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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGCCAGAAGGATCCGAAGGCCAACTAGCACAGATTTTGTGATATCTCTGGTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAGgtatgtggtcactgcttatgctaatgatctttgtgcaatcttcatcttatgattccaatgatttatgaacaatttctatcag

Basic information

species Vitis vinifera
transcript Vv04s0023g01950.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g01950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G07410.2 (Glycine max), 5'ss of exon 4
CAGCCAGAAGGATCCGAAGGCCAACTAGCACAGATTTTGTGATATCTCTGGTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAGgtatgt--------ggtcact--gcttatgctaatgatctttgtgcaatcttcatcttatgattccaatgatttatgaacaatttctatcag
| || | || | |  ||||| ||||  ||||||| ||  | |||||| ||||||||||||||||||||||  ||||||| ||||||||||||||||| ||| | ||        | | |||   ||| |  |  | ||  || | ||   | |  ||||  ||  |    | ||    ||||  | |  |||
CTGCAAAAAAGGTAAGAAGGGCAACAGGCACAGACTTCATCATATCTTTGGTTGCAGATGATTTTTCTCGCTCCAGCAACACATATGTTGGAAAACTCAGgcaagttttggtttgataacttgccttcttttttttattatttttcatcttgctccttaccatatctgcaacttgatgacaaactttgacag

upper sequence: Vv04s0023g01950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA01G37940.1 (Glycine max), 5'ss of exon 4
CAGCCAGAAGGATCCGAAGGCCAACTAGCACAGATTTTGTGATATCTCTGGTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAGgtatgt--------ggtcactgcttatgctaatgatctttgtgcaatcttcatcttatgattccaatgatttatgaacaatttctatcag
| |||| || | |  ||||| ||||  ||||||| || || |||||| |||||||||||||||||| |||  ||||||| ||||||||||||||||| ||| | ||        | |     |||    |  |  |  || | ||   | |  ||||  ||  |    | ||    ||||  | |  |||
CTGCCAAAAAGGTAAGAAGGGCAACAGGCACAGACTTCGTCATATCTTTGGTTGCAGATGATTTTTTTCGCTCCAGCAACACATATGTTGGAAAACTCAGgcaagttttagtttgattgaaacttgccttcttttttatttttcatcttgctccttaccatatctgcaactttatgacaaactttgacag

upper sequence: Vv04s0023g01950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA16G25210.1 (Glycine max), 5'ss of exon 4
CAGCCAGAAGGATCCGAAGGCCAACTAGCACAGATTTTGTGATATCTCTGGTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAGgtatgtg----gtcactgcttatgctaatgatctttgtg-caatcttcatcttatgattccaatgatttatgaacaatttc-tatcag-----------
| |||| ||||||  ||||| ||||  |||| || ||| | |||||  ||| ||||||||||||||||||||||||||| | ||||||||| ||||| ||| | |||    |||  |    |   || | | |||  |  |||| |||| |||    ||  |     ||||  |||| ||  |||              
CTGCCAAAAGGATAAGAAGGGCAACGGGCACTGACTTTATCATATCCTTGGCTGCAGATGATTTTTCTCGAGCCAGCAACAAATATGTTGGTAAACTAAGgcaagtgtttggtctatagaaactttactaaccttcatatcaattttcaccttgcc-ttttatcatcttatctacaacttaatattgtccttttggcag

upper sequence: Vv04s0023g01950.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G06180.1 (Glycine max), 5'ss of exon 4
CAGCCAGAAGGATCCGAAGGCCAACTAGCACAGATTTTGTGATATCTCTGGTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAGgtatgtggtcactgcttatgctaatgatctttgtg-caatcttcatcttatgattccaatgatttatgaacaatttc-tatcag-----------
| |||| ||||||  ||||| ||||  |||| | |||||| |||||  ||| ||| ||||||||||||||||||||||| | ||||||||| ||||| ||| | ||  |   |   ||      | |  ||  |  |||| ||||  ||    || ||     ||||  |||| ||  | |              
CTGCCAAAAGGATAAGAAGGGCAACAGGCACCGGTTTTGTCATATCCTTGGCTGCTGATGATTTTTCTCGAGCCAGCAACAAATATGTTGGTAAACTAAGgcaagtttttggtctatagaaaccttacattcatatcaattttcaaattgcc-ttacatcatcttatccacaacttaatgttgcccttttggcag

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|110718379|gb|EE095148.1|EE095148
EST:     GTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAG                         ATCCAATTTTCTGGGCACGAAGTTCACAATATACGACAGCCAACCTCCATA
genomic: GTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAGgtatgtggtc ... tttctatcagATCCAATTTTCTGGGCACGAAGTTCACAATATACGACAGCCAACCTCCATA
EST: gi|33403641|gb|CF209268.1|CF209268
EST:     GTTGCAGATGATTTTTCTCCAGTCAGCAATACATATGTTGGAAAACTGAG                         ATCCAATTTTCTGGGCACAAAGTTCACAATATACGACAGCCAACCTCCATA
genomic: GTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAGgtatgtggtc ... tttctatcagATCCAATTTTCTGGGCACGAAGTTCACAATATACGACAGCCAACCTCCATA
EST: gi|33403597|gb|CF209224.1|CF209224
EST:     GTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAG                         ATCCAATTTTCTGGGCACGAAGTTCACAATATACGACAGCCAACCTCCATA
genomic: GTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAGgtatgtggtc ... tttctatcagATCCAATTTTCTGGGCACGAAGTTCACAATATACGACAGCCAACCTCCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGCCAGAAGGATCCGAAGGCCAACTAGCACAGATTTTGTGATATCTCTGGTTGCAGATGATTTTTCTCGAGCCAGCAATACATATGTTGGAAAACTGAGgtatgtggtcactgcttatgctaatgatctttgtgcaatcttcatcttatgattccaatgatttatgaacaatttctatcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG