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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGGGGAGATTTAGTGGCAGACATGCCACTGAAGATATGTTACCCTGCTCTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattccatcttactgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcag

Basic information

species Vitis vinifera
transcript Vv13s0074g00720.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os04g33490.1 (Oryza sativa), 5'ss of exon 4
AATGGGGAGATTTAGTGGCAGACATGCCACTGAAGATATGTTACCCTGCTCTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaatt----ccatcttactgcctatgctattcctttttttttttttccctttgatttgattgttttca-tgtcactattggattgcattttgatgcag
|||||   ||||||||||| || |||||| |||||||||| || ||||||||||| | |||||| ||| || | || || || || || ||||| || |||| ||   |      ||| |    ||  ||  |||     | |||   || | | | ||||| || |||||  | ||| |   |                  
AATGGTCTGATTTAGTGGCGGATATGCCAATGAAGATATGCTATCCTGCTCTTGAGGATCAGGAGTGGAAATTCATTACAGGGAGCGACCCTAAAAATACgtgagccctatgattatcatgtaacccgtgtaatttagactgtttggatttcatcttatttgttttttttctctttcaatgcag------------------

upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os02g32730.1 (Oryza sativa), 5'ss of exon 5
AATGGGGAGATTTAGTGGCAGACATGCCACTGAAGATATGTTACCCTGCTCTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattccatcttactgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcag
|||||   |||||||||||||| |||||| |||||||||| || |||||||| ||    ||||||||| | || || || || ||||| || ||||| |||| ||  |||    | | |  || |||   ||  | |   | ||     |   ||  ||   | ||| |   | |||   |||| |||  |      
AATGGTCTGATTTAGTGGCAGAGATGCCATTGAAGATATGCTATCCTGCTCTAGAGAACCAGGAATGGAAGATCATTACTGGAAGTGACCCAAAGAATACgtgagttttcggaataattatctttgca--tctatgtacatgttcaagttccaat--gagcatcttcttagtaatatct-attg-attcag------

upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G040843_T01 (Zea mays), 5'ss of exon 5
AATGGGGAGATTTAGTGGCAGACATGCCACTGAAGATATGTTACCCTGCTCTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattccatcttactgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcag
|||||   |||||||| ||||| |||||||| |||||||| || ||||||||||||   ||||||||| |||| ||||| || ||||| ||||| ||||||| ||  ||  || ||  | |   |  ||  |  |   |    |     |    ||    | ||| ||||   ||     ||| | ||||  | |||
AATGGTCTGATTTAGTTGCAGAGATGCCACTAAAGATATGCTATCCTGCTCTTGAAAACCAGGAATGGAAAATCATCACTGGGAGTGACCCTAAAAACACgtgagccttagatgttttttcaatttttaccctctacctgggatcatgttgcagttc--ctttttacatg---cttggcaatttctttttcgtacag

upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G040843_T03 (Zea mays), 5'ss of exon 1
-----AATGGGGAGATT-TAGTGGCAGACATGCCACTGAAGATATGTTACCCTGCTCTTGAAGGTCAGGAAT-----------GGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattccatcttactgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgc-attttgatgcag--------
     | |||  |  |  ||  ||  |  |    | || | |  |   | || |||| |   |       ||           || || ||||   |  |||| | |       ||   ||    ||  ||  | ||||  |      | | ||   | |      | ||||||  |||     ||| |||||  |   ||| ||  || |   |        
TGTTGAGTGGATACCTCCTAAGGGTGGTTACTTTATTGGAAACCT-CCAGCCAGCTCATATGGACTTCCGATTCTTTTCACTGGGAAATTTATGGTCAATAgtaagcagcttggca-acaactcatcagtcgca-tgccattttagaccttattgagtctaaatggtctgatttagttgcagagatgccactaaagatatgctatcctgctcttgaaaaccag

upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G15220.1 (Glycine max), 5'ss of exon 5
AATGGGGAGATTTAGTGGCAGACATGCCACTGAAGATATGTTACCCTGCTCTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattccatcttac--tgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcag
|||||  |||||| |||||||| |||||| | ||||| ||||| ||||||||||| |||||||| ||||| || ||||| || ||||||||||||||||||||     || |  || |  ||  |||| | |||  || | || || |   ||| ||   ||  ||||        ||||  |||   |||||  ||||
AATGGTCAGATTTGGTGGCAGAGATGCCATTCAAGATTTGTTATCCTGCTCTTGATGGTCAGGAGTGGCAGATAATCACAGGCAGTGATCCTAAGAACACgtactgtatctaatttgccgtgtttatgtttttctgttatcttattatatttttcatcaaatgattttt------ttatttaattattttttg--gcag

upper sequence: Vv13s0074g00720.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G31920.1 (Glycine max), 5'ss of exon 4
AATGGGGAGATTTAGTGGCAGACATGCCACTGAAGATATGTTACCCTGCTCTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattccatcttactgcct--atgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcag
|||||  |||||| |||||||| |||||| | ||||| ||||| ||||| ||||| |||||||| ||||| || ||||| || ||||||||||||||||||||     || |  || |||  |  ||| | || || || | || ||    |||   |  | || |||  |     |||| | ||   |||||  ||||
AATGGTCAGATTTGGTGGCAGAGATGCCATTCAAGATTTGTTATCCTGCACTTGATGGTCAGGAGTGGCAGATAATCACAGGCAGTGATCCTAAGAACACgtacagtatctaatttgctgtgttaatgttttttctattatcttattatatttttcatcaaatgatttttt-----tatttgtttattttttg--gcag

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|294964217|gb|GW838020.1|GW838020
EST:     TGAAGGTCCAGGAATTGGCAA-TTATCACCGGTAGTGATCCTAAAAACAC                         GCCTTGGTCCTACCAT
genomic: TGAAGGTC-AGGAAT-GGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattc ... tttgatgcagGCCTTGGTCCTACCAT
EST: gi|110382317|gb|EC939148.1|EC939148
EST:     CTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACAC                         GCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
genomic: CTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattc ... tttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
EST: gi|110687834|gb|EE065698.1|EE065698
EST:     CTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACAC                         GCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG
genomic: CTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattc ... tttgatgcagGCCTTGGTCCTACCATAATGCAGGTTCCTGGCCAACTTTGCTCTGGCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGGGGAGATTTAGTGGCAGACATGCCACTGAAGATATGTTACCCTGCTCTTGAAGGTCAGGAATGGCAAATTATCACCGGTAGTGATCCTAAGAACACgtaagaattccatcttactgcctatgctattcctttttttttttttccctttgatttgattgttttcatgtcactattggattgcattttgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC