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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCAATTCGGGTGGTTTCACACAGGGGATCTCGGGTTCTTTGACCCGGATGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttcttctccatatttttcttatccatatatgcatatatacttaagctgtagttgttttgcttttagagaagaaagagcattatggcatattgt...

Basic information

species Vitis vinifera
transcript Vv16s0050g00390.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00390.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA20G29850.1 (Glycine max), 5'ss of exon 3
TTTCAATTCGGGTGGTTTCACACAGGGGATCTCGGGTTCTTTGACCCGGATGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttcttctccatatttttcttatccatatatgcatatatacttaagctgtagttgttttgcttttagagaagaaagagcattatggcatattgt
||||||||||||||||| ||||| || ||| ||||||| |||||  ||||||| |||||||| ||||||||||| |||||||| || || |||||||||||||        | |  |||| |||  |||  ||   |  ||| ||     |   |||||  || ||| |    |            | |  |   |  | 
TTTCAATTCGGGTGGTTCCACACTGGTGATATCGGGTTTTTTGATTCGGATGGGTATTTGCACCTTGTTGGTCGCATCAAGGAGCTTATTAACCGTGGAGgtatataactatatatatatattttatatttatggttttataaattgcacactagtagtcattatgcatggcaaatgtttgtgatttcacagttaagagg

upper sequence: Vv16s0050g00390.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA11G31310.2 (Glycine max), 5'ss of exon 2
TTTCAATTCGGGTGGTTTCACACAGGGGATCTCGGGTTCTTTGACCCGGATGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgta---atgtttcttctccatatttttcttatccatatatgcatatatacttaagctgtagttgttttgcttttagagaagaaagagcattatggcatattgt
||||  ||||  |||||||| || || ||| | || | ||||||  | ||||| ||||||||||| || ||||| |||||||||||||||||||| |||||||   || ||  ||||  ||| | |  | || ||| ||| || | |  | |||  | || ||  | |   || |   |||    | |    |    ||    
TTTCTGTTCGATTGGTTTCATACTGGTGATATTGGATACTTTGATTCTGATGGGTATTTGCATCTCGTGGGTCGGATCAAGGAACTCATCAACCGAGGAGgtacatatattatttctttataatataat-attcat-tattcaaaaacgcataatttataattaatatatattcattaaagttttatctcactaatttacct-

upper sequence: Vv16s0050g00390.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA09G25470.4 (Glycine max), 5'ss of exon 2
TTTCAATTCGGGTGGTTTCACACAGGGGATCTCGGGTTCTTTGACCCGGATGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttcttctccatatttttcttatccatatatgcatatatacttaag----ctgtagttgttttgcttttagagaagaaagagcattatggcatattgt
|||   || || ||||||||||| || ||| | |||| ||| ||  | ||||| ||||||||||| || ||||| |||||||| ||||||||||| |||||||   ||  || |   ||||| |  ||| || | |   ||  ||  | |||      | |  |  |    | ||          ||   |  |    |  || 
TTTTTGTTTGGTTGGTTTCACACCGGTGATGTTGGGTACTTGGATTCTGATGGGTATTTGCATCTCGTGGGTCGGATCAAGGAGCTCATCAACCGAGGAGgta-cattaattgttattatttat--tattcaaaaactgattaattataaaggatatcgaaagtagtaaaatgttgttttgctttgaatttggtatttttctg-

upper sequence: Vv16s0050g00390.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT3G48990.1 (Arabidopsis thaliana), 5'ss of exon 3
TTTCAATTCGGGTGGTTTCACACAGGGGATCTCGGGTTCTTTGACCCGGATGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttcttctccatatttttctta-tccatatatgcatatatac-ttaagctgtagttgttttgcttttagagaagaaagagcattatggcatattgt
||  | || |||||||| ||||| || ||| |||| | ||||||  | ||||| ||||||||||| || ||||| ||||| || || || |||||||||||| |   |  ||  |  ||||||  |   |  |    | || |   |   ||  || |   |       | || |   ||     |    | |  |  ||| 
TTCGAGTTTGGGTGGTTCCACACTGGTGATATCGGTTACTTTGATACCGATGGGTATTTGCATCTGGTGGGTCGGATCAAAGAGCTTATTAACCGTGGAGgttagtctcatttactctattttgatggctttactgtttcacaagaatactagtctatgtctagcagtttatttgtatagtctcggtgg-aggctactttg-

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|110358426|gb|EC922630.1|EC922630
EST:     TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAG                         GAGAGAAGATATCACCAATTGAAGTGGATGCTGTCCTTTTATCACATCCAG
genomic: TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttc ... atattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
EST: gi|110373141|gb|EC937354.1|EC937354
EST:     TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAG                         GAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
genomic: TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttc ... atattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
EST: gi|110383709|gb|EC948098.1|EC948098
EST:     TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAG                         GAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
genomic: TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttc ... atattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
EST: gi|110407659|gb|EC973268.1|EC973268
EST:     TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAG                         GAGAGAAGATATCACCAATTGAAGTGGATGCTGTCCTTTTATCACATCCAG
genomic: TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttc ... atattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
EST: gi|110371806|gb|EC935930.1|EC935930
EST:     TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAG                         GAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
genomic: TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttc ... atattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
EST: gi|30329927|gb|CD013189.1|CD013189
EST:     TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAG                         GAGAGAAGATATCACCAATTGAAGTGGATGCTGTCCTTTTATCACATCCAG
genomic: TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttc ... atattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
EST: gi|83275734|gb|DV939742.1|DV939742
EST:     TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAG                         GAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
genomic: TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttc ... atattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
EST: gi|110714911|gb|EE092360.1|EE092360
EST:     GAACTCATCAACCGTGGAG                         GAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
genomic: GAACTCATCAACCGTGGAGgtaatgtttc ... atattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG
EST: gi|27586211|gb|CB008906.1|CB008906
EST:     TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAG                         GAGAGAAGAT-TCACCAATTGAAGTGGATGCTGTCCTTTTATCACATCCAG
genomic: TGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttc ... atattttcagGAGAGAAGATATCACCAATCGAAGTGGATGCTGTCCTTTTATCACATCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCAATTCGGGTGGTTTCACACAGGGGATCTCGGGTTCTTTGACCCGGATGGTTATTTGCATCTTGTTGGTCGAATCAAGGAACTCATCAACCGTGGAGgtaatgtttcttctccatatttttcttatccatatatgcatatatacttaagctgtagttgttttgcttttagagaagaaagagcattatggcatattgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaagaaa