCCTGGCCATATCGTAGGCAAAATTTGTTACGAGAAATAGTTGGTTACCGTGCTGATATTATTTGTCTTCAGGAGgtatgtaaatgt-tgttttggctgtgattttgttggtcattaaacttattttaataaca--gtactgatcttcaactcatttattttcaagattttttttaga-----

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA03G36550.1 (Glycine max), 5'ss of exon 2
CAGTTACTGCCCCTCATGGGCTCTTTCTTGGCCTTACCGCAAGCAGAATTTATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgaggttacactttaattgttattcaatttctc-ttgtgttgctagcaatgt--attgagactttcaggtta--agcttctgaccttttttgacatgtgt
|| ||||||||| || ||||||||||| ||||| || |||| ||| ||| | ||||| ||||||||||| || ||||| || ||| | ||||| || ||||||  | |   |    |||   ||| |||   ||  || ||  | |  |   |||     |   ||  ||||  | |     ||   |  |||||| | ||    
CAATTACTGCCCTTCGTGGGCTCTTTCCTGGCCATATCGCAGGCAAAATCTGTTACGAGAAATAGTTGGTTACCGTGCAGATATTATTTGTCTTCAGGAGgtacataaatgt-tgttttggctgtgattttgttggtcattaagcttattttaataacagtactgatcttcaactcatttattttcaagatttttttagat----

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 5'ss of exon 2
CAGTTACTGCCCCTCATGGGCTCTTTCTTGGCCTTACCGCAAGCAGAATTTATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgagg---ttacactttaattgttattcaattt----ctcttgtgttgctagc-aatgtattgagactttcaggttaagcttctgaccttttttgacatgtgt
||||||||||||| ||||||||||  ||||| | ||||| |  |||||||| ||||||||||| ||    || ||||| || || || ||||| |||||||||| | |     |||      || |  || | | ||     |  ||   |||||||  |||| ||  | || |       ||  || |  | |||||   | ||   
CAGTTACTGCCCCACATGGGCTCTCGCTTGGACATACCGTAGACAGAATTTGTTACGGGAAATTGTCAAGTACCGTGCAGATATAGTTTGTCTACAAGAGgtatgttaaatatttatggcacaagttgtactgacttggaaacgtttcaattgctagttaatggataaatacctct---ccaatatttt--cgtttttcatcttgcag

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|294965969|gb|GW839308.1|GW839308
EST:     TATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAG                         ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACAT
genomic: TATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgagg ... ctcctttcagATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACAT
EST: gi|110705484|gb|EE082386.1|EE082386
EST:     TATTACNGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAA                         ATTCAA-GTGATCATTTTGAGGAATTTTTTGCCC-AGAGCTGGACNAACAT
genomic: TATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgagg ... ctcctttcagATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACAT
EST: gi|71862579|gb|DT011634.1|DT011634
EST:     TATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAG                         ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACAT
genomic: TATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgagg ... ctcctttcagATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACAT
EST: gi|110697952|gb|EE075410.1|EE075410
EST:     TATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAG                         ATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACAT
genomic: TATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgagg ... ctcctttcagATTCAAAGTGATCATTTTGAGGAATTTTTTGCCCCAGAGCTGGACAAACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTTACTGCCCCTCATGGGCTCTTTCTTGGCCTTACCGCAAGCAGAATTTATTACGGGAAATAGTTGGATATCGTGCTGACATTGTCTGTCTGCAAGAGgtatctgaggttacactttaattgttattcaatttctcttgtgttgctagcaatgtattgagactttcaggttaagcttctgaccttttttgacatgtgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA