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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgtttagatttatatatcagttgttggagtttaagatttaagtttcagttttggagttgatttctgttctgttgaaatggaaatgaagacaat...

Basic information

species Vitis vinifera
transcript Vv04s0008g06040.t01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: LOC_Os02g55420.1 (Oryza sativa), 5'ss of exon 8
CAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgtttagatttat-atatcagttgttggagtttaagatttaagtttcagttttggagttgatttctgttctgttgaaatggaaatgaagacaat
|||||||||||| || || |||||||| ||||| ||||| || ||||| |||||||||||||||||||| ||||| |||||||||||||||||||| |||||       | |   ||||| || ||  || |    |  | | |   ||  |     |    ||   || | |  ||||  |                   
CAACCCAACTGGAATAGACCCAACTCCGGAACAATGGGAGAAAATTGCAGATGTCATTCAAGAGAAGAAACACATGCCTTTCTTTGATGTTGCATATCAGgtgaaatgttctcactttattatttcgtttttctctgcatgaaaacaaatatcttactgactagcaaatattt-ctctgcag-------------------

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GRMZM5G836910_T01 (Zea mays), 5'ss of exon 8
CAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgtttagatttatatatcagttgttggagtttaagatttaagtttcagttttggag-ttgatttctgttctgttgaaatggaaatgaagacaat
|||||||||||| || || |||||||||||||||||||| || ||||| ||||||||||||||||| || || || || ||||||||||||||||| |||||      ||||    ||   || |   | |   |  |    ||   | | ||  ||     |  || |     |||  || |                  
CAACCCAACTGGAATAGACCCAACTCCTGAACAGTGGGAGAAAATTGCAGATGTCATTCAAGAGAAAAAGCATATGCCATTCTTTGATGTTGCATATCAGgtg--aacgtttttgcttgagtaccttgtctcctacgtatgtatcgcaatatctcttccactgactggtaggctttccttttag-----------------

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA14G13480.1 (Glycine max), 5'ss of exon 8
CAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgtttagatttatatatcagttgttgg--agtttaagatttaagtt-tcagt---tttggagt--tgatttctgttctgttgaaatggaaatgaagacaat
 ||||| |||||||| |||||||| ||||||||||||||||| || |||||||| |||||||| || || |||||||| || ||||||||||| |||||||||    | ||| | |  ||  |  | ||  |||  ||  ||   |  ||    | ||    ||  || |  ||| ||    | ||||   || |  |  |       
TAACCCTACTGGTATCGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATGTAATTCAAGAAAAAAACCACATTCCCTTTTTTGATGTTGCTTACCAGgtaccaatctttgggtaaatg-agaattttctggctagcctatattaaaaaccattagcatattaagaattatgacttaaagtgtgtttggatagctacca-------

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: GLYMA17G33050.4 (Glycine max), 5'ss of exon 8
CAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgtttagatttatatatcagttgttgg-agtttaagatttaagtt-tcagt---tttggagt--tgatttctgttctgttgaaatggaaatgaagacaat
 || || ||||||||||||||||| ||||||||||||||||| || |||||| | ||| |||| ||||| |||||||| || ||||||||||| |||||||||    | ||| | |  |      | || | |  ||  ||   | |||    | ||    ||  || |  ||| ||    | ||||   || |  |  |       
TAATCCTACTGGTATTGATCCAACACCTGAACAGTGGGAAAAAATAGCTGATTTAATTGAAGAAAAGAACCACATTCCCTTTTTTGATGTTGCTTACCAGgtaccaatctttgggtaaaggagaaatttctggatagcatatattataaaccattagcatattaagaattatgacttaaagtgtgtttggatagctacca-------

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: AT4G31990.4 (Arabidopsis thaliana), 5'ss of exon 9
CAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgtttagatttatatatcagttgttggagtttaagatttaagtttcagttttggagttgatttctgttctgttgaaatggaaatgaagacaat
|||||||||||| ||||| ||||| || |||||||||| ||| ||||||||||||||||| || ||||| || || || || || |||||||||||||||||||  |    ||    || || || |    | | ||||  ||   ||||   ||    | |      || |||   | | | ||| |  |     | | 
CAACCCAACTGGAATTGACCCAACACCAGAACAGTGGGTAAAAATTGCTGATGTCATTCAGGAAAAGAACCATATCCCATTTTTCGATGTTGCATACCAGgtatcccc--ctattcctacatttccgaatatcgtgtttccgagagaagta--agc---gaaaccatattatgtaacgct-acatgcacctattttccag

upper sequence: Vv04s0008g06040.t01 (Vitis vinifera), 5'ss of exon 10
lower sequence: PP1S540_7V6.3 (Physcomitrella patens), 5'ss of exon 8
CAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgta--ttgctgtttagatttatatatcagttgttggagtttaagatttaagtttcagt-tttgga--gttgatttctgttct---gttgaaatggaaatgaagacaat------------------------------------------------------------------------------------
|||||||||||| ||||| ||||| || || || ||||| |||||||||||| | |||||  | ||||| || ||  | ||||||||||| || |||||||||  || || |||  |||||   ||   |  ||| ||   |     |  | |||  | | ||||  | | |||  ||||||   ||| || | |   ||| |||  |                                                                                    
CAACCCAACTGGCATTGACCCAACACCAGACCAATGGGAGAAGATTGCTGATCTTATTCAGCAAAAGAACCATATGGCATTCTTTGATGTAGCTTACCAGgtaatttcctctttccatttacgcat--atcattgcaggaaacatgatcggcttcgatgtctggatggctaattagtgttcttcagtttaattagttgtgacgactttttatcaagtctcattgagccacatgagaaacatgagtgacttaccagtgttcgaggattcatttgtcgtcggatggtacaccag

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|110396712|gb|EC962407.1|EC962407
EST:     ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAG                         GGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
genomic: ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgt ... cactttgtagGGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
EST: gi|32270026|gb|CD719185.1|CD719185
EST:     ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAG                         GGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
genomic: ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgt ... cactttgtagGGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
EST: gi|32272538|gb|CD721697.1|CD721697
EST:     ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAG                         GGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
genomic: ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgt ... cactttgtagGGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
EST: gi|30326281|gb|CD009543.1|CD009543
EST:     ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAG                         GGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
genomic: ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgt ... cactttgtagGGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
EST: gi|30326632|gb|CD009894.1|CD009894
EST:     ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAG                         GGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
genomic: ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgt ... cactttgtagGGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
EST: gi|161714230|gb|FC063508.1|FC063508
EST:     ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAG                         GGATTTGCAAGTGGAAGCCTTGATGCATATGCGTCATCCGTGAGATTGTTT
genomic: ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgt ... cactttgtagGGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
EST: gi|29785081|gb|CB341792.2|CB341792
EST:     ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAG                         GGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
genomic: ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgt ... cactttgtagGGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
EST: gi|32271796|gb|CD720955.1|CD720955
EST:     ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAG                         GGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT
genomic: ATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgt ... cactttgtagGGATTTGCAAGTGGAAGCCTTGATGCAGATGCGTCATCCGTGAGATTGTTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCCAACTGGTATTGATCCAACTCCTGAACAGTGGGAAAAGATTGCTGATGTCATTCAAGAGAAGAATCACATTCCTTTCTTTGATGTTGCATACCAGgtattgctgtttagatttatatatcagttgttggagtttaagatttaagtttcagttttggagttgatttctgttctgttgaaatggaaatgaagacaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atggaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagacaa